diff --git a/doc/src/Build.rst b/doc/src/Build.rst index 7e4f749743..2e046451cf 100644 --- a/doc/src/Build.rst +++ b/doc/src/Build.rst @@ -6,9 +6,9 @@ either traditional makefiles for use with GNU make (which may require manual editing), or using a build environment generated by CMake (Unix Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more). -As an alternative you can download a package with pre-built executables -or automated build trees as described on the :doc:`Install ` -page. +As an alternative, you can download a package with pre-built executables +or automated build trees as described in the :doc:`Install ` +section of the manual. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 91b23f000f..62979d34df 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -60,7 +60,7 @@ standard. A more detailed discussion of that is below. Any ``make machine`` command will look up the make settings from a file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its - sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a + subdirectories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a folder ``Obj_machine`` with all objects and generated files and an executable called ``lmp_machine``\ . The standard parallel build with ``make mpi`` assumes a standard MPI installation with MPI diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 9bee18146c..1ab86badc8 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -9,10 +9,10 @@ page. The following text assumes some familiarity with CMake and focuses on using the command line tool ``cmake`` and what settings are supported -for building LAMMPS. A more detailed tutorial on how to use ``cmake`` -itself, the text mode or graphical user interface, change the generated -output files for different build tools and development environments is -on a :doc:`separate page `. +for building LAMMPS. A more detailed tutorial on how to use CMake +itself, the text mode or graphical user interface, to change the +generated output files for different build tools and development +environments is on a :doc:`separate page `. .. note:: @@ -22,12 +22,12 @@ on a :doc:`separate page `. .. warning:: You must not mix the :doc:`traditional make based ` - LAMMPS build procedure with using CMake. Thus no packages may be + LAMMPS build procedure with using CMake. No packages may be installed or a build been previously attempted in the LAMMPS source directory by using ``make ``. CMake will detect if this is the case and generate an error. To remove conflicting files from the ``src`` you can use the command ``make no-all purge`` which will - un-install all packages and delete all auto-generated files. + uninstall all packages and delete all auto-generated files. Advantages of using CMake @@ -44,9 +44,9 @@ software or for people that want to modify or extend LAMMPS. and adapt the LAMMPS default build configuration accordingly. - CMake can generate files for different build tools and integrated development environments (IDE). -- CMake supports customization of settings with a text mode or graphical - user interface. No knowledge of file formats or and complex command - line syntax required. +- CMake supports customization of settings with a command line, text + mode, or graphical user interface. No knowledge of file formats or + complex command line syntax is required. - All enabled components are compiled in a single build operation. - Automated dependency tracking for all files and configuration options. - Support for true out-of-source compilation. Multiple configurations @@ -55,23 +55,23 @@ software or for people that want to modify or extend LAMMPS. source tree. - Simplified packaging of LAMMPS for Linux distributions, environment modules, or automated build tools like `Homebrew `_. -- Integration of automated regression testing (the LAMMPS side for that - is still under development). +- Integration of automated unit and regression testing (the LAMMPS side + of this is still under active development). .. _cmake_build: Getting started ^^^^^^^^^^^^^^^ -Building LAMMPS with CMake is a two-step process. First you use CMake -to generate a build environment in a new directory. For that purpose -you can use either the command-line utility ``cmake`` (or ``cmake3``), -the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical -utility ``cmake-gui``, or use them interchangeably. The second step is -then the compilation and linking of all objects, libraries, and -executables. Here is a minimal example using the command line version of -CMake to build LAMMPS with no add-on packages enabled and no -customization: +Building LAMMPS with CMake is a two-step process. In the first step you +use CMake to generate a build environment in a new directory. For that +purpose you can use either the command-line utility ``cmake`` (or +``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the +graphical utility ``cmake-gui``, or use them interchangeably. The +second step is then the compilation and linking of all objects, +libraries, and executables using the selected build tool. Here is a +minimal example using the command line version of CMake to build LAMMPS +with no add-on packages enabled and no customization: .. code-block:: bash @@ -96,17 +96,17 @@ Compilation can take a long time, since LAMMPS is a large project with many features. If your machine has multiple CPU cores (most do these days), you can speed this up by compiling sources in parallel with ``make -j N`` (with N being the maximum number of concurrently executed -tasks). Also installation of the `ccache `_ (= -Compiler Cache) software may speed up repeated compilation even more, -e.g. during code development. +tasks). Installation of the `ccache `_ (= Compiler +Cache) software may speed up repeated compilation even more, e.g. during +code development, especially when repeatedly switching between branches. After the initial build, whenever you edit LAMMPS source files, enable or disable packages, change compiler flags or build options, you must re-compile and relink the LAMMPS executable with ``cmake --build .`` (or ``make``). If the compilation fails for some reason, try running ``cmake .`` and then compile again. The included dependency tracking -should make certain that only the necessary subset of files are -re-compiled. You can also delete compiled objects, libraries and +should make certain that only the necessary subset of files is +re-compiled. You can also delete compiled objects, libraries, and executables with ``cmake --build . --target clean`` (or ``make clean``). After compilation, you may optionally install the LAMMPS executable into @@ -132,12 +132,12 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the ``CMakeCache.txt``, which is generated at the end of the CMake configuration step. The cache file contains all current CMake settings. -To modify settings, enable or disable features, you need to set *variables* -with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or -change them in the text mode of graphical user interface. The *-D* flag -can be used several times in one command. +To modify settings, enable or disable features, you need to set +*variables* with either the *-D* command line flag (``-D +VARIABLE1_NAME=value``) or change them in the text mode of the graphical +user interface. The *-D* flag can be used several times in one command. -For your convenience we provide :ref:`CMake presets ` +For your convenience, we provide :ref:`CMake presets ` that combine multiple settings to enable optional LAMMPS packages or use a different compiler tool chain. Those are loaded with the *-C* flag (``-C ../cmake/presets/basic.cmake``). This step would only be needed @@ -155,22 +155,23 @@ specific CMake version is given when running ``cmake --help``. Multi-configuration build systems ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Throughout this manual it is mostly assumed that LAMMPS is being built +Throughout this manual, it is mostly assumed that LAMMPS is being built on a Unix-like operating system with "make" as the underlying "builder", -since this is the most common case. In this case the build "configuration" -is chose using ``-D CMAKE_BUILD_TYPE=`` with ```` -being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel". -Some build tools, however, can also use or even require to have a so-called -multi-configuration build system setup. For those the built type (or -configuration) is chosen at compile time using the same build files. E.g. -with: +since this is the most common case. In this case the build +"configuration" is chose using ``-D CMAKE_BUILD_TYPE=`` +with ```` being one of "Release", "Debug", +"RelWithDebInfo", or "MinSizeRel". Some build tools, however, can also +use or even require having a so-called multi-configuration build system +setup. For a multi-configuration build, the built type (or +configuration) is selected at compile time using the same build +files. E.g. with: .. code-block:: bash cmake --build build-multi --config Release In that case the resulting binaries are not in the build folder directly -but in sub-directories corresponding to the build type (i.e. Release in +but in subdirectories corresponding to the build type (i.e. Release in the example from above). Similarly, for running unit tests the configuration is selected with the *-C* flag: @@ -184,7 +185,7 @@ particular applicable to compiling packages that require additional libraries that would be downloaded and compiled by CMake. The "windows" preset file tries to keep track of which packages can be compiled natively with the MSVC compilers out-of-the box. Not all of those external libraries are -portable to Windows either. +portable to Windows, either. Installing CMake diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index d7bbe65a18..e284f11721 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -288,7 +288,7 @@ your machine are not correct, the LAMMPS build will fail, and .. note:: If you re-build the GPU library in ``lib/gpu``, you should always - un-install the GPU package in ``lammps/src``, then re-install it and + uninstall the GPU package in ``lammps/src``, then re-install it and re-build LAMMPS. This is because the compilation of files in the GPU package uses the library settings from the ``lib/gpu/Makefile.machine`` used to build the GPU library. diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index c7b063e8a9..efa9332cce 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -20,21 +20,22 @@ with :doc:`CMake `. The makefiles of the traditional make based build process and the scripts they are calling expect a few additional tools to be available and functioning. - * a working C/C++ compiler toolchain supporting the C++11 standard; on - Linux these are often the GNU compilers. Some older compilers + * A working C/C++ compiler toolchain supporting the C++11 standard; on + Linux, these are often the GNU compilers. Some older compiler versions require adding flags like ``-std=c++11`` to enable the C++11 mode. - * a Bourne shell compatible "Unix" shell program (often this is ``bash``) - * a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname`` - * python (optional, required for ``make lib-`` in the src folder). - python scripts are currently tested with python 2.7 and 3.6. The procedure - for :doc:`building the documentation ` requires python 3.5 or later. + * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``) + * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname`` + * Python (optional, required for ``make lib-`` in the src + folder). Python scripts are currently tested with python 2.7 and + 3.6 to 3.11. The procedure for :doc:`building the documentation + ` *requires* Python 3.5 or later. Getting started ^^^^^^^^^^^^^^^ To include LAMMPS packages (i.e. optional commands and styles) you must enable (or "install") them first, as discussed on the :doc:`Build -package ` page. If a packages requires (provided or +package ` page. If a package requires (provided or external) libraries, you must configure and build those libraries **before** building LAMMPS itself and especially **before** enabling such a package with ``make yes-``. :doc:`Building LAMMPS with @@ -56,17 +57,17 @@ Compilation can take a long time, since LAMMPS is a large project with many features. If your machine has multiple CPU cores (most do these days), you can speed this up by compiling sources in parallel with ``make -j N`` (with N being the maximum number of concurrently executed -tasks). Also installation of the `ccache `_ (= -Compiler Cache) software may speed up repeated compilation even more, -e.g. during code development. +tasks). Installation of the `ccache `_ (= Compiler +Cache) software may speed up repeated compilation even more, e.g. during +code development, especially when repeatedly switching between branches. After the initial build, whenever you edit LAMMPS source files, or add or remove new files to the source directory (e.g. by installing or uninstalling packages), you must re-compile and relink the LAMMPS executable with the same ``make `` command. The makefile's -dependency tracking should insure that only the necessary subset of -files are re-compiled. If you change settings in the makefile, you have -to recompile *everything*. To delete all objects you can use ``make +dependency tracking should ensure that only the necessary subset of +files is re-compiled. If you change settings in the makefile, you have +to recompile *everything*. To delete all objects, you can use ``make clean-``. .. note:: @@ -84,8 +85,8 @@ Customized builds and alternate makefiles The ``src/MAKE`` directory tree contains the ``Makefile.`` files included in the LAMMPS distribution. Typing ``make example`` uses -``Makefile.example`` from one of those folders, if available. Thus the -``make serial`` and ``make mpi`` lines above use +``Makefile.example`` from one of those folders, if available. The +``make serial`` and ``make mpi`` lines above, for example, use ``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``, respectively. Other makefiles are in these directories: @@ -106,12 +107,13 @@ a new name, please edit the first line with the description and machine name, so you will not confuse yourself, when looking at the machine summary. -Makefiles you may wish to try include these (some require a package -first be installed). Many of these include specific compiler flags -for optimized performance. Please note, however, that some of these -customized machine Makefile are contributed by users. Since both -compilers, OS configurations, and LAMMPS itself keep changing, their -settings may become outdated: +Makefiles you may wish to try out, include those listed below (some +require a package first be installed). Many of these include specific +compiler flags for optimized performance. Please note, however, that +some of these customized machine Makefile are contributed by users, and +thus may have modifications specific to the systems of those users. +Since compilers, OS configurations, and LAMMPS itself keep changing, +their settings may become outdated, too: .. code-block:: bash diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 9b0f00276c..eaa9f44a1c 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -2,7 +2,7 @@ Build the LAMMPS documentation ============================== Depending on how you obtained LAMMPS and whether you have built the -manual yourself, this directory has a number of sub-directories and +manual yourself, this directory has a number of subdirectories and files. Here is a list with descriptions: .. code-block:: bash diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 938ffec306..cde210780d 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -4,7 +4,7 @@ Include packages in build In LAMMPS, a package is a group of files that enable a specific set of features. For example, force fields for molecular systems or rigid-body constraints are in packages. In the src directory, each -package is a sub-directory with the package name in capital letters. +package is a subdirectory with the package name in capital letters. An overview of packages is given on the :doc:`Packages ` doc page. Brief overviews of each package are on the :doc:`Packages details ` page. @@ -94,7 +94,7 @@ versus make. If you switch between building with CMake and make builds, no packages in the src directory can be installed when you invoke ``cmake``. CMake will give an error if that is not the case, - indicating how you can un-install all packages in the src dir. + indicating how you can uninstall all packages in the src dir. .. tab:: Traditional make @@ -103,7 +103,7 @@ versus make. cd lammps/src make ps # check which packages are currently installed make yes-name # install a package with name - make no-name # un-install a package with name + make no-name # uninstall a package with name make mpi # build LAMMPS with whatever packages are now installed Examples: @@ -119,13 +119,13 @@ versus make. .. note:: You must always re-build LAMMPS (via make) after installing or - un-installing a package, for the action to take effect. The + uninstalling a package, for the action to take effect. The included dependency tracking will make certain only files that are required to be rebuilt are recompiled. .. note:: - You cannot install or un-install packages and build LAMMPS in a + You cannot install or uninstall packages and build LAMMPS in a single make command with multiple targets, e.g. ``make yes-colloid mpi``. This is because the make procedure creates a list of source files that will be out-of-date for the build @@ -150,7 +150,7 @@ other files dependent on that package are also excluded. if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE) were pre-installed via the traditional make procedure in the ``src`` directory. That is no longer the case, so that CMake will build - as-is without needing to un-install those packages. + as-is without needing to uninstall those packages. ---------- @@ -227,7 +227,7 @@ The following commands are useful for managing package source files and their installation when building LAMMPS via traditional make. Just type ``make`` in lammps/src to see a one-line summary. -These commands install/un-install sets of packages: +These commands install/uninstall sets of packages: .. code-block:: bash @@ -243,40 +243,40 @@ These commands install/un-install sets of packages: make yes-ext # install packages that require external libraries make no-ext # uninstall packages that require external libraries -which install/un-install various sets of packages. Typing ``make +which install/uninstall various sets of packages. Typing ``make package`` will list all the these commands. .. note:: - Installing or un-installing a package for the make based build process + Installing or uninstalling a package for the make based build process works by simply copying files back and forth between the main source - directory src and the sub-directories with the package name (e.g. + directory src and the subdirectories with the package name (e.g. src/KSPACE, src/ATC), so that the files are included or excluded when LAMMPS is built. Only source files in the src folder will be compiled. The following make commands help manage files that exist in both the -src directory and in package sub-directories. You do not normally +src directory and in package subdirectories. You do not normally need to use these commands unless you are editing LAMMPS files or are updating LAMMPS via git. Type ``make package-status`` or ``make ps`` to show which packages are currently installed. For those that are installed, it will list any files that are different in the src directory and package -sub-directory. +subdirectory. Type ``make package-installed`` or ``make pi`` to show which packages are currently installed, without listing the status of packages that are not installed. Type ``make package-update`` or ``make pu`` to overwrite src files with -files from the package sub-directories if the package is installed. It +files from the package subdirectories if the package is installed. It should be used after the checkout has been :doc:`updated or changed withy git `, this will only update the files in the package -sub-directories, but not the copies in the src folder. +subdirectories, but not the copies in the src folder. Type ``make package-overwrite`` to overwrite files in the package -sub-directories with src files. +subdirectories with src files. Type ``make package-diff`` to list all differences between pairs of files in both the source directory and the package directory. diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index 63ff30abfe..563dae7b69 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -7,7 +7,7 @@ but there are small a number of files in several other languages like C, Fortran, Shell script, or Python. The core of the code is located in the ``src`` folder and its -sub-directories. A sizable number of these files are in the ``src`` +subdirectories. A sizable number of these files are in the ``src`` directory itself, but there are plenty of :doc:`packages `, which can be included or excluded when LAMMPS is built. See the :doc:`Include packages in build ` section of the manual @@ -16,11 +16,11 @@ currently supports building with :doc:`conventional makefiles ` and through :doc:`CMake `. Those procedures differ in how packages are enabled or disabled for inclusion into a LAMMPS binary so they cannot be mixed. The source files for each -package are in all-uppercase sub-directories of the ``src`` folder, for +package are in all-uppercase subdirectories of the ``src`` folder, for example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``. The ``src/STUBS`` -sub-directory is not a package but contains a dummy MPI library, that is +subdirectory is not a package but contains a dummy MPI library, that is used when building a serial version of the code. The ``src/MAKE`` -directory and its sub-directories contain makefiles with settings and +directory and its subdirectories contain makefiles with settings and flags for a variety of configuration and machines for the build process with traditional makefiles. @@ -28,7 +28,7 @@ The ``lib`` directory contains the source code for several supporting libraries or files with configuration settings to use globally installed libraries, that are required by some of the optional packages. They may include python scripts that can transparently download additional source -code on request. Each sub-directory, like ``lib/poems`` or ``lib/gpu``, +code on request. Each subdirectory, like ``lib/poems`` or ``lib/gpu``, contains the source files, some of which are in different languages such as Fortran or CUDA. These libraries included in the LAMMPS build, if the corresponding package is installed. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index bbd4db8508..de3eae8714 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -1,7 +1,7 @@ Example scripts =============== -The LAMMPS distribution includes an examples sub-directory with many +The LAMMPS distribution includes an examples subdirectory with many sample problems. Many are 2d models that run quickly and are straightforward to visualize, requiring at most a couple of minutes to run on a desktop machine. Each problem has an input script (in.\*) and @@ -29,7 +29,7 @@ be quickly post-processed into a movie using commands described on the Animations of many of the examples can be viewed on the Movies section of the `LAMMPS website `_. -There are two kinds of sub-directories in the examples folder. Lower +There are two kinds of subdirectories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run problems. Upper case named directories contain up to several complex scripts that illustrate a particular kind of simulation method or @@ -221,10 +221,10 @@ Uppercase directories Nearly all of these directories have README files which give more details on how to understand and use their contents. -The PACKAGES directory has a large number of sub-directories which +The PACKAGES directory has a large number of subdirectories which correspond by name to specific packages. They contain scripts that illustrate how to use the command(s) provided in those packages. Many -of the sub-directories have their own README files which give further +of the subdirectories have their own README files which give further instructions. See the :doc:`Packages_details ` doc page for more info on specific packages. diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 8ac957f554..c997aa52bf 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -89,7 +89,7 @@ different options (``build-parallel``, ``build-serial``) or with different compilers (``build-gnu``, ``build-clang``, ``build-intel``) and so on. All the auxiliary files created by one build process (executable, object files, log files, etc) are stored in this directory -or sub-directories within it that CMake creates. +or subdirectories within it that CMake creates. Running CMake diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index a182d4a050..9a9fef5efc 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -392,7 +392,7 @@ IPyLammps Examples ------------------ Examples of IPython notebooks can be found in the python/examples/pylammps -sub-directory. To open these notebooks launch *jupyter notebook* inside this +subdirectory. To open these notebooks launch *jupyter notebook* inside this directory and navigate to one of them. If you compiled and installed a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. diff --git a/doc/src/Install.rst b/doc/src/Install.rst index b327dfcbff..5ebcc4c8ed 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -33,7 +33,7 @@ you **must** build LAMMPS from the source code. ---- -These are the files and sub-directories in the LAMMPS distribution: +These are the files and subdirectories in the LAMMPS distribution: +------------+---------------------------------------------+ | README | Short description of the LAMMPS package | diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index 8856da2600..5140e4e17d 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -1,10 +1,10 @@ Download an executable for Linux or Mac via Conda ------------------------------------------------- -Pre-compiled LAMMPS binaries are available for macOS or Linux via the +Pre-compiled LAMMPS binaries are available for macOS and Linux via the `Conda `_ package management system. -First, one must setup the Conda package manager on your system. Follow the +First, one must set up the Conda package manager on your system. Follow the instructions to install `Miniconda `_, then create a conda environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS install: @@ -21,19 +21,19 @@ Then, you can install LAMMPS on your system with the following command: conda activate my-lammps-env conda install lammps -The LAMMPS binary is built with the :ref:`KIM package ` which +The LAMMPS binary is built with the :ref:`KIM package `, which results in Conda also installing the `kim-api` binaries when LAMMPS is -installed. In order to use potentials from `openkim.org `_, you can -install the `openkim-models` package +installed. In order to use potentials from `openkim.org `_, +you can install the `openkim-models` package .. code-block:: bash conda install openkim-models -If you have problems with the installation you can post issues to -`this link `_. -Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting -up the Conda capability. +If you have problems with the installation, you can post issues to `this +link `_. Thanks to Jan Janssen +(Max-Planck-Institut fuer Eisenforschung) for setting up the Conda +capability. .. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues .. _openkim: https://openkim.org diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 99c57044e2..de948b3671 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -1,16 +1,16 @@ Download the LAMMPS source with git ----------------------------------- -All LAMMPS development is coordinated through the "LAMMPS GitHub -site". If you clone the LAMMPS repository onto your local machine, it -has several advantages: +LAMMPS development is coordinated through the "LAMMPS GitHub site". +If you clone the LAMMPS repository onto your local machine, it has +several advantages: * You can stay current with changes to LAMMPS with a single git command. * You can create your own development branches to add code to LAMMPS. * You can submit your new features back to GitHub for inclusion in - LAMMPS. For that you should first create your own :doc:`fork on - GitHub `. + LAMMPS. For that, you should first create your own :doc:`fork on + GitHub `, though. You must have `git `_ installed on your system to use the commands explained below to communicate with the git servers on @@ -31,8 +31,8 @@ You can follow the LAMMPS development on 3 different git branches: * **stable** : this branch is updated from the *release* branch with every stable release version and also has selected bug fixes and updates back-ported from the *develop* branch -* **release** : this branch is updated with every patch release; - updates are always "fast forward" merges from *develop* +* **release** : this branch is updated with every patch or feature release; + updates are always "fast-forward" merges from *develop* * **develop** : this branch follows the ongoing development and is updated with every merge commit of a pull request @@ -58,12 +58,12 @@ between them at any time using "git checkout ".) commit history (most people don't), you can speed up the "cloning" process and reduce local disk space requirements by using the *--depth* git command line flag. That will create a "shallow clone" - of the repository containing only a subset of the git history. Using - a depth of 1000 is usually sufficient to include the head commits of - the *develop* and the *release* branches. To include the head commit - of the *stable* branch you may need a depth of up to 10000. If you - later need more of the git history, you can always convert the - shallow clone into a "full clone". + of the repository, which contains only a subset of the git history. + Using a depth of 1000 is usually sufficient to include the head + commits of the *develop* and the *release* branches. To include the + head commit of the *stable* branch you may need a depth of up + to 10000. If you later need more of the git history, you can always + convert the shallow clone into a "full clone". Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with the exception, that @@ -84,11 +84,11 @@ from within the "mylammps" directory: git pull Doing a "pull" will not change any files you have added to the LAMMPS -directory structure. It will also not change any existing LAMMPS -files you have edited, unless those files have changed in the -repository. In that case, git will attempt to merge the new -repository file with your version of the file and tell you if there -are any conflicts. See the git documentation for details. +directory structure. It will also not change any existing LAMMPS files +you have edited, unless those files have changed in the repository. In +that case, git will attempt to merge the changes from the repository +file with your version of the file and tell you if there are any +conflicts. See the git documentation for details. If you want to access a particular previous release version of LAMMPS, you can instead "check out" any version with a published tag. See the @@ -146,13 +146,13 @@ changed. How to do this depends on the build system you are using. and package directories. This is OK to do even if you don't use any packages. The ``make purge`` command removes any deprecated src files if they were removed by the patch from a package - sub-directory. + subdirectory. .. warning:: If you wish to edit/change a src file that is from a package, you should edit the version of the file inside the package - sub-directory with src, then re-install the package. The + subdirectory with src, then re-install the package. The version in the source directory is merely a copy and will be wiped out if you type "make package-update". @@ -164,5 +164,5 @@ changed. How to do this depends on the build system you are using. GitHub account, you may also use SSH protocol with the URL "git@github.com:lammps/lammps.git". -The LAMMPS GitHub project is currently managed by Axel Kohlmeyer +The LAMMPS GitHub project is currently overseen by Axel Kohlmeyer (Temple U, akohlmey at gmail.com). diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index 2d2035d68d..bf33e35ee2 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -3,7 +3,7 @@ Download an executable for Linux Binaries are available for different versions of Linux: -- :ref:`Pre-built Ubuntu Linux executables ` +- :ref:`Pre-built Ubuntu and Debian Linux executables ` - :ref:`Pre-built Fedora Linux executables ` - :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) ` - :ref:`Pre-built OpenSuse Linux executables ` @@ -14,21 +14,23 @@ Binaries are available for different versions of Linux: If you have questions about these pre-compiled LAMMPS executables, you need to contact the people preparing those packages. The LAMMPS - developers have no control over their choices of how they configure - and build their packages and when they update them. + developers have no control over how they configure and build their + packages and when they update them. They may only provide packages + for stable release versions and not always update the packages in a + timely fashion after a new LAMMPS release is made. ---------- .. _ubuntu: -Pre-built Ubuntu Linux executables -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Pre-built Ubuntu and Debian Linux executables +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -A pre-built LAMMPS executable suitable for running on the latest Ubuntu -Linux versions, can be downloaded as a Debian package. This allows you -to install LAMMPS with a single command, and stay (mostly) up-to-date -with the current stable version of LAMMPS by simply updating your -operating system. +A pre-built LAMMPS executable, suitable for running on the latest Ubuntu +and Debian Linux versions, can be downloaded as a Debian package. This +allows you to install LAMMPS with a single command, and stay (mostly) +up-to-date with the current stable version of LAMMPS by simply updating +your operating system. To install LAMMPS do the following once: @@ -38,8 +40,22 @@ To install LAMMPS do the following once: This downloads an executable named ``lmp`` to your box and multiple packages with supporting data, examples and libraries as well as any -missing dependencies. This executable can then be used in the usual way -to run input scripts: +missing dependencies. For example, the LAMMPS binary in this package is +built with the :ref:`KIM package ` enabled, which results in the +above command also installing the ``kim-api`` binaries when LAMMPS is +installed, unless they were installed already. In order to use +potentials from `openkim.org `_, you can also install the +``openkim-models`` package: + +.. code-block:: bash + + sudo apt-get install openkim-models + +Or use the `KIM-API commands `_ +to download and install individual models. + +This LAMMPS executable can then be used in the usual way to run input +scripts: .. code-block:: bash @@ -51,20 +67,9 @@ To update LAMMPS to the latest packaged version, do the following: sudo apt-get update -which will also update other packages on your system. +This will also update other packages on your system. -The ``lmp`` binary is built with the :ref:`KIM package ` included, -which results in the above command also installing the ``kim-api`` -binaries when LAMMPS is installed. In order to use potentials from -`openkim.org `_, you can also install the ``openkim-models`` -package - -.. code-block:: bash - - sudo apt-get install openkim-models - -Or use the KIM-API commands to download and install individual models. -To un-install LAMMPS, do the following: +To uninstall LAMMPS, do the following: .. code-block:: bash @@ -83,8 +88,9 @@ Ubuntu package capability. Pre-built Fedora Linux executables ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Pre-built LAMMPS packages for stable releases are available in the -Fedora Linux distribution as of Fedora version 28. The packages can be +Pre-built `LAMMPS packages for stable releases +`_ are available in the +Fedora Linux distribution since Fedora version 28. The packages can be installed via the dnf package manager. There are 3 basic varieties (lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi = OpenMPI MPI library) and for each support for linking to the C library @@ -107,9 +113,9 @@ To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do: module load mpi/openmpi-x86_64 mpirun -np 2 lmp -in in.lj -The ``dnf install`` command is needed only once. In case of a new LAMMPS +The ``dnf install`` command is needed only once. In case of a new LAMMPS stable release, ``dnf update`` will automatically update to the newer -version as soon at the RPM files are built and uploaded to the download +version as soon as the RPM files are built and uploaded to the download mirrors. The ``module load`` command is needed once per (shell) session or shell terminal instance, unless it is automatically loaded from the shell profile. @@ -165,7 +171,7 @@ in OpenSuse as of Leap 15.0. You can install the package with: zypper install lammps This includes support for OpenMPI. The name of the LAMMPS executable -is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do: +is ``lmp``. To run an input in parallel on 2 CPUs you would do: .. code-block:: bash @@ -192,17 +198,18 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse. Gentoo Linux executable ^^^^^^^^^^^^^^^^^^^^^^^ -LAMMPS is part of Gentoo's main package tree and can be installed by -typing: +LAMMPS is part of `Gentoo's main package tree +`_ and can be +installed by typing: .. code-block:: bash emerge --ask lammps -Note that in Gentoo the LAMMPS source is downloaded and the package is -built on the your machine. +Note that in Gentoo the LAMMPS source code is downloaded and the package is +then compiled and installed on your machine. -Certain LAMMPS packages can be enable via USE flags, type +Certain LAMMPS packages can be enabled via USE flags, type .. code-block:: bash @@ -221,8 +228,11 @@ Archlinux build-script ^^^^^^^^^^^^^^^^^^^^^^ LAMMPS is available via Arch's unofficial Arch User repository (AUR). -There are three scripts available, named lammps, lammps-beta and lammps-git. -They respectively package the stable, patch and git releases. +There are three scripts available, named `lammps +`_, `lammps-beta +`_ and `lammps-git +`_. They respectively +package the stable, patch and git releases. To install, you will need to have the git package installed. You may use any of the above names in-place of lammps. @@ -234,9 +244,9 @@ any of the above names in-place of lammps. makepkg -s makepkg -i -To update, you may repeat the above, or change into the cloned directory, -and execute the following, after which, if there are any changes, you may -use makepkg as above. +To update LAMMPS, you may repeat the above, or change into the cloned +directory, and execute the following, after which, if there are any +changes, you may use makepkg as above. .. code-block:: bash @@ -244,12 +254,5 @@ use makepkg as above. Alternatively, you may use an AUR helper to install these packages. -Note that the AUR provides build-scripts that download the source and -the build the package on your machine. - -.. note:: - - It looks like the Arch Linux AUR repository build scripts for LAMMPS - have not been updated since the 29 October 2020 version. You may want - to consider installing a more current version of LAMMPS from source - directly. +Note that the AUR provides build-scripts that download the source code +and then build and install the package on your machine. diff --git a/doc/src/Install_mac.rst b/doc/src/Install_mac.rst index 3b7be3722c..39146c5afc 100644 --- a/doc/src/Install_mac.rst +++ b/doc/src/Install_mac.rst @@ -2,10 +2,11 @@ Download an executable for Mac ------------------------------ LAMMPS can be downloaded, built, and configured for OS X on a Mac with -`Homebrew `_. (Alternatively, see the install instructions for -:doc:`Download an executable via Conda `.) The following LAMMPS -packages are unavailable at this time because of additional needs not yet met: -GPU, KOKKOS, LATTE, MSCG, MPIIO, POEMS, VORONOI. +`Homebrew `_. (Alternatively, see the installation +instructions for :doc:`downloading an executable via Conda +`.) The following LAMMPS packages are unavailable at +this time because of additional requirements not yet met: GPU, KOKKOS, +LATTE, MSCG, MPIIO, POEMS, VORONOI. After installing Homebrew, you can install LAMMPS on your system with the following commands: @@ -24,16 +25,16 @@ Lennard-Jones benchmark file: brew test lammps -v -The LAMMPS binary is built with the :ref:`KIM package ` which -results in Homebrew also installing the `kim-api` binaries when LAMMPS is -installed. In order to use potentials from `openkim.org `_, you can -install the `openkim-models` package +The LAMMPS binary is built with the :ref:`KIM package `, which +results in Homebrew also installing the `kim-api` binaries when LAMMPS +is installed. In order to use potentials from `openkim.org +`_, you can install the `openkim-models` package .. code-block:: bash brew install openkim-models -If you have problems with the installation you can post issues to +If you have problems with the installation, you can post issues to `this link `_. .. _homebrew: https://brew.sh diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index e17ab2bd46..0765d71044 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -9,17 +9,19 @@ of the `LAMMPS website `_. .. _older: https://download.lammps.org/tars/ .. _lws: https://www.lammps.org -You have two choices of tarballs, either the most recent stable -release or the most current patch release. Stable releases occur a -few times per year, and undergo more testing before release. Patch -releases occur a couple times per month. The new contents in all -releases are listed on the `bug and feature page `_ of the website. +You have two choices of tarballs, either the most recent stable release +or the most current patch or feature release. Stable releases occur a +few times per year, and undergo more testing before release. Feature +releases occur every 4 to 8 weeks. The new contents in all feature +releases are listed on the `bug and feature page `_ of the LAMMPS +homepage. Both tarballs include LAMMPS documentation (HTML and PDF files) corresponding to that version. The download page also has an option to download the current-version LAMMPS documentation by itself. -Older versions of LAMMPS can also be downloaded from `this page `_. +Tarballs of older LAMMPS versions can also be downloaded from `this page +`_. Once you have a tarball, unzip and untar it with the following command: @@ -36,14 +38,13 @@ in its name, e.g. lammps-23Jun18. You can also download a compressed tar or zip archives from the "Assets" sections of the `LAMMPS GitHub releases site `_. The file name will be lammps-.zip which can be unzipped -with the following command, to create a lammps- dir: +with the following command, to create a lammps- directory: .. code-block:: bash unzip lammps*.zip -This version corresponds to the selected LAMMPS patch or stable -release. +This version corresponds to the selected LAMMPS patch or stable release. .. _git: https://github.com/lammps/lammps/releases diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index fc167d7e68..da9441fc49 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -33,7 +33,7 @@ Windows, once it is installed, in both serial and parallel. When you download the installer package, you run it on your Windows machine. It will then prompt you with a dialog, where you can choose the installation directory, unpack and copy several executables, -potential files, documentation pdfs, selected example files, etc. It +potential files, documentation PDFs, selected example files, etc. It will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS) and add an entry into the Start Menu (with references to the documentation, LAMMPS homepage and more). From that menu, there is @@ -41,10 +41,10 @@ also a link to an uninstaller that removes the files and undoes the environment manipulations. Note that to update to a newer version of LAMMPS, you should typically -uninstall the version you currently have, download a new installer, -and go through the install procedure described above. I.e. the same +uninstall the version you currently have, download a new installer, and +go through the installation procedure described above. I.e. the same procedure for installing/updating most Windows programs. You can -install multiple versions of LAMMPS (in different directories), but -only the executable for the last-installed package will be found +install multiple versions of LAMMPS (in different directories), but only +the executable for the last-installed package will be found automatically, so this should only be done for debugging purposes. diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 933294a9f7..4497a1788e 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -8,7 +8,7 @@ systems or rigid-body constraints are in packages. You can see the list of all packages and "make" commands to manage them by typing "make package" from within the src directory of the LAMMPS distribution. The :doc:`Build package ` page gives -general info on how to install and un-install packages as part of the +general info on how to install and uninstall packages as part of the LAMMPS build process. .. toctree:: diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 21a9e3accf..0a893cfb4a 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2210,7 +2210,7 @@ packages, which have styles optimized for CPUs. See src/MAKE/OPTIONS/Makefile.omp for an example. Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner: +install/uninstall the package and build LAMMPS in the usual manner: **Install:** diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index 9e5727bb0e..ea253b8100 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -8,7 +8,7 @@ Packages are supported by either the LAMMPS developers or the contributing authors and written in a syntax and style consistent with the rest of LAMMPS. -The "Examples" column is a sub-directory in the examples directory of the +The "Examples" column is a subdirectory in the examples directory of the distribution which has one or more input scripts that use the package. E.g. "peptide" refers to the examples/peptide directory; PACKAGES/atc refers to the examples/PACKAGES/atc directory. The "Lib" column indicates diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index f795827230..14912b9e0e 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -33,7 +33,7 @@ with ``gl`` or ``atomeye`` or ``pymol`` or ``vmd``, depending on what visualization package you have installed. Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the Pizza.py doc pages for more info: +which is included in the pizza subdirectory. See the Pizza.py doc pages for more info: * `https://lammps.github.io/pizza `_ diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 4dbd6f7d2f..6270443dcf 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -324,7 +324,7 @@ writes log information to file.N. If file is none, then no partition log files are created. This overrides the filename specified in the -log command-line option. This option is useful when working with large numbers of partitions, allowing the partition log files to be -suppressed (-plog none) or placed in a sub-directory (-plog +suppressed (-plog none) or placed in a subdirectory (-plog replica_files/log.lammps) If this option is not used the log file for partition N is log.lammps.N or whatever is specified by the -log command-line option. @@ -341,7 +341,7 @@ partition screen files are created. This overrides the filename specified in the -screen command-line option. This option is useful when working with large numbers of partitions, allowing the partition screen files to be suppressed (-pscreen none) or placed in a -sub-directory (-pscreen replica_files/screen). If this option is not +subdirectory (-pscreen replica_files/screen). If this option is not used the screen file for partition N is screen.N or whatever is specified by the -screen command-line option. diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index d36864b454..0c0a07f4c7 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -33,7 +33,7 @@ path for the default location of this MPI package. After the installation of the MPICH2 software, it needs to be integrated into the system. For this you need to start a Command Prompt in *Administrator Mode* (right click on the icon and select it). Change -into the MPICH2 installation directory, then into the sub-directory +into the MPICH2 installation directory, then into the subdirectory **bin** and execute **smpd.exe -install**\ . Exit the command window. * Get a new, regular command prompt by going to Start->Run... , diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 05069ce9c5..0421cf33e4 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -29,11 +29,11 @@ actively supported by the LAMMPS developers, as they were contributed by LAMMPS users. If you have problems using them, we can direct you to the authors. -The source code for each of these codes is in the tools sub-directory +The source code for each of these codes is in the tools subdirectory of the LAMMPS distribution. There is a Makefile (which you may need to edit for your platform) which will build several of the tools which reside in that directory. Most of them are larger packages in their -own sub-directories with their own Makefiles and/or README files. +own subdirectories with their own Makefiles and/or README files. ---------- @@ -109,7 +109,7 @@ Tool descriptions amber2lmp tool -------------------------- -The amber2lmp sub-directory contains two Python scripts for converting +The amber2lmp subdirectory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information. @@ -145,7 +145,7 @@ since binary files are not compatible across all platforms. ch2lmp tool ------------------------ -The ch2lmp sub-directory contains tools for converting files +The ch2lmp subdirectory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. They are intended to make it easy to use CHARMM as a builder and as a @@ -156,7 +156,7 @@ CHARMM22 and later is available as an option. This tool can also add solvent water molecules and Na+ or Cl- ions to the system. Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. -See the README file in the ch2lmp sub-directory for more information. +See the README file in the ch2lmp subdirectory for more information. These tools were created by Pieter in't Veld (pjintve at sandia.gov) and Paul Crozier (pscrozi at sandia.gov) at Sandia. @@ -638,7 +638,7 @@ you first need to use the :doc:`clear` command. lmp2arc tool ------------ -The lmp2arc sub-directory contains a tool for converting LAMMPS output +The lmp2arc subdirectory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly MSI/Biosym and its Discover MD code). See the README file for more information. @@ -657,7 +657,7 @@ Greathouse at Sandia (jagreat at sandia.gov). lmp2cfg tool ---------------------- -The lmp2cfg sub-directory contains a tool for converting LAMMPS output +The lmp2cfg subdirectory contains a tool for converting LAMMPS output files into a series of \*.cfg files which can be read into the `AtomEye `_ visualizer. See the README file for more information. @@ -704,7 +704,7 @@ detect most LAMMPS restarts, dump, data and log files. Examples: matlab tool ------------------------ -The matlab sub-directory contains several `MATLAB `_ scripts for +The matlab subdirectory contains several `MATLAB `_ scripts for post-processing LAMMPS output. The scripts include readers for log and dump files, a reader for EAM potential files, and a converter that reads LAMMPS dump files and produces CFG files that can be visualized @@ -747,7 +747,7 @@ definition file. This tool was used to create the system for the moltemplate tool ---------------------------------- -The moltemplate sub-directory contains instructions for installing +The moltemplate subdirectory contains instructions for installing moltemplate, a Python-based tool for building molecular systems based on a text-file description, and creating LAMMPS data files that encode their molecular topology as lists of bonds, angles, dihedrals, etc. @@ -765,7 +765,7 @@ The latest sources can be found `on its GitHub page ` command in the PHONON package. @@ -900,7 +900,7 @@ University. polybond tool ---------------------------- -The polybond sub-directory contains a Python-based tool useful for +The polybond subdirectory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file lmpsdata.py provides a "Lmpsdata" class with various methods which can be invoked by a user-written Python script to create data files with @@ -917,7 +917,7 @@ This tool was written by Zachary Kraus at Georgia Tech. pymol_asphere tool ------------------------------- -The pymol_asphere sub-directory contains a tool for converting a +The pymol_asphere subdirectory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the `PyMol visualization package `_ or its `open source variant `_. @@ -938,7 +938,7 @@ This tool was written by Mike Brown at Sandia. python tool ----------------------------- -The python sub-directory contains several Python scripts +The python subdirectory contains several Python scripts that perform common LAMMPS post-processing tasks, such as: * extract thermodynamic info from a log file as columns of numbers @@ -975,7 +975,7 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) smd tool ------------------ -The smd sub-directory contains a C++ file dump2vtk_tris.cpp and +The smd subdirectory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output files created by the Smooth-Mach Dynamics (MACHDYN) package into a VTK-compatible unstructured grid file. It could then be read in and @@ -994,7 +994,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). spin tool -------------------- -The spin sub-directory contains a C file interpolate.c which can +The spin subdirectory contains a C file interpolate.c which can be compiled and used to perform a cubic polynomial interpolation of the MEP following a GNEB calculation. @@ -1011,7 +1011,7 @@ Ivanov, at University of Iceland (ali5 at hi.is). singularity/apptainer tool -------------------------- -The singularity sub-directory contains container definitions files that +The singularity subdirectory contains container definitions files that can be used to build container images for building and testing LAMMPS on specific OS variants using the `Apptainer `_ or `Singularity `_ container software. Contributions for diff --git a/doc/src/pair_reaxff.rst b/doc/src/pair_reaxff.rst index 4640307105..4dac9baf85 100644 --- a/doc/src/pair_reaxff.rst +++ b/doc/src/pair_reaxff.rst @@ -110,7 +110,7 @@ control variable. The format of the control file is described below. not agree. Examples using *pair_style reaxff* are provided in the examples/reax -sub-directory. +subdirectory. Use of this pair style requires that a charge be defined for every atom. See the :doc:`atom_style ` and diff --git a/doc/src/shell.rst b/doc/src/shell.rst index 50f148565c..fb9baffe08 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -74,7 +74,7 @@ will use the new directory. All processors execute this command. The *mkdir* command creates directories similar to the Unix ``mkdir -p`` command. That is, it will attempt to create the entire path of -sub-directories if they do not exist yet. +subdirectories if they do not exist yet. The *mv* command renames a file and/or moves it to a new directory. It cannot rename files across filesystem boundaries or between drives. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index bcc269e451..d86305283d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3432,6 +3432,8 @@ Subclassed subcutoff subcycle subcycling +subdirectory +subdirectories subdomain subdomains subhi @@ -3710,6 +3712,7 @@ undump uniaxial uniaxially unimodal +uninstall unitarg unitless Universite