diff --git a/doc/src/Build.rst b/doc/src/Build.rst index 2e046451cf..7cf2a01992 100644 --- a/doc/src/Build.rst +++ b/doc/src/Build.rst @@ -7,7 +7,7 @@ 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 in the :doc:`Install ` +or automated build trees, as described in the :doc:`Install ` section of the manual. .. toctree:: diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 62979d34df..25326897b8 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -44,7 +44,7 @@ standard. A more detailed discussion of that is below. The executable created by CMake (after running make) is named ``lmp`` unless the ``LAMMPS_MACHINE`` option is set. When setting - ``LAMMPS_MACHINE=name`` the executable will be called + ``LAMMPS_MACHINE=name``, the executable will be called ``lmp_name``. Using ``BUILD_MPI=no`` will enforce building a serial executable using the MPI STUBS library. @@ -107,9 +107,9 @@ MPI and OpenMP support in LAMMPS ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you are installing MPI yourself to build a parallel LAMMPS -executable, we recommend either MPICH or OpenMPI which are regularly +executable, we recommend either MPICH or OpenMPI, which are regularly used and tested with LAMMPS by the LAMMPS developers. MPICH can be -downloaded from the `MPICH home page `_ and +downloaded from the `MPICH home page `_, and OpenMPI can be downloaded correspondingly from the `OpenMPI home page `_. Other MPI packages should also work. No specific vendor provided and standard compliant MPI library is currently @@ -130,12 +130,12 @@ package can be compiled to include OpenMP threading. In addition, there are a few commands in LAMMPS that have native OpenMP support included as well. These are commands in the ``MPIIO``, -``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition +``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore, some packages support OpenMP threading indirectly through the libraries -they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``. -See the :doc:`Packages details ` page for more -info on these packages and the pages for their respective commands -for OpenMP threading info. +they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``. See the +:doc:`Packages details ` page for more info on these +packages, and the pages for their respective commands for OpenMP +threading info. For CMake, if you use ``BUILD_OMP=yes``, you can use these packages and turn on their native OpenMP support and turn on their native OpenMP @@ -144,9 +144,9 @@ variable before you launch LAMMPS. For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS`` variables in Makefile.machine need to include the compiler flag that -enables OpenMP. For GNU compilers it is ``-fopenmp``\ . For (recent) Intel -compilers it is ``-qopenmp``\ . If you are using a different compiler, -please refer to its documentation. +enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ . +For (recent) Intel compilers, it is ``-qopenmp``\ . If you are using a +different compiler, please refer to its documentation. .. _default-none-issues: @@ -174,15 +174,16 @@ Choice of compiler and compile/link options The choice of compiler and compiler flags can be important for maximum performance. Vendor provided compilers for a specific hardware can produce faster code than open-source compilers like the GNU compilers. -On the most common x86 hardware most popular C++ compilers are quite -similar in performance of C/C++ code at high optimization levels. When -using the ``INTEL`` package, there is a distinct advantage in using -the `Intel C++ compiler `_ due to much improved vectorization -through SSE and AVX instructions on compatible hardware as the source -code includes changes and Intel compiler specific directives to enable -high degrees of vectorization. This may change over time as equivalent -vectorization directives are included into OpenMP standard revisions and -other compilers adopt them. +On the most common x86 hardware, the most popular C++ compilers are +quite similar in their ability to optimize regular C/C++ source code at +high optimization levels. When using the ``INTEL`` package, there is a +distinct advantage in using the `Intel C++ compiler `_ due to +much improved vectorization through SSE and AVX instructions on +compatible hardware. The source code in that package conditionally +includes compiler specific directives to enable these high degrees of +vectorization. This may change over time as equivalent vectorization +directives are included into the OpenMP standard and other compilers +adopt them. .. _intel: https://software.intel.com/en-us/intel-compilers @@ -196,7 +197,7 @@ LAMMPS. .. tab:: CMake build By default CMake will use the compiler it finds according to - internal preferences and it will add optimization flags + internal preferences, and it will add optimization flags appropriate to that compiler and any :doc:`accelerator packages ` you have included in the build. CMake will check if the detected or selected compiler is compatible with the @@ -250,9 +251,9 @@ LAMMPS. and `-C ../cmake/presets/pgi.cmake` will switch the compiler to the PGI compilers. - In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add - compiler flags to tune for optimal performance on given hosts. By - default this variable is empty. + Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add + compiler flags to tune for optimal performance on given hosts. + This variable is empty by default. .. note:: @@ -368,10 +369,10 @@ running LAMMPS from Python via its library interface. # no default value The compilation will always produce a LAMMPS library and an - executable linked to it. By default this will be a static library - named ``liblammps.a`` and an executable named ``lmp`` Setting - ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library - called ``liblammps.so`` (or ``liblammps.dylib`` or + executable linked to it. By default, this will be a static + library named ``liblammps.a`` and an executable named ``lmp`` + Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared + library called ``liblammps.so`` (or ``liblammps.dylib`` or ``liblammps.dll`` depending on the platform) If ``LAMMPS_MACHINE=name`` is set in addition, the name of the generated libraries will be changed to either ``liblammps_name.a`` @@ -429,7 +430,7 @@ You may need to use ``sudo make install`` in place of the last line if you do not have write privileges for ``/usr/local/lib`` or use the ``--prefix`` configuration option to select an installation folder, where you do have write access. The end result should be the file -``/usr/local/lib/libmpich.so``. On many Linux installations the folder +``/usr/local/lib/libmpich.so``. On many Linux installations, the folder ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does not require superuser or sudo access. In that case the configuration step becomes: @@ -438,9 +439,10 @@ step becomes: ./configure --enable-shared --prefix=${HOME}/.local -Avoiding to use "sudo" for custom software installation (i.e. from source -and not through a package manager tool provided by the OS) is generally -recommended to ensure the integrity of the system software installation. +Avoiding the use of "sudo" for custom software installation (i.e. from +source and not through a package manager tool provided by the OS) is +generally recommended to ensure the integrity of the system software +installation. ---------- @@ -514,11 +516,11 @@ using CMake or Make. Install LAMMPS after a build ------------------------------------------ -After building LAMMPS, you may wish to copy the LAMMPS executable of -library, along with other LAMMPS files (library header, doc files) to -a globally visible place on your system, for others to access. Note -that you may need super-user privileges (e.g. sudo) if the directory -you want to copy files to is protected. +After building LAMMPS, you may wish to copy the LAMMPS executable or +library, along with other LAMMPS files (library header, doc files), to a +globally visible place on your system, for others to access. Note that +you may need super-user privileges (e.g. sudo) if the directory you want +to copy files to is protected. .. tabs:: @@ -536,7 +538,7 @@ you want to copy files to is protected. environment variable, if you are installing LAMMPS into a non-system location and/or are linking to libraries in a non-system location that depend on such runtime path settings. - As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH`` + As an alternative, you may set the CMake variable ``LAMMPS_INSTALL_RPATH`` to ``on`` and then the runtime paths for any linked shared libraries and the library installation folder for the LAMMPS library will be embedded and thus the requirement to set environment variables is avoided. diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 1ab86badc8..9be2c33165 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -63,9 +63,9 @@ software or for people that want to modify or extend LAMMPS. Getting started ^^^^^^^^^^^^^^^ -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 +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, diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index c2645a2118..416b49c685 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -46,7 +46,7 @@ It can be enabled for all C++ code with the following CMake flag With this flag enabled all source files will be processed twice, first to be compiled and then to be analyzed. Please note that the analysis can be -significantly more time consuming than the compilation itself. +significantly more time-consuming than the compilation itself. ---------- diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index 79868de83c..3800e41e21 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -1,33 +1,32 @@ Link LAMMPS as a library to another code ======================================== -LAMMPS is designed as a library of C++ objects that can be -integrated into other applications including Python scripts. -The files ``src/library.cpp`` and ``src/library.h`` define a -C-style API for using LAMMPS as a library. See the -:doc:`Howto_library` page -for a description of the interface and how to use it for your needs. +LAMMPS is designed as a library of C++ objects that can be integrated +into other applications, including Python scripts. The files +``src/library.cpp`` and ``src/library.h`` define a C-style API for using +LAMMPS as a library. See the :doc:`Howto_library` page for a +description of the interface and how to use it for your needs. -The :doc:`Build_basics` page explains how to build -LAMMPS as either a shared or static library. This results in a file -in the compilation folder called ``liblammps.a`` or ``liblammps_.a`` -in case of building a static library. In case of a shared library -the name is the same only that the suffix is going to be either ``.so`` -or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS. -In some cases the ``.so`` file may be a symbolic link to a file with -the suffix ``.so.0`` (or some other number). +The :doc:`Build_basics` page explains how to build LAMMPS as either a +shared or static library. This results in a file in the compilation +folder called ``liblammps.a`` or ``liblammps_.a`` in case of +building a static library. In case of a shared library, the name is the +same only that the suffix is going to be either ``.so`` or ``.dylib`` or +``.dll`` instead of ``.a`` depending on the OS. In some cases, the +``.so`` file may be a symbolic link to a file with the suffix ``.so.0`` +(or some other number). .. note:: Care should be taken to use the same MPI library for the calling code - and the LAMMPS library unless LAMMPS is to be compiled without (real) - MPI support using the include STUBS MPI library. + and the LAMMPS library, unless LAMMPS is to be compiled without (real) + MPI support using the included STUBS MPI library. Link with LAMMPS as a static library ------------------------------------ The calling application can link to LAMMPS as a static library with -compilation and link commands as in the examples shown below. These +compilation and link commands, as in the examples shown below. These are examples for a code written in C in the file ``caller.c``. The benefit of linking to a static library is, that the resulting executable is independent of that library since all required @@ -142,10 +141,10 @@ Link with LAMMPS as a shared library When linking to LAMMPS built as a shared library, the situation becomes much simpler, as all dependent libraries and objects are either included in the shared library or registered as a dependent library in the shared -library file. Thus those libraries need not to be specified when -linking the calling executable. Only the *-I* flags are needed. So the -example case from above of the serial version static LAMMPS library with -the POEMS package installed becomes: +library file. Thus, those libraries need not be specified when linking +the calling executable. Only the *-I* flags are needed. So the example +case from above of the serial version static LAMMPS library with the +POEMS package installed becomes: .. tabs:: diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index efa9332cce..f1e34bbc55 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -73,12 +73,12 @@ clean-``. .. note:: Before the actual compilation starts, LAMMPS will perform several - steps to collect information from the configuration and setup that - is then embedded into the executable. When you build LAMMPS for - the first time, it will also compile a tool to quickly assemble - a list of dependencies, that are required for the make program to - correctly detect which parts need to be recompiled after changes - were made to the sources. + steps to collect information from the configuration and setup that is + then embedded into the executable. When you build LAMMPS for the + first time, it will also compile a tool to quickly determine a list + of dependencies. Those are required for the make program to + correctly detect, which files need to be recompiled or relinked + after changes were made to the sources. Customized builds and alternate makefiles ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index cde210780d..896edc7d4b 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -7,10 +7,11 @@ rigid-body constraints are in packages. In the src directory, each 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. +page. Brief overviews of each package are on the :doc:`Packages details +` page. When building LAMMPS, you can choose to include or exclude each -package. In general there is no need to include a package if you +package. Generally, there is no need to include a package if you never plan to use its features. If you get a run-time error that a LAMMPS command or style is @@ -167,9 +168,9 @@ control flow constructs for more complex operations. LAMMPS includes several of these files to define configuration "presets", similar to the options that exist for the Make based -system. Using these files you can enable/disable portions of the -available packages in LAMMPS. If you need a custom preset you can take -one of them as a starting point and customize it to your needs. +system. Using these files, you can enable/disable portions of the +available packages in LAMMPS. If you need a custom preset, you can +make a copy of one of them and modify it to suit your needs. .. code-block:: bash @@ -183,7 +184,7 @@ one of them as a starting point and customize it to your needs. cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages - mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross compilers + mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers Presets that have names starting with "windows" are specifically for compiling LAMMPS :doc:`natively on Windows ` and @@ -272,7 +273,7 @@ not installed. Type ``make package-update`` or ``make pu`` to overwrite src files with 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 +with git `, this will only update the files in the package subdirectories, but not the copies in the src folder. Type ``make package-overwrite`` to overwrite files in the package diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 2d83908bb1..c2e7b94b0e 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -1,8 +1,8 @@ Optional build settings ======================= -LAMMPS can be built with several optional settings. Each sub-section -explain how to do this for building both with CMake and make. +LAMMPS can be built with several optional settings. Each subsection +explains how to do this for building both with CMake and make. * `C++11 standard compliance`_ when building all of LAMMPS * `FFT library`_ for use with the :doc:`kspace_style pppm ` command @@ -41,7 +41,7 @@ FFT library When the KSPACE package is included in a LAMMPS build, the :doc:`kspace_style pppm ` command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT -library is included with LAMMPS but other libraries can be faster. +library is included with LAMMPS, but other libraries can be faster. LAMMPS can use them if they are available on your system. .. tabs:: @@ -63,9 +63,9 @@ LAMMPS can use them if they are available on your system. Usually these settings are all that is needed. If FFTW3 is selected, then CMake will try to detect, if threaded FFTW libraries are available and enable them by default. This setting - is independent of whether OpenMP threads are enabled and a - packages like KOKKOS or OPENMP is used. If CMake cannot detect - the FFT library, you can set these variables to assist: + is independent of whether OpenMP threads are enabled and a package + like KOKKOS or OPENMP is used. If CMake cannot detect the FFT + library, you can set these variables to assist: .. code-block:: bash @@ -141,18 +141,18 @@ The Intel MKL math library is part of the Intel compiler suite. It can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting above). -Performing 3d FFTs in parallel can be time consuming due to data -access and required communication. This cost can be reduced by -performing single-precision FFTs instead of double precision. Single -precision means the real and imaginary parts of a complex datum are -4-byte floats. Double precision means they are 8-byte doubles. Note -that Fourier transform and related PPPM operations are somewhat less -sensitive to floating point truncation errors and thus the resulting -error is less than the difference in precision. Using the ``-DFFT_SINGLE`` -setting trades off a little accuracy for reduced memory use and -parallel communication costs for transposing 3d FFT data. +Performing 3d FFTs in parallel can be time-consuming due to data access +and required communication. This cost can be reduced by performing +single-precision FFTs instead of double precision. Single precision +means the real and imaginary parts of a complex datum are 4-byte floats. +Double precision means they are 8-byte doubles. Note that Fourier +transform and related PPPM operations are somewhat less sensitive to +floating point truncation errors, and thus the resulting error is +generally less than the difference in precision. Using the +``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory +use and parallel communication costs for transposing 3d FFT data. -When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW +When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW library a second time with support for single-precision. For FFTW3, do the following, which should produce the additional @@ -177,11 +177,11 @@ ARRAY mode. Size of LAMMPS integer types and size limits -------------------------------------------- -LAMMPS has a few integer data types which can be defined as either -4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time. -This has an impact on the size of a system that can be simulated -or how large counters can become before "rolling over". -The default setting of "smallbig" is almost always adequate. +LAMMPS uses a few custom integer data types, which can be defined as +either 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time. +This has an impact on the size of a system that can be simulated, or how +large counters can become before "rolling over". The default setting of +"smallbig" is almost always adequate. .. tabs:: @@ -254,7 +254,7 @@ topology information, though IDs are enabled by default. The :doc:`atom_modify id no ` command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Similarly, some force or compute or fix styles -require atom IDs. Thus if you model a molecular system or use one of +require atom IDs. Thus, if you model a molecular system or use one of those styles with more than 2 billion atoms, you need the "bigbig" setting. @@ -264,7 +264,7 @@ systems and 500 million for systems with bonds (the additional restriction is due to using the 2 upper bits of the local atom index in neighbor lists for storing special bonds info). -Image flags store 3 values per atom in a single integer which count the +Image flags store 3 values per atom in a single integer, which count the number of times an atom has moved through the periodic box in each dimension. See the :doc:`dump ` manual page for a discussion. If an atom moves through the periodic box more than this limit, the value @@ -285,7 +285,7 @@ Output of JPG, PNG, and movie files -------------------------------------------------- The :doc:`dump image ` command has options to output JPEG or -PNG image files. Likewise the :doc:`dump movie ` command +PNG image files. Likewise, the :doc:`dump movie ` command outputs movie files in a variety of movie formats. Using these options requires the following settings: @@ -354,7 +354,7 @@ Read or write compressed files If this option is enabled, large files can be read or written with compression by ``gzip`` or similar tools by several LAMMPS commands, including :doc:`read_data `, :doc:`rerun `, and -:doc:`dump `. Currently supported compression tools are: +:doc:`dump `. Supported compression tools are currently ``gzip``, ``bzip2``, ``zstd``, and ``lzma``. .. tabs:: @@ -394,7 +394,7 @@ Memory allocation alignment --------------------------------------- This setting enables the use of the "posix_memalign()" call instead of -"malloc()" when LAMMPS allocates large chunks or memory. Vector +"malloc()" when LAMMPS allocates large chunks of memory. Vector instructions on CPUs may become more efficient, if dynamically allocated memory is aligned on larger-than-default byte boundaries. On most current operating systems, the "malloc()" implementation returns @@ -496,7 +496,7 @@ Trigger selected floating-point exceptions ------------------------------------------ Many kinds of CPUs have the capability to detect when a calculation -results in an invalid math operation like a division by zero or calling +results in an invalid math operation, like a division by zero or calling the square root with a negative argument. The default behavior on most operating systems is to continue and have values for ``NaN`` (= not a number) or ``Inf`` (= infinity). This allows software to detect and diff --git a/doc/src/Developer_grid.rst b/doc/src/Developer_grid.rst index cbc3610c9f..2b0838ab6c 100644 --- a/doc/src/Developer_grid.rst +++ b/doc/src/Developer_grid.rst @@ -160,7 +160,7 @@ cells (the entire allocated grid). Grid class constructors ^^^^^^^^^^^^^^^^^^^^^^^ -The following sub-sections describe the public methods of the Grid3d +The following subsections describe the public methods of the Grid3d class which a style command can invoke. The Grid2d methods are similar; simply remove arguments which refer to the z-dimension. diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index ab7723e8fb..0b465d318b 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -315,7 +315,7 @@ add changes. Please watch the comments to the pull requests. The two "test" labels are used to trigger extended tests before the code is merged. This is sometimes done by LAMMPS developers, if they suspect that there may be some subtle side effects from your changes. It is not -done by default, because those tests are very time consuming. The +done by default, because those tests are very time-consuming. The *ready_for_merge* label is usually attached when the LAMMPS developer assigned to the pull request considers this request complete and to trigger a final full test evaluation. diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 6c76eef184..851b7703fd 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -26,7 +26,7 @@ discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS ` which can then generate values that can then be output with these commands. -The following sub-sections discuss different LAMMPS commands related +The following subsections discuss different LAMMPS commands related to output and the kind of data they operate on and produce: * :ref:`Global/per-atom/local/per-grid data ` diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index f23198e36f..9e14bdf2aa 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -93,7 +93,7 @@ With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be tested via benchmark runs for a specific simulation running on a specific machine, paying attention to guidelines discussed in the next -sub-section. +subsection. A description of the multi-threading strategy used in the OPENMP package and some performance examples are diff --git a/doc/src/balance.rst b/doc/src/balance.rst index bb66598546..a18d25c7ce 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -350,7 +350,7 @@ particles in that sub-box. .. _weighted_balance: -This sub-section describes how to perform weighted load balancing +This subsection describes how to perform weighted load balancing using the *weight* keyword. By default, all particles have a weight of 1.0, which means each diff --git a/doc/src/compute_efield_wolf_atom.rst b/doc/src/compute_efield_wolf_atom.rst index c6845c5045..45ec123ebb 100644 --- a/doc/src/compute_efield_wolf_atom.rst +++ b/doc/src/compute_efield_wolf_atom.rst @@ -81,7 +81,7 @@ cutoff of any pair style force computation. :class: note This compute will loop over a full neighbor list just like a pair - style does when computing forces, thus it can be quite time consuming + style does when computing forces, thus it can be quite time-consuming and slow down a calculation significantly when its data is used in every time step. The :doc:`compute efield/atom ` command of the DIELECTRIC package is more diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 1953aee7e7..413c5f5c3c 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -86,7 +86,7 @@ Matter papers: :ref:`(Duffy) ` and :ref:`(Rutherford) a primary knock-on atom (PKA) was initialized with a high velocity to simulate a radiation event. -The description in this sub-section applies to all 3 fix styles: +The description in this subsection applies to all 3 fix styles: *ttm*, *ttm/grid*, and *ttm/mod*. Fix *ttm/grid* distributes the regular grid across processors consistent diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index a03036de1c..d4d69c7af0 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -136,7 +136,7 @@ where bx,by,bz are the 3 values specified for the *basis* keyword. ---------- -This sub-section discusses the arguments that determine how the +This subsection discusses the arguments that determine how the idealized unit cell is transformed into a lattice of points within the simulation box. diff --git a/doc/src/processors.rst b/doc/src/processors.rst index 64959ec6b2..be11ed3e32 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -134,8 +134,8 @@ processors to the grid is determined by the *map* keyword setting. The *twolevel* style can be used on machines with multicore nodes to minimize off-node communication. It insures that contiguous -sub-sections of the 3d grid are assigned to all the cores of a node. -For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of +subsections of the 3d grid are assigned to all the cores of a node. +For example if *Nc* is 4, then 2x2x1 or 2x1x2 or 1x2x2 subsections of the 3d grid will correspond to the cores of each node. This affects both the factorization and mapping steps. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index d86305283d..2d12ce6845 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3016,6 +3016,7 @@ reinit reinitflag relaxbox relink +relinked relres relTol relu