diff --git a/doc/Makefile b/doc/Makefile index 81f3623499..9069fa1d60 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt)) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) -.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check +.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check # ------------------------------------------ @@ -42,6 +42,8 @@ help: @echo " old create old-style HTML doc pages in old dir" @echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " epub create ePUB format manual for e-book readers" + @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" + @echo " (requires ebook-convert tool from calibre)" @echo " clean remove all intermediate RST files" @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" @@ -106,6 +108,11 @@ epub: $(OBJECTS) @rm -rf epub @echo "Build finished. The ePUB manual file is created." +mobi: epub + @rm -f LAMMPS.mobi + @ebook-convert LAMMPS.epub LAMMPS.mobi + @echo "Conversion finished. The MOBI manual file is created." + pdf: utils/txt2html/txt2html.exe @(\ set -e; \ diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index cee78aced3..6924e73417 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -61,7 +61,7 @@ library files. Failing this, these 3 variables can be used to specify where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH) are found, and the name of the library files (MPI_LIB). -For a serial build, you need to specify the 3 varaibles, as shown +For a serial build, you need to specify the 3 variables, as shown above. For a serial LAMMPS build, use the dummy MPI library provided in @@ -145,7 +145,7 @@ By default CMake will use a compiler it finds and it will add optimization flags appropriate to that compiler and any "accelerator packages"_Speed_packages.html you have included in the build. -You can tell CMake to look for a specific compiler with these varaible +You can tell CMake to look for a specific compiler with these variable settings. Likewise you can specify the FLAGS variables if you want to experiment with alternate optimization flags. You should specify all 3 compilers, so that the small number of LAMMPS source files written @@ -216,8 +216,8 @@ LAMMPS can be built as either an executable or as a static or shared library. The LAMMPS library can be called from another application or a scripting language. See the "Howto couple"_Howto_couple.html doc page for more info on coupling LAMMPS to other codes. See the -"Python"_Python doc page for more info on wrapping and running LAMMPS -from Python via its library interface. +"Python"_Python_head.html doc page for more info on wrapping and +running LAMMPS from Python via its library interface. [CMake variables]: @@ -247,7 +247,7 @@ Note that for a shared library to be usable by a calling program, all the auxiliary libraries it depends on must also exist as shared libraries. This will be the case for libraries included with LAMMPS, such as the dummy MPI library in src/STUBS or any package libraries in -the lib/packages directroy, since they are always built as shared +the lib/packages directory, since they are always built as shared libraries using the -fPIC switch. However, if a library like MPI or FFTW does not exist as a shared library, the shared library build will generate an error. This means you will need to install a shared @@ -299,7 +299,7 @@ Install LAMMPS after a build :h4,link(install) 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 priveleges (e.g. sudo) if the directory +that you may need super-user privileges (e.g. sudo) if the directory you want to copy files to is protected. [CMake variable]: diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 08c1c72180..f8b52056fc 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -40,7 +40,7 @@ executable called "lmp" and a library called "liblammps.a" in the If your machine has multiple CPU cores (most do these days), using a command like "make -jN" (with N being the number of available local CPU cores) can be much faster. If you plan to do development on -LAMMPS or need to recompile LAMMPS repeatedly, installation of the +LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up compilation even more. After compilation, you can optionally copy the LAMMPS executable and @@ -50,7 +50,7 @@ make install # optional, copy LAMMPS executable & library elsewhere :pre :line -There are 3 variants of CMake: a command-line verison (cmake), a text mode +There are 3 variants of CMake: a command-line version (cmake), a text mode UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use any of them interchangeably to configure and create the LAMMPS build environment. On Linux all the versions produce a Makefile as their @@ -188,7 +188,7 @@ module list # is a cmake module already loaded? module avail # is a cmake module available? module load cmake3 # load cmake module with appropriate name :pre -Most Linux distributions offer precompiled cmake packages through +Most Linux distributions offer pre-compiled cmake packages through their package management system. If you do not have CMake or a new enough version, you can download the latest version at "https://cmake.org/download/"_https://cmake.org/download/. diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 5c33a0a4d4..088ffd8972 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -340,7 +340,7 @@ NOTE: the use of the MEAM package is discouraged, as it has been superseded by the USER-MEAMC package, which is a direct translation of the Fortran code in the MEAM library to C++. The code in USER-MEAMC should be functionally equivalent to the MEAM package, fully supports -use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn +use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does not), and has optimizations that make it significantly faster than the MEAM package. @@ -470,7 +470,7 @@ lib/python/README for more details. -D PYTHON_EXECUTABLE=path # path to Python executable to use :pre -Without this setting, CMake will ues the default Python on your +Without this setting, CMake will guess the default Python on your system. To use a different Python version, you can either create a virtualenv, activate it and then run cmake. Or you can set the PYTHON_EXECUTABLE variable to specify which Python interpreter should @@ -687,7 +687,7 @@ the HDF5 library. No additional settings are needed besides "-D PKG_USER-H5MD=yes". -This should autodetect the H5MD library on your system. Several +This should auto-detect the H5MD library on your system. Several advanced CMake H5MD options exist if you need to specify where it is installed. Use the ccmake (terminal window) or cmake-gui (graphical) tools to see these options and set them interactively from their user @@ -777,7 +777,7 @@ on your system. No additional settings are needed besides "-D PKG_USER-NETCDF=yes". -This should autodetect the NETCDF library if it is installed on your +This should auto-detect the NETCDF library if it is installed on your system at standard locations. Several advanced CMake NETCDF options exist if you need to specify where it was installed. Use the ccmake (terminal window) or cmake-gui (graphical) tools to see these options @@ -905,7 +905,7 @@ Eigen3 is a template library, so you do not need to build it. -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and -inside the CMake build directory. If the Eig3n3 library is already on +inside the CMake build directory. If the Eigen3 library is already on your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR is the directory the Eigen3++ include file is in. @@ -936,7 +936,7 @@ your system. No additional settings are needed besides "-D PKG_USER-VTK=yes". -This should autodetect the VTK library if it is installed on your +This should auto-detect the VTK library if it is installed on your system at standard locations. Several advanced VTK options exist if you need to specify where it was installed. Use the ccmake (terminal window) or cmake-gui (graphical) tools to see these options and set diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt index c00ce1f420..ad18695e46 100644 --- a/doc/src/Build_make.txt +++ b/doc/src/Build_make.txt @@ -35,16 +35,16 @@ This initial 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), using a command like "make -jN mpi" (with N = the number of available CPU cores) can be much faster. If you plan to -do development on LAMMPS or need to recompile LAMMPS repeatedly, the +do development on LAMMPS or need to re-compile LAMMPS repeatedly, the installation of the ccache (= Compiler Cache) software may speed up compilation even more. 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 recompile and relink the LAMMPS +uninstalling packages), you must re-compile and relink the LAMMPS executable with the same "make" command. This makefiles dependencies should insure that only the subset of files that need to be are -recompiled. +re-compiled. NOTE: When you build LAMMPS for the first time, a long list of *.d files will be printed out rapidly. This is not an error; it is the @@ -71,8 +71,8 @@ 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 configs, and LAMMPS itself keep changing, their settings -may become outdated: +compilers, OS configurations, and LAMMPS itself keep changing, their +settings may become outdated: make mac # build serial LAMMPS on a Mac make mac_mpi # build parallel LAMMPS on a Mac diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index 773217e3a0..500130ecee 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -80,8 +80,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run using the "kspace_style -pppm"_kspace_style.html command. The "Run output"_doc page gives more -details. +pppm"_kspace_style.html command. The "Run output"_Run_output.html +doc page gives more details. FFTW is a fast, portable FFT library that should also work on any platform and can be faster than the KISS FFT library. You can @@ -101,7 +101,7 @@ 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 precesion means they are 8-byte doubles. Note +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 @@ -193,7 +193,7 @@ Output of JPG, PNG, and movie files :h4,link(graphics) The "dump image"_dump_image.html command has options to output JPEG or PNG image files. Likewise the "dump movie"_dump_image.html command -ouputs movie files in MPEG format. Using these options requires the +outputs movie files in MPEG format. Using these options requires the following settings: [CMake variables]: @@ -206,7 +206,7 @@ following settings: # default = yes if CMake can find ffmpeg, else no :pre Usually these settings are all that is needed. If CMake cannot find -the graphics header, library, executuable files, you can set these +the graphics header, library, executable files, you can set these variables: -D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index da257ccbc8..0caad589fb 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -84,7 +84,7 @@ with the cross-compiler environment on Fedora machines. Please keep in mind, though, that this only applies to compiling LAMMPS. Whether the resulting binaries do work correctly is no tested by the LAMMPS developers. We instead rely on the feedback of the users -of these precompiled LAMMPS packages for Windows. We will try to resolve +of these pre-compiled LAMMPS packages for Windows. We will try to resolve issues to the best of our abilities if we become aware of them. However this is subject to time constraints and focus on HPC platforms. diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index 13db1272b9..aec5a9db8b 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -19,7 +19,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c All commands :h3 -An alphabetic list of all LAMMPS commmands. +An alphabetic list of all LAMMPS commands. "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index 48069d3120..0cf433d53a 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -95,7 +95,7 @@ OPT. "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, "nharmonic (o)"_dihedral_nharmonic.html, -"opls (iko)"_dihedral_opls.htm;, +"opls (iko)"_dihedral_opls.html, "quadratic (o)"_dihedral_quadratic.html, "spherical (o)"_dihedral_spherical.html, "table (o)"_dihedral_table.html, diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt index cbe2261986..1d7c754fa7 100644 --- a/doc/src/Commands_parse.txt +++ b/doc/src/Commands_parse.txt @@ -14,7 +14,7 @@ LAMMPS commands are case sensitive. Command names are lower-case, as are specified command arguments. Upper case letters may be used in file names or user-chosen ID strings. -Here are 6 rulse for how each line in the input script is parsed by +Here are 6 rules for how each line in the input script is parsed by LAMMPS: (1) If the last printable character on the line is a "&" character, @@ -71,7 +71,7 @@ floating-point value. The format string is used to output the result of the variable expression evaluation. If a format string is not specified a high-precision "%.20g" is used as the default. -This can be useful for formatting print output to a desired precion: +This can be useful for formatting print output to a desired precision: print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index d279b5e975..a74182967c 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -743,7 +743,7 @@ Self-explanatory. :dd Self-explanatory. :dd -{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt +{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt Single precision cannot be used with MSM. :dd @@ -5078,7 +5078,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/point requires atom attribute q} :dt @@ -5092,7 +5092,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/shielded requires atom attribute q} :dt @@ -5110,7 +5110,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/slater requires atom attribute q} :dt @@ -5541,7 +5541,7 @@ See the package gpu command. :dd {GPUs are requested but Kokkos has not been compiled for CUDA} :dt -Recompile Kokkos with CUDA support to use GPUs. :dd +Re-compile Kokkos with CUDA support to use GPUs. :dd {Ghost velocity forward comm not yet implemented with Kokkos} :dt diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index dd3402ba86..98b66f2aa5 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -13,7 +13,7 @@ This is an alphabetic list of the WARNING messages LAMMPS prints out and the reason why. If the explanation here is not sufficient, the documentation for the offending command may help. Warning messages also list the source file and line number where the warning was -generated. For example, a message lile this: +generated. For example, a message like this: WARNING: Bond atom missing in box size check (domain.cpp:187) :pre diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt index 7c3db89152..3323334600 100644 --- a/doc/src/Howto_barostat.txt +++ b/doc/src/Howto_barostat.txt @@ -64,11 +64,11 @@ Thermodynamic output, which can be setup via the "thermo_style"_thermo_style.html command, often includes pressure values. As explained on the doc page for the "thermo_style"_thermo_style.html command, the default pressure is -setup by the thermo command itself. It is NOT the presure associated +setup by the thermo command itself. It is NOT the pressure associated with any barostatting fix you have defined or with any compute you -have defined that calculates a presure. The doc pages for the +have defined that calculates a pressure. The doc pages for the barostatting fixes explain the ID of the pressure compute they create. -Thus if you want to view these pressurse, you need to specify them +Thus if you want to view these pressures, you need to specify them explicitly via the "thermo_style custom"_thermo_style.html command. Or you can use the "thermo_modify"_thermo_modify.html command to re-define what pressure compute is used for default thermodynamic diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt index 3535349b46..3e7db9bc8e 100644 --- a/doc/src/Howto_body.txt +++ b/doc/src/Howto_body.txt @@ -337,7 +337,7 @@ the sphere that surrounds each vertex. The diameter value can be different for each body particle. These floating-point values can be listed on as many lines as you wish; see the "read_data"_read_data.html command for more details. Because the -maxmimum vertices per face is hard-coded to be 4 +maximum number of vertices per face is hard-coded to be 4 (i.e. quadrilaterals), faces with more than 4 vertices need to be split into triangles or quadrilaterals. For triangular faces, the last vertex index should be set to -1. diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt index 741078e7eb..9a9656784c 100644 --- a/doc/src/Howto_library.txt +++ b/doc/src/Howto_library.txt @@ -171,16 +171,16 @@ void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, The gather functions collect peratom info of the requested type (atom coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter +same vector of values to each calling processor. The scatter functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. +passed by all calling processors, to individual atoms, which may be +owned by different processors. The lammps_gather_atoms() function does this for all N atoms in the system, ordered by atom ID, from 1 to N. The lammps_gather_atoms_concat() function does it for all N atoms, but simply concatenates the subset of atoms owned by each processor. The -resulting vector is not ordered by atom ID. Atom IDs can be requetsed +resulting vector is not ordered by atom ID. Atom IDs can be requested by the same function if the caller needs to know the ordering. The lammps_gather_subset() function allows the caller to request values for only a subset of atoms (identified by ID). diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt index 8be4b66e78..a12bf13f2e 100644 --- a/doc/src/Howto_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -73,7 +73,7 @@ that package into your current Python installation. cd $LAMMPS_DIR/python python install.py :pre -NOTE: Recompiling the shared library requires reinstalling the Python package +NOTE: Recompiling the shared library requires re-installing the Python package Installation inside of a virtualenv :h5 diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt index 1e737df655..4dfe4e2f6c 100644 --- a/doc/src/Howto_spherical.txt +++ b/doc/src/Howto_spherical.txt @@ -159,7 +159,7 @@ ellipsoidal particles: The advantage of these fixes is that those which thermostat the particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The "fix langevin"_fix_langevin +calculation and thermostatting. The "fix langevin"_fix_langevin.html command can also be used with its {omgea} or {angmom} options to thermostat the rotational degrees of freedom for spherical or ellipsoidal particles. Other thermostatting fixes only operate on the diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index 1b9adb49a5..b549f99be2 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Magnetic spins :h3 -The magnetic spin simualtions are enabled by the SPIN package, whose +The magnetic spin simulations are enabled by the SPIN package, whose implementation is detailed in "Tranchida"_#Tranchida7. -The model representents the simulation of atomic magnetic spins coupled +The model represents the simulation of atomic magnetic spins coupled to lattice vibrations. The dynamics of those magnetic spins can be used to simulate a broad range a phenomena related to magneto-elasticity, or or to study the influence of defects on the magnetic properties of @@ -43,7 +43,7 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate the thermal energy of the Langevin thermostat, or to perform a relaxation of the magnetic configuration toward an equilibrium state. -All the computed magnetic properties can be outputed by two main +All the computed magnetic properties can be output by two main commands. The first one is "compute spin"_compute_spin.html, that enables to evaluate magnetic averaged quantities, such as the total magnetization of the system along x, y, or z, the spin temperature, or diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt index 3d0b27370e..ff9b14c12c 100644 --- a/doc/src/Install_patch.txt +++ b/doc/src/Install_patch.txt @@ -17,10 +17,11 @@ how to stay current are on the "Install git"_Install_git.html and If you prefer to download a tarball, as described on the "Install git"_Install_tarball.html doc page, you can stay current by downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the "bug and feature page"_bug of the -website, along with a list of changed files and details about what is -in the new patch release. This page explains how to apply the patch -file to your local LAMMPS directory. +a patch file is posted on the "bug and feature +page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along +with a list of changed files and details about what is in the new patch +release. This page explains how to apply the patch file to your local +LAMMPS directory. NOTE: You should not apply patch files to a local Git or SVN repo of LAMMPS, only to an unpacked tarball. Use Git and SVN commands to diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt index 49c14bc5f0..cd822c778f 100644 --- a/doc/src/Intro_overview.txt +++ b/doc/src/Intro_overview.txt @@ -17,7 +17,7 @@ variety of interatomic potentials (force fields) and boundary conditions. It can model 2d or 3d systems with only a few particles up to millions or billions. -LAMMPS can be built and run on a laptop or destop machine, but is +LAMMPS can be built and run on a laptop or desktop machine, but is designed for parallel computers. It will run on any parallel machine that supports the "MPI"_mpi message-passing library. This includes shared-memory boxes and distributed-memory clusters and @@ -45,7 +45,7 @@ nature; some long-range models are included as well. LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes -too large. This is in contrast to methods used for modeling plasmas +too large. This is in contrast to methods used for modeling plasma or gravitational bodies (e.g. galaxy formation). On parallel machines, LAMMPS uses spatial-decomposition techniques to diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt index a6b881cb79..ac12dd7b2e 100644 --- a/doc/src/Manual_build.txt +++ b/doc/src/Manual_build.txt @@ -10,15 +10,16 @@ Section"_Manual.html :c Building the LAMMPS manual :h2 -Depending on how you obtained LAMMPS, the doc directory has -2 or 3 sub-directories and optionally 2 PDF files and an ePUB file: +Depending on how you obtained LAMMPS, the doc directory has 2 or 3 +sub-directories and optionally 2 PDF files and 2 e-book format files: src # content files for LAMMPS documentation html # HTML version of the LAMMPS manual (see html/Manual.html) tools # tools and settings for building the documentation Manual.pdf # large PDF version of entire manual Developer.pdf # small PDF with info about how LAMMPS is structured -LAMMPS.epub # Manual in ePUB format :pre +LAMMPS.epub # Manual in ePUB e-book format +LAMMPS.mobi # Manual in MOBI e-book format :pre If you downloaded LAMMPS as a tarball from the web site, all these directories and files should be included. @@ -40,7 +41,7 @@ HTML files already exist. This requires various tools including Sphinx, which the build process will attempt to download and install on your system, if not already available. See more details below. -(c) You can genererate an older, simpler, less-fancy style of HTML +(c) You can generate an older, simpler, less-fancy style of HTML documentation by typing "make old". This will create an "old" directory. This can be useful if (b) does not work on your box for some reason, or you want to quickly view the HTML version of a doc @@ -61,6 +62,7 @@ make old # generate old-style HTML pages in old dir via txt2html make fetch # fetch HTML doc pages and 2 PDF files from web site # as a tarball and unpack into html dir and 2 PDFs make epub # generate LAMMPS.epub in ePUB format using Sphinx +make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert make clean # remove intermediate RST files created by HTML build make clean-all # remove entire build folder and any cached data :pre @@ -68,7 +70,7 @@ make clean-all # remove entire build folder and any cached data :pre Installing prerequisites for HTML build :h3 -To run the HTML documention build toolchain, Python 3 and virtualenv +To run the HTML documentation build toolchain, Python 3 and virtualenv have to be installed. Here are instructions for common setups: Ubuntu :h4 @@ -115,10 +117,8 @@ ePUB :h4 Same as for HTML. This uses the same tools and configuration files as the HTML tree. -For converting the generated ePUB file to a mobi format file +For converting the generated ePUB file to a MOBI format file (for e-book readers like Kindle, that cannot read ePUB), you also need to have the 'ebook-convert' tool from the "calibre" software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/ -You first create the ePUB file with 'make epub' and then do: - -ebook-convert LAMMPS.epub LAMMPS.mobi :pre +You first create the ePUB file and then convert it with 'make mobi' diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt index cf94b40281..4ab1eddf21 100644 --- a/doc/src/Modify_overview.txt +++ b/doc/src/Modify_overview.txt @@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Overview :h3 The best way to add a new feature to LAMMPS is to find a similar -featureand look at the corresponding source and header files to figure +feature and look at the corresponding source and header files to figure out what it does. You will need some knowledge of C++ to be able to understand the hi-level structure of LAMMPS and its class organization, but functions (class methods) that do actual diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 892774be38..381dc2e995 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -297,7 +297,7 @@ lib/gpu/README "Section 2.6 -sf gpu"_Run_options.html "Section 2.6 -pk gpu"_Run_options.html "package gpu"_package.html -"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g) +"Commands all"_lc pages (pair,kspace) for styles followed by (g) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -412,7 +412,7 @@ lib/kokkos/README "Section 2.6 -sf kk"_Run_options.html "Section 2.6 -pk kokkos"_Run_options.html "package kokkos"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -851,7 +851,7 @@ multi-replica simulations in LAMMPS. Methods in the package include nudged elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated dynamics (TAD), parallel tempering, and a verlet/split algorithm for performing long-range Coulombics on one set -of processors, and the remainder of the force field calcalation on +of processors, and the remainder of the force field calculation on another set. [Supporting info:] @@ -874,7 +874,7 @@ RIGID package :link(PKG-RIGID),h4 [Contents:] Fixes which enforce rigid constraints on collections of atoms or -particles. This includes SHAKE and RATTLE, as well as varous +particles. This includes SHAKE and RATTLE, as well as various rigid-body integrators for a few large bodies or many small bodies. Also several computes which calculate properties of rigid bodies. @@ -1370,7 +1370,7 @@ which have styles optimized for CPUs and KNLs. You need to have an Intel compiler, version 14 or higher to take full advantage of this package. While compilation with GNU compilers is -supported, performance will be suboptimal. +supported, performance will be sub-optimal. NOTE: the USER-INTEL package contains styles that require using the -restrict flag, when compiling with Intel compilers. @@ -1392,7 +1392,7 @@ src/USER-INTEL/README "Section 2.6 -sf intel"_Run_options.html "Section 2.6 -pk intel"_Run_options.html "package intel"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i) src/USER-INTEL/TEST "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul @@ -1582,8 +1582,6 @@ molecular visualization and analysis program, to enable LAMMPS to dump snapshots in formats compatible with various molecular simulation tools. -:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd) - To use this package you must have the desired VMD plugins available on your system. @@ -1593,7 +1591,7 @@ plugin via the "dump molfile"_dump_molfile.html command. Plugins can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD or other -programs that use them) without having to recompile the application +programs that use them) without having to re-compile the application itself. More information about the VMD molfile plugins can be found at "http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile. @@ -1635,6 +1633,7 @@ tools: "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul :link(ovito,http://www.ovito.org) +:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/) :link(atomeye,http://www.libatoms.org) [Author:] Lars Pastewka (Karlsruhe Institute of Technology). @@ -1698,7 +1697,7 @@ src/USER-OMP/README "Section 2.6 -sf omp"_Run_options.html "Section 2.6 -pk omp"_Run_options.html "package omp"_package.html -"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o) +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -1998,3 +1997,5 @@ src/USER-VTK: filenames -> commands src/USER-VTK/README lib/vtk/README "dump vtk"_dump_vtk.html :ul + + diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt index 55d0d616f4..2feb4e142d 100644 --- a/doc/src/Packages_standard.txt +++ b/doc/src/Packages_standard.txt @@ -47,7 +47,7 @@ Package, Description, Doc page, Example, Library "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int -"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, n/a, no, no +"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no "MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no "MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index c1a52fd0d0..7db2fa895c 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -58,7 +58,7 @@ Package, Description, Doc page, Example, Library "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no -"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext +"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt index 029c8f831c..3c382de1ba 100644 --- a/doc/src/Python_call.txt +++ b/doc/src/Python_call.txt @@ -59,9 +59,9 @@ and callbacks to LAMMPS. The "fix python/invoke"_fix_python_invoke.html command can execute Python code at selected timesteps during a simulation run. -The "pair_style python"_pair_python command allows you to define +The "pair_style python"_pair_python.html command allows you to define pairwise potentials as python code which encodes a single pairwise -interaction. This is useful for rapid-developement and debugging of a +interaction. This is useful for rapid development and debugging of a new potential. To use any of these commands, you only need to build LAMMPS with the diff --git a/doc/src/Python_head.txt b/doc/src/Python_head.txt index 1f02368429..54f995c565 100644 --- a/doc/src/Python_head.txt +++ b/doc/src/Python_head.txt @@ -62,11 +62,11 @@ library interface provided in src/library.h and src/library.h. That interface is exposed to Python either when calling LAMMPS from Python or when calling Python from a LAMMPS input script and then calling back to LAMMPS from Python code. The library interface is designed to -be easy to add funcionality to. Thus the Python interface to LAMMPS +be easy to add functionality to. Thus the Python interface to LAMMPS is also easy to extend as well. If you create interesting Python scripts that run LAMMPS or interesting Python functions that can be called from a LAMMPS input -script, that you think would be genearlly useful, please post them as +script, that you think would be generally useful, please post them as a pull request to our "GitHub site"_https://github.com/lammps/lammps, and they can be added to the LAMMPS distribution or webpage. diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt index 9a3ea93fc3..e76af83962 100644 --- a/doc/src/Python_library.txt +++ b/doc/src/Python_library.txt @@ -186,20 +186,20 @@ keyword as a float. The get_natoms() method returns the total number of atoms in the simulation, as an int. -The set_variable() methosd sets an existing string-style variable to a +The set_variable() method sets an existing string-style variable to a new string value, so that subsequent LAMMPS commands can access the variable. -The reset_box() emthods resets the size and shape of the simulation +The reset_box() method resets the size and shape of the simulation box, e.g. as part of restoring a previously extracted and saved state of a simulation. The gather methods collect peratom info of the requested type (atom coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter +same vector of values to each calling processor. The scatter functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. +passed by all calling processors, to individual atoms, which may be +owned by different processors. Note that the data returned by the gather methods, e.g. gather_atoms("x"), is different from the data structure returned diff --git a/doc/src/Run_basics.txt b/doc/src/Run_basics.txt index 02139a8c69..1b7387b46b 100644 --- a/doc/src/Run_basics.txt +++ b/doc/src/Run_basics.txt @@ -75,7 +75,7 @@ setenv OMP_NUM_THREADS 2 # csh or tcsh :pre This can also be done via the "package"_package.html command or via the "-pk command-line switch"_Run_options.html which invokes the package command. See the "package"_package.html command or -"Speed"_Speed.html doc pages for more details about which accerlarator +"Speed"_Speed.html doc pages for more details about which accelerator packages and which commands support multi-threading. :line diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt index 2b93cc7d49..85c9a6550d 100644 --- a/doc/src/Run_windows.txt +++ b/doc/src/Run_windows.txt @@ -33,8 +33,8 @@ in parallel, follow these steps. Download and install a compatible MPI library binary package: -for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi -for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul +for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi +for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul The LAMMPS Windows installer packages will automatically adjust your path for the default location of this MPI package. After the diff --git a/doc/src/Speed_bench.txt b/doc/src/Speed_bench.txt index 8e407d14ea..a3d0bf4f46 100644 --- a/doc/src/Speed_bench.txt +++ b/doc/src/Speed_bench.txt @@ -11,7 +11,7 @@ Benchmarks :h3 Current LAMMPS performance is discussed on the "Benchmarks page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws -where timings and parallel efficiencies are listed. The page has +where timings and parallel efficiency are listed. The page has several sections, which are briefly described below: CPU performance on 5 standard problems, strong and weak scaling @@ -77,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated. Performance on a parallel machine can also be predicted from one-core or one-node timings if the parallel efficiency can be estimated. The communication bandwidth and latency of a particular parallel machine -affects the efficiency. On most machines LAMMPS will give parallel -efficiencies on these benchmarks above 50% so long as the number of +affects the efficiency. On most machines LAMMPS will give a parallel +efficiency on these benchmarks above 50% so long as the number of atoms/core is a few 100 or greater, and closer to 100% for large numbers of atoms/core. This is for all-MPI mode with one MPI task per core. For nodes with accelerator options or hardware (OpenMP, GPU, diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt index acef5bf6c1..bddefc5031 100644 --- a/doc/src/Speed_gpu.txt +++ b/doc/src/Speed_gpu.txt @@ -62,7 +62,7 @@ Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-d installed. There can be multiple of them for the same or different hardware (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those as 'platforms'. The GPU library will select the [first] suitable platform, -but this can be overridded using the device option of the "package"_package.html +but this can be overridden using the device option of the "package"_package.html command. run lammps/lib/gpu/ocl_get_devices to get a list of available platforms and devices with a suitable ICD available. diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index ef876a7d42..bf078fb576 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -68,7 +68,7 @@ In most molecular dynamics software, parallelization parameters to changing the order of operations with finite-precision calculations. The USER-INTEL package is deterministic. This means that the results should be reproducible from run to run with the -{same} parallel configurations and when using determinstic +{same} parallel configurations and when using deterministic libraries or library settings (MPI, OpenMP, FFT). However, there are differences in the USER-INTEL package that can change the order of operations compared to LAMMPS without acceleration: @@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to styles when USER-INTEL styles are not available. NOTE: For simulations on higher node counts, add "processors * * * -grid numa"_processors.html" to the beginning of the input script for +grid numa"_processors.html to the beginning of the input script for better scalability. When running on many nodes, performance might be better when using diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index eb787df5d6..04cf53691b 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -93,12 +93,12 @@ The "t Nt" option specifies how many OpenMP threads per MPI task to use with a node. The default is Nt = 1, which is MPI-only mode. Note that the product of MPI tasks * OpenMP threads/task should not exceed the physical number of cores (on a node), otherwise performance will -suffer. If hyperthreading is enabled, then the product of MPI tasks * -OpenMP threads/task should not exceed the physical number of cores * -hardware threads. The "-k on" switch also issues a "package kokkos" -command (with no additional arguments) which sets various KOKKOS -options to default values, as discussed on the "package"_package.html -command doc page. +suffer. If Hyper-Threading (HT) is enabled, then the product of MPI +tasks * OpenMP threads/task should not exceed the physical number of +cores * hardware threads. The "-k on" switch also issues a +"package kokkos" command (with no additional arguments) which sets +various KOKKOS options to default values, as discussed on the +"package"_package.html command doc page. The "-sf kk" "command-line switch"_Run_options.html will automatically append the "/kk" suffix to styles that support it. In this manner no @@ -149,7 +149,7 @@ Intel Knight's Landing (KNL) Xeon Phi: KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are reserved for the OS, and only 64 or 66 cores are used. Each core has 4 -hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66) +Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit, otherwise performance will suffer. Note that with the KOKKOS package you do not need to specify how many KNLs there @@ -228,7 +228,7 @@ for details and default settings. Experimenting with its options can provide a speed-up for specific calculations. For example: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre +mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre NOTE: For good performance of the KOKKOS package on GPUs, you must have Kepler generation GPUs (or later). The Kokkos library exploits diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt index 647ff71e36..dd12685dc5 100644 --- a/doc/src/Speed_measure.txt +++ b/doc/src/Speed_measure.txt @@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when communication occurs for other processors to catch up. Thus the reported times for "Communication" or "Other" may be higher than they really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile +uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile LAMMPS, to obtain synchronized timings. diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt index 0abf54430e..238909d1b4 100644 --- a/doc/src/Speed_omp.txt +++ b/doc/src/Speed_omp.txt @@ -29,7 +29,7 @@ instructions. [Run with the USER-OMP package from the command line:] -These example asume one or more 16-core nodes. +These examples assume one or more 16-core nodes. env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt index 6c837885cd..4c87091e7e 100644 --- a/doc/src/Speed_packages.txt +++ b/doc/src/Speed_packages.txt @@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html: "pair_style lj/cut/opt"_pair_lj.html :ul To see what accelerate styles are currently available for a particular -style, find the style name in the "Commands_all"_Commands_all.html +style, find the style name in the "Commands_all"_lc style pages (fix,compute,pair,etc) and see what suffixes are listed (g,i,k,o,t) with it. The doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html index 8d9625e1bd..4e7810aa61 100644 --- a/doc/src/USER/atc/man_add_molecule.html +++ b/doc/src/USER/atc/man_add_molecule.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html index 9beded1b16..a990ab626f 100644 --- a/doc/src/USER/atc/man_add_species.html +++ b/doc/src/USER/atc/man_add_species.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html index 6725170928..a5707d280e 100644 --- a/doc/src/USER/atc/man_atom_element_map.html +++ b/doc/src/USER/atc/man_atom_element_map.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html index 28bc90fa01..350ab13b92 100644 --- a/doc/src/USER/atc/man_atom_weight.html +++ b/doc/src/USER/atc/man_atom_weight.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html index ef787f53ac..17e854a37f 100644 --- a/doc/src/USER/atc/man_atomic_charge.html +++ b/doc/src/USER/atc/man_atomic_charge.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html index 61596d3b31..8dcf328dd3 100644 --- a/doc/src/USER/atc/man_boundary.html +++ b/doc/src/USER/atc/man_boundary.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html index 40b82f3f61..335ff2d209 100644 --- a/doc/src/USER/atc/man_boundary_dynamics.html +++ b/doc/src/USER/atc/man_boundary_dynamics.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html index 7eb950f78e..6c2fb84940 100644 --- a/doc/src/USER/atc/man_boundary_faceset.html +++ b/doc/src/USER/atc/man_boundary_faceset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html index 0663dba176..c4b0d4865e 100644 --- a/doc/src/USER/atc/man_boundary_integral.html +++ b/doc/src/USER/atc/man_boundary_integral.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index a731b09116..baa306a1c8 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html index 690f0fcc98..16f6d9abad 100644 --- a/doc/src/USER/atc/man_contour_integral.html +++ b/doc/src/USER/atc/man_contour_integral.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html index 900952ba0b..e94a9a52ef 100644 --- a/doc/src/USER/atc/man_control.html +++ b/doc/src/USER/atc/man_control.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html index 8f4f486595..e3074eae8f 100644 --- a/doc/src/USER/atc/man_control_momentum.html +++ b/doc/src/USER/atc/man_control_momentum.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html index eab186f715..8d32f1c4f9 100644 --- a/doc/src/USER/atc/man_control_thermal.html +++ b/doc/src/USER/atc/man_control_thermal.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html index a337a495e0..d28ec334f5 100644 --- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html +++ b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html index d54a201034..98eedafa6c 100644 --- a/doc/src/USER/atc/man_decomposition.html +++ b/doc/src/USER/atc/man_decomposition.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html index ab454c16d2..7cf40f6813 100644 --- a/doc/src/USER/atc/man_electron_integration.html +++ b/doc/src/USER/atc/man_electron_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html index d01253c4b3..8c81ce5925 100644 --- a/doc/src/USER/atc/man_equilibrium_start.html +++ b/doc/src/USER/atc/man_equilibrium_start.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html index 4f1f5962d9..f4d1b01e88 100644 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ b/doc/src/USER/atc/man_extrinsic_exchange.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html index e517dd4855..e39ddd3cec 100644 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ b/doc/src/USER/atc/man_fe_md_boundary.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html index b8ba584816..485b8c95a0 100644 --- a/doc/src/USER/atc/man_fem_mesh.html +++ b/doc/src/USER/atc/man_fem_mesh.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html index 7a871f5c81..e2190dea21 100644 --- a/doc/src/USER/atc/man_filter_scale.html +++ b/doc/src/USER/atc/man_filter_scale.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html index 2711d128e9..0928139d7d 100644 --- a/doc/src/USER/atc/man_filter_type.html +++ b/doc/src/USER/atc/man_filter_type.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html index 7cc6cfea5b..f6f7b43a38 100644 --- a/doc/src/USER/atc/man_fix_atc.html +++ b/doc/src/USER/atc/man_fix_atc.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html index 42815def6b..31bd5619a3 100644 --- a/doc/src/USER/atc/man_fix_flux.html +++ b/doc/src/USER/atc/man_fix_flux.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index 03cf86eb92..2245e32607 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html index b45b7dfb01..ec2dc3ccb9 100644 --- a/doc/src/USER/atc/man_hardy_computes.html +++ b/doc/src/USER/atc/man_hardy_computes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index 17903aabd0..483e5be6bd 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 00935f0ae2..1874ad152e 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index f97037784c..620b9b1d36 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html index e51cbc9873..337a92517e 100644 --- a/doc/src/USER/atc/man_hardy_rates.html +++ b/doc/src/USER/atc/man_hardy_rates.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index 41ae06eb8c..c8348c45ed 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html index dfa19474e5..f76607cc91 100644 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ b/doc/src/USER/atc/man_internal_atom_integrate.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html index 849e8f0671..a5d893f2a3 100644 --- a/doc/src/USER/atc/man_internal_element_set.html +++ b/doc/src/USER/atc/man_internal_element_set.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html index 7f10e17076..6af543cbae 100644 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ b/doc/src/USER/atc/man_internal_quadrature.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html index 92db590198..cb02c05c23 100644 --- a/doc/src/USER/atc/man_kernel_function.html +++ b/doc/src/USER/atc/man_kernel_function.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index fd845d0a71..88442d63a1 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html index 31c18b4f1f..ea5a6e357b 100644 --- a/doc/src/USER/atc/man_mask_direction.html +++ b/doc/src/USER/atc/man_mask_direction.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html index 140b745f09..fd744e5bbf 100644 --- a/doc/src/USER/atc/man_mass_matrix.html +++ b/doc/src/USER/atc/man_mass_matrix.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html index c31ab4938d..1646abc671 100644 --- a/doc/src/USER/atc/man_material.html +++ b/doc/src/USER/atc/man_material.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html index 25a5c2cdae..c4976f699d 100644 --- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html +++ b/doc/src/USER/atc/man_mesh_add_to_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html index a7ee112614..98989bd015 100644 --- a/doc/src/USER/atc/man_mesh_create.html +++ b/doc/src/USER/atc/man_mesh_create.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html index 2ac383a974..735d462b73 100644 --- a/doc/src/USER/atc/man_mesh_create_elementset.html +++ b/doc/src/USER/atc/man_mesh_create_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html index 39bfffd119..0e3624cf8a 100644 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ b/doc/src/USER/atc/man_mesh_create_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html index 60a2fe59a1..e39cc54d41 100644 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ b/doc/src/USER/atc/man_mesh_delete_elements.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html index d05429ebab..66b55a48fb 100644 --- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html +++ b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html index f768a29c41..1d2983afff 100644 --- a/doc/src/USER/atc/man_mesh_output.html +++ b/doc/src/USER/atc/man_mesh_output.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html index e0571ccf88..315180e1db 100644 --- a/doc/src/USER/atc/man_mesh_read.html +++ b/doc/src/USER/atc/man_mesh_read.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html index 756cf49922..f709c02a84 100644 --- a/doc/src/USER/atc/man_mesh_write.html +++ b/doc/src/USER/atc/man_mesh_write.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html index 60fbfcd888..ee0505847c 100644 --- a/doc/src/USER/atc/man_momentum_time_integration.html +++ b/doc/src/USER/atc/man_momentum_time_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html index aec1d5d55a..d0a08fa0da 100644 --- a/doc/src/USER/atc/man_output.html +++ b/doc/src/USER/atc/man_output.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html index 54079027c5..18afe0aa97 100644 --- a/doc/src/USER/atc/man_output_elementset.html +++ b/doc/src/USER/atc/man_output_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html index 2fc6e02681..7906c5fc52 100644 --- a/doc/src/USER/atc/man_output_nodeset.html +++ b/doc/src/USER/atc/man_output_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html index 2cb2cb6113..3ec2eecc60 100644 --- a/doc/src/USER/atc/man_pair_interactions.html +++ b/doc/src/USER/atc/man_pair_interactions.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html index b6fabbb27c..3e22a51f3e 100644 --- a/doc/src/USER/atc/man_poisson_solver.html +++ b/doc/src/USER/atc/man_poisson_solver.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html index 5fc21282f6..d13151a12e 100644 --- a/doc/src/USER/atc/man_read_restart.html +++ b/doc/src/USER/atc/man_read_restart.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html index e6ad418de6..54e4e3419f 100644 --- a/doc/src/USER/atc/man_remove_molecule.html +++ b/doc/src/USER/atc/man_remove_molecule.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html index acea7a5607..c15e0ca46d 100644 --- a/doc/src/USER/atc/man_remove_source.html +++ b/doc/src/USER/atc/man_remove_source.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html index 561364518f..ee063ce57f 100644 --- a/doc/src/USER/atc/man_remove_species.html +++ b/doc/src/USER/atc/man_remove_species.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html index 88e6748001..3c43861054 100644 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html index a6429bf6d6..9607848e1a 100644 --- a/doc/src/USER/atc/man_reset_time.html +++ b/doc/src/USER/atc/man_reset_time.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html index 4e48c4bb29..9a9a8e3a02 100644 --- a/doc/src/USER/atc/man_sample_frequency.html +++ b/doc/src/USER/atc/man_sample_frequency.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html index cf775c9b36..55ad8d952b 100644 --- a/doc/src/USER/atc/man_set.html +++ b/doc/src/USER/atc/man_set.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html index c7239f2c41..78fb1652eb 100644 --- a/doc/src/USER/atc/man_source.html +++ b/doc/src/USER/atc/man_source.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html index 3f43340af8..3b261b7810 100644 --- a/doc/src/USER/atc/man_source_integration.html +++ b/doc/src/USER/atc/man_source_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html index a07ba29cab..c317c06c00 100644 --- a/doc/src/USER/atc/man_temperature_definition.html +++ b/doc/src/USER/atc/man_temperature_definition.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html index fe293138be..830591921e 100644 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ b/doc/src/USER/atc/man_thermal_time_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html index 732eaa3a36..5000fb079d 100644 --- a/doc/src/USER/atc/man_time_filter.html +++ b/doc/src/USER/atc/man_time_filter.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html index f5410816d7..2c7cf26150 100644 --- a/doc/src/USER/atc/man_track_displacement.html +++ b/doc/src/USER/atc/man_track_displacement.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html index 95e1f4be5a..551896431a 100644 --- a/doc/src/USER/atc/man_unfix_flux.html +++ b/doc/src/USER/atc/man_unfix_flux.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html index 78495c928a..4dfd9b3cfc 100644 --- a/doc/src/USER/atc/man_unfix_nodes.html +++ b/doc/src/USER/atc/man_unfix_nodes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html index 8a0e5b62a8..1722d74f67 100644 --- a/doc/src/USER/atc/man_write_atom_weights.html +++ b/doc/src/USER/atc/man_write_atom_weights.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html index 6dca57673b..74c6e2d289 100644 --- a/doc/src/USER/atc/man_write_restart.html +++ b/doc/src/USER/atc/man_write_restart.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 4b4ac3862d..0f0b241b76 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -67,7 +67,7 @@ when required. An example are the bond (angle, etc) methods which need to find the local index of an atom with a specific global ID which is a bond (angle, etc) partner. LAMMPS performs this operation efficiently by creating a "map", which is either an {array} or {hash} -table, as descibed below. +table, as described below. When the {map} keyword is not specified in your input script, LAMMPS only creates a map for "atom_styles"_atom_style.html for molecular diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 7d9e443e7d..8facb4de63 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -173,7 +173,7 @@ There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accerlerated styles exist. +(g,i,k,o,t) to indicate which accelerated styles exist. "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle/local"_compute_bond_local.html - theta and energy of each angle diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index cda4a36b34..46db81eb9e 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -32,7 +32,7 @@ according to the formulation given in "(Ackland)"_#Ackland. Historically, LAMMPS had two, slightly different implementations of the algorithm from the paper. With the {legacy} keyword, it is possible to switch between the pre-2015 ({legacy yes}) and post-2015 -implemention ({legacy no}). The post-2015 variant is the default. +implementation ({legacy no}). The post-2015 variant is the default. In contrast to the "centro-symmetry parameter"_compute_centro_atom.html this method is stable against diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 66eecd195d..ddc4cc82d3 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -67,7 +67,7 @@ identify crystal-like atoms in a system, as discussed in "ten Wolde"_#tenWolde1. The ID of the previously specified "compute -orientorder/atom"_compute_orientorder/atom command is specified as +orientorder/atom"_compute_orientorder_atom.html command is specified as {orientorderID}. The compute must invoke its {components} option to calculate components of the {Ybar_lm} vector for each atoms, as described in its documentation. Note that orientorder/atom compute diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 669ab9f7ca..7cea62c7b3 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -85,7 +85,7 @@ dump 1 all custom 100 tmp.dump id type x y z dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} & refresh c_dsp delay 100 :pre -The "dump_modify thresh"_dump_modify.html command will only ouptut +The "dump_modify thresh"_dump_modify.html command will only output atoms that have displaced more than 0.6 Angstroms on each snapshot (assuming metal units). The dump_modify {refresh} option triggers a call to this compute at the end of every dump. diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt index b3891841b8..04f0fd0b82 100644 --- a/doc/src/compute_entropy_atom.txt +++ b/doc/src/compute_entropy_atom.txt @@ -14,7 +14,7 @@ compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :l entropy/atom = style name of this compute command :l -sigma = width of gaussians used in the g(r) smoothening :l +sigma = width of gaussians used in the g(r) smoothing :l cutoff = cutoff for the g(r) calculation :l one or more keyword/value pairs may be appended :l keyword = {avg} or {local} @@ -49,14 +49,14 @@ This parameter for atom i is computed using the following formula from where r is a distance, g(r) is the radial distribution function of atom i and rho is the density of the system. The g(r) computed for each -atom i can be noisy and therefore it is smoothened using: +atom i can be noisy and therefore it is smoothed using: :c,image(Eqs/pair_entropy2.jpg) where the sum in j goes through the neighbors of atom i, and sigma is a -parameter to control the smoothening. +parameter to control the smoothing. -The input parameters are {sigma} the smoothening parameter, and the +The input parameters are {sigma} the smoothing parameter, and the {cutoff} for the calculation of g(r). If the keyword {avg} has the setting {yes}, then this compute also @@ -82,7 +82,7 @@ If the {local yes} option is used, the g(r) is normalized by the local density around each atom, that is to say the density around each atom is the number of neighbors within the neighbor list cutoff divided by the corresponding volume. This option can be useful when dealing with -inhomogeneus systems such as those that have surfaces. +inhomogeneous systems such as those that have surfaces. Here are typical input parameters for fcc aluminum (lattice constant 4.05 Angstroms), diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index 192ea0bc9e..5ba2100fba 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l 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 recompute the number of degrees of freedom (DOF) contributing to the temperature + 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 :pre :ule diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt index c4c0fc405f..72ed0ba5c4 100644 --- a/doc/src/compute_pressure_uef.txt +++ b/doc/src/compute_pressure_uef.txt @@ -27,8 +27,8 @@ compute 2 all pressure/uef my_temp_uef virial :pre This command is used to compute the pressure tensor in the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html" or -"fix npt/uef"_fix_nh_uef.html" is used. +"fix nvt/uef"_fix_nh_uef.html or +"fix npt/uef"_fix_nh_uef.html is used. It is not necessary to use this command to compute the scalar value of the pressure. A "compute pressure"_compute_pressure.html may be used for that purpose. diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index 512009093c..bc1e3049fa 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -158,7 +158,7 @@ corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. For the spin quantities, sp is in the units of the Bohr magneton, spx, -spy, and spz are adimentional quantities, and fmx, fmy and fmz are +spy, and spz are adimensional quantities, and fmx, fmy and fmz are given in rad.THz. [Restrictions:] none diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index 04b38682cc..d11ae9e3bf 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -182,7 +182,7 @@ change from zero to one at the location of the spike in g(r). NOTE: compute rdf can handle dynamic groups and systems where atoms are added or removed, but this causes that certain normalization -parameters need to be recomputed in every step and include collective +parameters need to be re-computed in every step and include collective communication operations. This will reduce performance and limit parallel efficiency and scaling. For systems, where only the type of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html), diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 9b829a70fc..67c6209bdf 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -92,7 +92,7 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\ This section explains the rigid body attributes that can be specified. -The {id} attribute is the atomID of the atom which owns the rigid body, which is +The {id} attribute is the atom-ID of the atom which owns the rigid body, which is assigned by the "fix rigid/small"_fix_rigid.html command. The {mol} attribute is the molecule ID of the rigid body. It should diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt index 92f5923de0..e9ff2e739b 100644 --- a/doc/src/compute_smd_tlsph_dt.txt +++ b/doc/src/compute_smd_tlsph_dt.txt @@ -25,7 +25,7 @@ Define a computation that outputs the CFL-stable time increment per particle. This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. Because both the speed of sound and the smoothing length typically change during the course of a -simulation, the stable time increment needs to be recomputed every +simulation, the stable time increment needs to be re-computed every time step. This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the stable time increment accessible for output purposes. diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index 787ff8cdcf..e6185a2dd8 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -48,7 +48,7 @@ variable temp_mag equal c_out_mag\[6\] :pre thermo 10 thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre -This serie of commands evaluates the total magnetization along z, the norm of +This series of commands evaluates the total magnetization along z, the norm of the total magnetization, and the magnetic temperature. Three variables are assigned to those quantities. The thermo and thermo_style commands print them every 10 timesteps. diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index 9a509da450..97e1d6e1ae 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -24,8 +24,8 @@ compute 2 sel temp/uef :pre This command is used to compute the kinetic energy tensor in the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html" or -"fix npt/uef"_fix_nh_uef.html" is used. +"fix nvt/uef"_fix_nh_uef.html or +"fix npt/uef"_fix_nh_uef.html is used. It is not necessary to use this command to compute the scalar value of the temperature. A "compute temp"_compute_temp.html may be used for that purpose. diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt index 57faf97ad1..a55288e1db 100644 --- a/doc/src/delete_atoms.txt +++ b/doc/src/delete_atoms.txt @@ -84,7 +84,7 @@ connectivity that has already been assigned. However, the "reset_ids"_reset_ids.html command can be used after this command to accomplish the same thing. -Note that the re-assignement of IDs is not really a compression, where +Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt index b29fa82f2d..4e33604696 100644 --- a/doc/src/delete_bonds.txt +++ b/doc/src/delete_bonds.txt @@ -140,7 +140,7 @@ enough for a processor to acquire the ghost atoms its needs to compute bond, angle, etc interactions. If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 -weighting list is not recomputed, this can cause a later "fix +weighting list is not re-computed, this can cause a later "fix shake"_fix_shake.html command to fail due to an atom's bonds being inconsistent with the weighting list. This should only happen if the group used in the fix command includes both atoms in the bond, in diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 98bcbc5e55..72f4935916 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -914,7 +914,7 @@ flush = yes format = %d and %g for each integer or floating point value image = no label = ENTRIES -maxifiles = -1 +maxfiles = -1 nfile = 1 pad = 0 pbc = no diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index dd2b212f0b..b5f157cf29 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -99,7 +99,7 @@ USER-MOLFILE package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD -or other programs that use them) without having to recompile the +or other programs that use them) without having to re-compile the application itself. The plugins are installed in the directory: /plugins//molfile diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 9c3a1d0349..ee0d006fe8 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -30,7 +30,7 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are hundredes of fixes +conditions, computing diagnostics, etc. There are hundreds of fixes defined in LAMMPS and new ones can be added; see the "Modify"_Modify.html doc page for details. @@ -164,7 +164,7 @@ There are also additional accelerated fix styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands fix"_Commands_fix.html doc page are followed by one or more of (g,i,k,o,t) to indicate which -accerlerated styles exist. +accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time "addforce"_fix_addforce.html - add a force to each atom diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index 7acc22d702..b7d4e7badf 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -56,7 +56,7 @@ value and its corresponding pressure correction. The volumes in the file should be uniformly spaced. Both the volumes and the pressure corrections should be provided in the proper units, e.g. if you are using {units real}, the volumes should all be in cubic angstroms, and the pressure corrections -should all be in atomspheres. Furthermore, the table should start/end at a +should all be in atmospheres. Furthermore, the table should start/end at a volume considerably smaller/larger than you expect your system to sample during the simulation. If the system ever reaches a volume outside of the range provided, the simulation will stop. diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 327088cb99..8e7cb1bdae 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -34,7 +34,7 @@ react = mandatory argument indicating new reaction specification :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l - map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l + map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l individual_keyword = {prob} or {stabilize_steps} :l {prob} values = fraction seed diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index be4fbd255b..0c5a4493ae 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -14,7 +14,7 @@ fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre ID, group-ID are documented in "fix"_fix.html command dt/reset = style name of this fix command -N = recompute dt every N timesteps +N = re-compute dt every N timesteps Tmin = minimum dt allowed which can be NULL (time units) Tmax = maximum dt allowed which can be NULL (time units) Xmax = maximum distance for an atom to move in one timestep (distance units) diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index b30966c2f9..4868761d42 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -47,7 +47,7 @@ this can significantly accelerate the simulation. The filter computes a cluster decomposition of the molecular structure following the criteria indicated by the options a, b, t and m. This process is similar to the approach in "fix shake"_fix_shake.html, -however, the clusters are not kept contrained. Instead, the position +however, the clusters are not kept constrained. Instead, the position is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index b115aba7df..64486a9cc7 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -63,7 +63,7 @@ electrostatics, or that contain parameters that depend on box size: all of these options will be initialized based on the cell size in the LAMMPS-side initial configuration and kept constant during the run. This is required to e.g. obtain reproducible and conserved forces. -If the cell varies too wildly, it may be advisable to reinitialize +If the cell varies too wildly, it may be advisable to re-initialize these interactions at each call. This behavior can be requested by setting the {reset} switch. diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index 7bb25e0a68..d4836706e2 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -34,7 +34,7 @@ the following stochastic differential equation: :c,image(Eqs/fix_langevin_spin_sLLG.jpg) -with lambda the transverse damping, and eta a random verctor. +with lambda the transverse damping, and eta a random vector. This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) equation. diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index bd61e29dcb..c97095bcfc 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -44,7 +44,7 @@ Once LAMMPS is built with the LATTE package, you can run the example input scripts for molecular dynamics or energy minimization that are found in examples/latte. -A step-by-step tutorial can be follwed at: "LAMMPS-LATTE +A step-by-step tutorial can be followed at: "LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS The {peID} argument is not yet supported by fix latte, so it must be diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index 1a52397822..d9012d8cb3 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -187,7 +187,7 @@ NOTE: Care must be taken when choosing both a value for dx, and a simulation domain size. This fix uses the same subdivision of the simulation domain among processors as the main LAMMPS program. In order to uniformly cover the simulation domain with lattice sites, the -lengths of the individual LAMMPS subdomains must all be evenly +lengths of the individual LAMMPS sub-domains must all be evenly divisible by dx. If the simulation domain size is cubic, with equal lengths in all dimensions, and the default value for dx is used, this will automatically be satisfied. diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index ddb5f9a4cd..f50747948a 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -21,7 +21,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} - yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature + yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature {bodyforces} value = {early} or {late} early/late = compute rigid-body forces/torques early or late in the timestep :pre :ule diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index d331d9ad75..521dfff12b 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -168,7 +168,7 @@ The difference between these two {estyle} options is as follows. When {estyle} is specified as {last/efirst}, no change is made to the inter-replica force applied to the intermediate replicas (neither first or last). If the initial path is too far from the MEP, an -intermediate repilica may relax "faster" and reach a lower energy than +intermediate replica may relax "faster" and reach a lower energy than the last replica. In this case the intermediate replica will be relaxing toward its own local minima. This behavior can be prevented by specifying {estyle} as {last/efirst/middle} which will alter the diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index ae403cafd1..dc05948de3 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -174,7 +174,7 @@ This fix can be used with the "fix_modify"_fix_modify.html {temp} and {press} options. The temperature and pressure computes used must be of type {temp/uef} and {pressure/uef}. -This fix computes the same global scalar and vecor quantities as "fix +This fix computes the same global scalar and vector quantities as "fix npt"_fix_nh.html. The fix is not invoked during "energy minimization"_minimize.html. diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt index a3d1ab702e..f013ebfae1 100644 --- a/doc/src/fix_rhok.txt +++ b/doc/src/fix_rhok.txt @@ -11,7 +11,7 @@ fix rhok command :h3 fix ID group-ID rhok nx ny nz K a :pre ID, group-ID are documented in "fix"_fix.html command -nx, ny, nz = k-vektor of collective density field +nx, ny, nz = k-vector of collective density field K = spring constant of bias potential a = anchor point of bias potential :ul diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index d489762e80..5d65856735 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -442,11 +442,11 @@ couple none :pre The keyword/value option pairs are used in the following ways. The {reinit} keyword determines, whether the rigid body properties -are reinitialized between run commands. With the option {yes} (the +are re-initialized between run commands. With the option {yes} (the default) this is done, with the option {no} this is not done. Turning -off the reinitialization can be helpful to protect rigid bodies against +off the re-initialization can be helpful to protect rigid bodies against unphysical manipulations between runs or when properties cannot be -easily recomputed (e.g. when read from a file). When using the {infile} +easily re-computed (e.g. when read from a file). When using the {infile} keyword, the {reinit} option is automatically set to {no}. The {langevin} and {temp} and {tparam} keywords perform thermostatting diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index 644c04eadb..774842c7cf 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -77,7 +77,7 @@ normalized. But since it represents the {absolute} displacement of group-ID2 relative to the fix group, (1,1,0) is a different spring than (-1,-1,0). For each vector component, the displacement can be described with the {auto} parameter. In this case the direction is -recomputed in every step, which can be useful for steering a local +re-computed in every step, which can be useful for steering a local process where the whole object undergoes some other change. When the relative positions and distance between the two groups are not in equilibrium, the same spring force described above is applied to atoms diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt index ade64d2056..2ee045141a 100644 --- a/doc/src/fix_surface_global.txt +++ b/doc/src/fix_surface_global.txt @@ -6,7 +6,7 @@ :line -fix wall/surface/globale command :h3 +fix wall/surface/global command :h3 [Description:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 57e122fdcd..75d199e0b4 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -338,9 +338,9 @@ energy gradient of image i. ReplicaForce is the two-norm of the 3N-length force vector (including nudging forces) for replica i. MaxAtomForce is the maximum force component of any atom in replica i. -When a NEB calculation does not converge properly, the suplementary +When a NEB calculation does not converge properly, the supplementary information can help understanding what is going wrong. For instance -when the path angle becomes accute the definition of tangent used in +when the path angle becomes accute, the definition of tangent used in the NEB calculation is questionable and the NEB cannot may diverge "(Maras)"_#Maras2. diff --git a/doc/src/package.txt b/doc/src/package.txt index 8b0581929f..65117ba3c3 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -363,7 +363,7 @@ specified with the OMP_NUM_THREADS environment variable or the {omp} keyword). The extra thread is dedicated for performing part of the "PPPM solver"_kspace_style.html computations and communications. This can improve parallel performance on processors supporting -Simultaneous Multithreading (SMT) such as Hyperthreading on Intel +Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel processors. In this mode, one additional thread is generated per MPI process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 4c43978fe5..d9780e0320 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -52,18 +52,18 @@ The latter corrects for artifacts occurring at short distances which become an issue for soft vdW potentials. The {buck6d} styles include a smoothing function which is invoked -according to the global smooting parameter within the specified +according to the global smoothing parameter within the specified cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing within 90% of the cutoff. No smoothing is applied at a value of 1.0. For the {gauss/dsf} style this smoothing is only applicable for the dispersion damped Buckingham potential. For the {gauss/long} styles the smoothing function can also be invoked for the real -space coulomb interactions which enforce continous energies and +space coulomb interactions which enforce continuous energies and forces at the cutoff. Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long} evaluate a Coulomb potential using spherical Gaussian type charge -distributions which effectively dampen electrostatic ineractions +distributions which effectively dampen electrostatic interactions for high charges at close distances. The electrostatic potential is thus evaluated as: diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index 63f85f23d5..88f95b5b2c 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -128,7 +128,7 @@ There are also additional accelerated pair styles (not listed on the distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands pair"_Commands_pair.html doc page are followed by one or more of (g,i,k,o,t) to indicate which -accerlerated styles exist. +accelerated styles exist. :line diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt index adaeeb8390..8b1ceab858 100644 --- a/doc/src/pair_dsmc.txt +++ b/doc/src/pair_dsmc.txt @@ -16,7 +16,7 @@ max_cell_size = global maximum cell size for DSMC interactions (distance units) seed = random # seed (positive integer) weighting = macroparticle weighting Tref = reference temperature (temperature units) -Nrecompute = recompute v*sigma_max every this many timesteps (timesteps) +Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps) Nsample = sample this many times in recomputing v*sigma_max :ul [Examples:] diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 02d0db7af2..c74028faa9 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -39,7 +39,7 @@ in "(Kolmogorov)"_#Kolmogorov2. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than -r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above +r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2. It is important to include all the pairs to build the neighbor list for diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index f557e6c731..912fca1657 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -30,7 +30,7 @@ which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) -It is important to have a suffiently large cutoff to ensure smooth forces. +It is important to have a sufficiently large cutoff to ensure smooth forces. Energies are shifted so that they go continously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index 23da86fc49..e8baf14d2e 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -29,7 +29,7 @@ The {python} pair style provides a way to define pairwise additive potential functions as python script code that is loaded into LAMMPS from a python file which must contain specific python class definitions. This allows to rapidly evaluate different potential functions without -having to modify and recompile LAMMPS. Due to python being an +having to modify and re-compile LAMMPS. Due to python being an interpreted language, however, the performance of this pair style is going to be significantly slower (often between 20x and 100x) than corresponding compiled code. This penalty can be significantly reduced @@ -98,7 +98,7 @@ verify, that the potential definition in the python class and in the LAMMPS input match. Here is an example for a single type Lennard-Jones potential class -{LJCutMelt} in reducted units, which defines an atom type {lj} for +{LJCutMelt} in reduced units, which defines an atom type {lj} for which the parameters epsilon and sigma are both 1.0: class LJCutMelt(LAMMPSPairPotential): diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index b33897c5aa..1441da2b61 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -93,7 +93,7 @@ There are also additional accelerated pair styles (not listed here) included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands pair"_Commands_pair.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accerlerated styles exist. +(g,i,k,o,t) to indicate which accelerated styles exist. "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index ef899a15b4..6aa30d9e63 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -124,14 +124,14 @@ bond atoms or bad dynamics. The three choices for the {add} argument affect how the atom IDs and molecule IDs of atoms in the data file are treated. If {append} is specified, atoms in the data file are added to the current system, -with their atom IDs reset so that an atomID = M in the data file -becomes atomID = N+M, where N is the largest atom ID in the current +with their atom IDs reset so that an atom-ID = M in the data file +becomes atom-ID = N+M, where N is the largest atom ID in the current system. This rule is applied to all occurrences of atom IDs in the data file, e.g. in the Velocity or Bonds section. This is also done for molecule IDs, if the atom style does support molecule IDs or they are enabled via fix property/atom. If {IDoffset} is specified, then {IDoffset} is a numeric value is given, e.g. 1000, so that an -atomID = M in the data file becomes atomID = 1000+M. For systems +atom-ID = M in the data file becomes atom-ID = 1000+M. For systems with enabled molecule IDs, another numerical argument {MOLoffset} is required representing the equivalent offset for molecule IDs. If {merge} is specified, the data file atoms @@ -139,7 +139,7 @@ are added to the current system without changing their IDs. They are assumed to merge (without duplication) with the currently defined atoms. It is up to you to insure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. For +by insuring the resulting max atom-ID >= the number of atoms. For molecule IDs, there is no check done at all. The {offset} and {shift} keywords can only be used if the {add} diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 0195dce911..79a481746e 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -14,7 +14,7 @@ replicate nx ny nz {keyword} :pre nx,ny,nz = replication factors in each dimension :ulb optional {keyword} = {bbox} :l - {bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule + {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule [Examples:] @@ -46,7 +46,7 @@ image flags that differ by 1. This will allow the bond to be unwrapped appropriately. The optional keyword {bbox} uses a bounding box to only check atoms -in replicas that overlap with a processor's subdomain when assigning +in replicas that overlap with a processor's sub-domain when assigning atoms to processors, and thus can result in substantial speedups for calculations using a large number of processors. It does require temporarily using more memory. diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt index 391b51fde9..8b217c7b1c 100644 --- a/doc/src/reset_ids.txt +++ b/doc/src/reset_ids.txt @@ -23,7 +23,7 @@ for bond, angle, dihedral, improper topology data. This will create a set of IDs that are numbered contiguously from 1 to N for a N atoms system. -This can be useful to do after perfoming a "delete_atoms" command for +This can be useful to do after performing a "delete_atoms" command for a molecular system. The delete_atoms compress yes option will not perform this operation due to the existence of bond topology. It can also be useful to do after any simulation which has lost atoms, diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 7c034f36e0..e0fae3909d 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -49,7 +49,7 @@ as it writes successive restart files. Note that you can specify the restart command twice, once with a single filename and once with two filenames. This would allow you, for example, to write out archival restart files every 100000 steps -using a single filenname, and more frequent temporary restart files +using a single filename, and more frequent temporary restart files every 1000 steps, using two filenames. Using restart 0 will turn off both modes of output. diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 6dd9b56908..9defd1314e 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -318,7 +318,7 @@ bond forces = level 1 (innermost loop) angle forces = same level as bond forces dihedral forces = same level as angle forces improper forces = same level as dihedral forces -pair forces = leven N (outermost level) +pair forces = level N (outermost level) kspace forces = same level as pair forces inner, middle, outer forces = no default :ul diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index a57b61664d..283aad6c2d 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -64,7 +64,7 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command. Thus LAMMPS ignores special_bonds settings when manybody potentials are calculated. Please note, that the existence of explicit bonds for atoms that are described by a manybody potential will alter the -neigborlist and thus can render the computation of those interactions +neighbor list and thus can render the computation of those interactions invalid, since those pairs are not only used to determine direct pairwise interactions but also neighbors of neighbors and more. The recommended course of action is to remove such bonds, or - if @@ -110,7 +110,7 @@ simulation. The two exceptions to this rule are (a) if the {angle} or {dihedral} keywords are set to {yes} (see below), or (b) if the "delete_bonds"_delete_bonds.html command is used with the {special} -option that recomputes the 1-2,1-3,1-4 topologies after bonds are +option that re-computes the 1-2,1-3,1-4 topologies after bonds are deleted; see the "delete_bonds"_delete_bonds.html command for more details. diff --git a/doc/utils/converters/lammpsdoc/lammps_filters.py b/doc/utils/converters/lammpsdoc/lammps_filters.py index 11460185db..7b1481ceb9 100644 --- a/doc/utils/converters/lammpsdoc/lammps_filters.py +++ b/doc/utils/converters/lammpsdoc/lammps_filters.py @@ -64,7 +64,7 @@ def filter_file_header_until_first_horizontal_line(content): common_links = "\n.. _lws: http://lammps.sandia.gov\n" \ ".. _ld: Manual.html\n" \ - ".. _lc: Section_commands.html#comm\n" + ".. _lc: Commands_all.html\n" if first_hr >= 0: return content[first_hr+len(hr):].lstrip() + common_links diff --git a/doc/utils/converters/tests/test_lammps_filters.py b/doc/utils/converters/tests/test_lammps_filters.py index 6c25c23a79..8d2fa2e577 100644 --- a/doc/utils/converters/tests/test_lammps_filters.py +++ b/doc/utils/converters/tests/test_lammps_filters.py @@ -47,7 +47,7 @@ class TestStructuralFilters(unittest.TestCase): self.assertEqual("Title\n\n" "\n.. _lws: http://lammps.sandia.gov\n" ".. _ld: Manual.html\n" - ".. _lc: Section_commands.html#comm\n", s) + ".. _lc: Commands_all.html\n", s) def test_filter_multiple_horizontal_rules(self): s = self.txt2rst.convert(":hline\n" diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html index 39ee684a0b..1eb53c70a2 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html @@ -18,7 +18,7 @@ View page source {% endif %} Website - Commands + Commands {% endif %} diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index fb08e4e97e..febd5c20a0 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -260,6 +260,8 @@ Caro cartesian Cates cbecker +ccache +ccmake CCu cd cdeam @@ -286,6 +288,9 @@ cgs Chalopin Champaign charmm +charmmfsw +charmmfsh +charmm CHARMM checkmark checkqeq @@ -308,6 +313,8 @@ Clebsch Clermont clo Clovertown +cmake +CMake cmap Cmax cmdlist @@ -410,6 +417,7 @@ Cval cvar cvff cwiggle +cygwin Cygwin Cyrot cyrstals @@ -585,6 +593,7 @@ ehanced ehex eHEX Ei +Eigen Eigensolve Eike eim @@ -713,7 +722,10 @@ fhg Fi figshare Fij -filenname +filename +filenames +Filename +Filenames fileper Fincham Finchham @@ -1385,6 +1397,7 @@ Mikami Militzer Minary mincap +mingw minima minimizations minimizer @@ -1456,6 +1469,7 @@ Mtotal Muccioli Mukherjee Mulders +multi multibody Multibody multicenter @@ -2489,6 +2503,7 @@ velocites Verlag verlet Verlet +versa ves vhi vibrational @@ -2566,6 +2581,7 @@ whitespace Wi Wicaksono wih +wildcard Wirnsberger wirtes witin diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 9f3221449b..efa2c87296 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -177,7 +177,7 @@ void MSM::init() if (sizeof(FFT_SCALAR) != 8) error->all(FLERR,"Cannot (yet) use single precision with MSM " - "(remove -DFFT_SINGLE from Makefile and recompile)"); + "(remove -DFFT_SINGLE from Makefile and re-compile)"); // extract short-range Coulombic cutoff from pair style @@ -419,7 +419,7 @@ void MSM::setup() boxlo = domain->boxlo_lamda; // ghost grid points depend on direct sum interaction limits, - // so need to recompute local grid + // so need to re-compute local grid set_grid_local(); diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 11bf2ae01e..785146a0d6 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -394,7 +394,7 @@ void PairAGNI::read_file(char *file) if (nwords == 0) continue; if (nwords > MAXWORD) - error->all(FLERR,"Increase MAXWORD and recompile"); + error->all(FLERR,"Increase MAXWORD and re-compile"); // words = ptrs to all words in line