diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 460d177c9236998897e0e7518708c44fb87956a2..51997593dbd6b1a896899a33ed4cd8cf300e4d58 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -276,11 +276,14 @@ endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
- if(NOT LAPACK_FOUND)
+ find_package(BLAS)
+ if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
+ else()
+ list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
endif()
diff --git a/cmake/README.md b/cmake/README.md
index 85375cd2aa49ca9ddb0bc97b0fa50d048a344f4a..21e728c1f02a696ede20bf6fe632200acd05f69e 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_EXE</code></td>
+ <td>control whether to build LAMMPS executable</td>
+ <td>
+ <dl>
+ <dt><code>on</code> (default)</dt>
+ <dt><code>off</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>BUILD_SHARED_LIBS</code></td>
<td>control whether to build LAMMPS as a shared-library</td>
diff --git a/doc/Makefile b/doc/Makefile
index 81f362349950be2123d2da4bd14255e7f9f27739..9069fa1d60dacb7484f54dda7b310e495d0c73ea 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.txt b/doc/src/Build.txt
index 1046171de1c58ecd8c1fc358bc4b598d661ecc38..df30af36f5df45a7621e10f7f3832be49e6e622d 100644
--- a/doc/src/Build.txt
+++ b/doc/src/Build.txt
@@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
Build_settings
Build_package
Build_extras
+ Build_windows
END_RST -->
@@ -39,7 +40,8 @@ END_RST -->
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html :all(b)
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html :all(b)
If you have problems building LAMMPS, it is often due to software
issues on your local machine. If you can, find a local expert to
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index cee78aced3faafce24586e4543d344185500fc7d..6924e7341782e7e782300f4201c988dc4724763f 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 08c1c72180a417b259078753dd1245d4f93cc6ce..f8b52056fc1616e1ac84174ddeab7aafb27d91ee 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 5c33a0a4d44f97545e8d94819161e2bce9fad78e..088ffd8972f3d8b5228ab73c454b03558fd7f9bd 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 c00ce1f4208ba04a8517b98a9128cb63e886ef8b..ad18695e46245686444a8ae5d3e8ec7728a1d64b 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 773217e3a0e205f4d818c349f7a96b09d7526eba..500130ecee81ba7622fe5e6851509e57ef98e56f 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
new file mode 100644
index 0000000000000000000000000000000000000000..0caad589fb4497938797092297e41dbc4fbc6ac2
--- /dev/null
+++ b/doc/src/Build_windows.txt
@@ -0,0 +1,97 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines. The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers). If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin. If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows. There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+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 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.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index 13db1272b928e558ceda0853df22162945e6c6e5..aec5a9db8b726453d16a36211fd54eddf7b35754 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 48069d3120048e9d59ead6a3f2959be296d078de..0cf433d53a5bef331c65654a97d76eb2f7347796 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 cbe2261986bb8f8f96089dac3dff3a03dc39dd42..1d7c754fa718a8a4b38e8a04c2cd657c7d704a90 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 d279b5e9758c0366169abb962e3d27b9fddaa56e..a74182967cc7f49987f0256c7427ded847dd5985 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 dd3402ba8641c487f1a6a4210fa27f1b6ae062ff..98b66f2aa569040bea2ea260b3cb37ddd84764f2 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 7c3db891524379f49fe38134186764e07eeff959..33233346006d2d2d7b25d04baeb01311d77e5a30 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 3535349b461589aa6ddafdf4e9a3d684a546c2e1..3e7db9bc8e4b735ad93014b8a86a8c7b2ffe3bc4 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 741078e7eb7cb74a574c0e0bada4cca4414cce89..9a9656784ce7e81b5d82e0e74f029b605ac122bc 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 8be4b66e78a511b404987929d247ce3836a40086..a12bf13f2e9ca2914012b1121cc0951b282bcbcc 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 1e737df655462c2fc0e1059ac7bc56ecdb120287..4dfe4e2f6c88eab104e813e0051138c25434b4ef 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 1b9adb49a5701789dafc9f86cebc23a87623411c..b549f99be2f2e8d27c0d54eb251cd9ab31105e78 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 3d0b27370e1285e293f247e02c7a4fac0c24c630..ff9b14c12c162dcd9112fde9298d18f5370e3220 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 49c14bc5f06d463037d294d28873b43fdf6c7f14..cd822c778f29db10193966d27b7f7f0cada6392d 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.txt b/doc/src/Manual.txt
index c5e5aff61b1ce5149ee2a2acef906bf31eb6bdd5..ad3e66a4b27b93645e0f7ed4b2ec628e160597b9 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Aug 2018 version">
+<META NAME="docnumber" CONTENT="22 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-16 Aug 2018 version :c,h2
+22 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt
index a6b881cb79708c37760dc482cac2a7017342d7df..ac12dd7b2ed3da973c726b6d4ded6a68745fb34e 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 cf94b40281417805515700d697dc84cbd476fc38..4ab1eddf218786a6dca4c2b4f77bcda26fa3d57f 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 892774be383f379ade01ca6265e69ea6b6f4bcfc..381dc2e99589f5702dfd4ebf3f5ec615c2dd307b 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 55d0d616f417a5511898b98f61d9b7b0b348edd9..2feb4e142d32f63c3008ffa3bc582dc2a2257062 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 c1a52fd0d0d864493d49f849aa5c531fcb1cd40f..7db2fa895ceaa020552d6e05502b67bc174ca54b 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 029c8f831cc537da73f898ac5ba3172036a54faf..3c382de1ba2b6661aceada829de918721d4f2673 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 1f0236842993a5a7492f3e805b32939a3c2fdff0..54f995c565b741456fcfc02cee75b4072c52b361 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 9a3ea93fc30ee932cbc1a85e374f37fb41bddee9..e76af83962336cb267a738f4cfee4ad84c41f9dc 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 02139a8c69ad9f7ddb37b7fa8e24e7b080de5d37..1b7387b46ba672c1cb92cfe1f49f7d98d2593166 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 2b93cc7d4944f4a3e61a826d9967986fb5d32516..85c9a6550d637036815cd58f53326dfe3c930363 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 8e407d14ea6bdb7428bff3818a670a9a84244f63..a3d0bf4f46f95c07f04c304449d4399a6c79c95f 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 3ae4639dc2391b492410a450c8f9b3ad56402684..bddefc50314d6d73879337bf84bb1a79238888bf 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
GPU package :h3
-The GPU package was developed by Mike Brown at ORNL and his
-collaborators, particularly Trung Nguyen (ORNL). It provides GPU
-versions of many pair styles, including the 3-body Stillinger-Weber
-pair style, and for "kspace_style pppm"_kspace_style.html for
-long-range Coulombics. It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+"kspace_style pppm"_kspace_style.html for long-range Coulombics.
+It has the following general features:
It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
e.g. within a node of a parallel machine. :ulb,l
-Atom-based data (e.g. coordinates, forces) moves back-and-forth
+Atom-based data (e.g. coordinates, forces) are moved back-and-forth
between the CPU(s) and GPU every timestep. :l
Neighbor lists can be built on the CPU or on the GPU :l
@@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l
-Asynchronous force computations can be performed simultaneously on the
-CPU(s) and GPU. :l
+Force computations of different style (pair vs. bond/angle/dihedral/improper)
+can be performed concurrently on the GPU and CPU(s), respectively. :l
It allows for GPU computations to be performed in single or double
precision, or in mixed-mode precision, where pairwise forces are
@@ -39,21 +39,32 @@ force vectors. :l
LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
-same functionality can eventually be supported on a variety of GPU
-hardware. :l
+same functionality is supported on a variety of hardware. :l
:ule
[Required hardware/software:]
-To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA CUDA software on your system:
-
-Check if you have an NVIDIA GPU: cat
-/proc/driver/nvidia/gpus/0/information Go to
-http://www.nvidia.com/object/cuda_get.html Install a driver and
-toolkit appropriate for your system (SDK is not necessary) Run
-lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
-below) to list supported devices and properties :ul
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
+
+Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
+Go to http://www.nvidia.com/object/cuda_get.html :l
+Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
+Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
+list supported devices and properties :ule,l
+
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
+Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
+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 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.
[Building LAMMPS with the GPU package:]
@@ -120,7 +131,10 @@ GPUs/node to use, as well as other options.
The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
-precision used on the GPU (double, single, mixed).
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the GPU package on various
@@ -146,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
performance. Neighbor lists can be built on the GPU or CPU. Force
calculations can be dynamically balanced across the CPU cores and
GPUs. GPU-specific settings can be made which can be optimized
-for different hardware. See the "packakge"_package.html command
+for different hardware. See the "package"_package.html command
doc page for details. :l
As described by the "package gpu"_package.html command, GPU
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index ef876a7d42108a3ae8aad4f6c2f65670f65e0223..bf078fb57652b747c99b17d12d4f441618e58d24 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 eb787df5d6ac8a1e97136453a8eda62f754bdc0b..04cf53691be0c7379bd031b8feefe46119627748 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 647ff71e36593f9a642c22360e74c36752e43e7d..dd12685dc547a4115229d68409ba0d6c544fd323 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 0abf54430ef042de4e04080cd741332cf5a7b85f..238909d1b47c1711562687b79f6f402a618c23e5 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 6c837885cd4dd5272e9b7925d84aa01ee8f9ab79..4c87091e7e20c675413c605738ec776813b52b9b 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 8d9625e1bd0e926742f0283c5229880681f89431..4e7810aa615c202f1c94158517552a8ec47d7aa5 100644
--- a/doc/src/USER/atc/man_add_molecule.html
+++ b/doc/src/USER/atc/man_add_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html
index 9beded1b164d22c57f5800d62d258bf0867e9999..a990ab626fbc62322b0c63cf346066298de3cf98 100644
--- a/doc/src/USER/atc/man_add_species.html
+++ b/doc/src/USER/atc/man_add_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html
index 6725170928a49b0887e1e09e3fc1634b94666773..a5707d280e831c83ab93de07a2b9e2476cba1894 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html
index 28bc90fa01c053c99983a594100b086ddd6b08a5..350ab13b92ad1e47baa672fed6448cfa9e4c55f6 100644
--- a/doc/src/USER/atc/man_atom_weight.html
+++ b/doc/src/USER/atc/man_atom_weight.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html
index ef787f53acc2632e066aaf14766b5df0ac350706..17e854a37f5e0472632918537b766ef5ae796be5 100644
--- a/doc/src/USER/atc/man_atomic_charge.html
+++ b/doc/src/USER/atc/man_atomic_charge.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html
index 61596d3b31899ea0a65cdd4332753b61b3436eeb..8dcf328dd3ba8df57c87b5c258314bc681da6980 100644
--- a/doc/src/USER/atc/man_boundary.html
+++ b/doc/src/USER/atc/man_boundary.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html
index 40b82f3f6113ba5b21416776a4927fc2f05de3de..335ff2d20957f62def15c506845d9601e0035548 100644
--- a/doc/src/USER/atc/man_boundary_dynamics.html
+++ b/doc/src/USER/atc/man_boundary_dynamics.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html
index 7eb950f78e54c7dfd17f4f7121332a592265f236..6c2fb8494028f4934a9af203c6f98806cd385c8a 100644
--- a/doc/src/USER/atc/man_boundary_faceset.html
+++ b/doc/src/USER/atc/man_boundary_faceset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html
index 0663dba176e57066ea8b878f5bf3b7b2e1280889..c4b0d4865e75e5b518c0f42285378f568de4a8e1 100644
--- a/doc/src/USER/atc/man_boundary_integral.html
+++ b/doc/src/USER/atc/man_boundary_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index a731b09116dd2a9e7fb677b5fcc12b433023bdfa..baa306a1c80afc280f2aa8d31551de329726fb8e 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html
index 690f0fcc986e9670071c54d30c5cdc70a1756601..16f6d9abadbb15176737ff7d6950ae7d8f0e81fa 100644
--- a/doc/src/USER/atc/man_contour_integral.html
+++ b/doc/src/USER/atc/man_contour_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html
index 900952ba0b39735f31d74d8a44b6c6fd80067667..e94a9a52ef84db97b7c5598182f97e249eb30379 100644
--- a/doc/src/USER/atc/man_control.html
+++ b/doc/src/USER/atc/man_control.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html
index 8f4f48659561834285e915632ec4dd8802cb1f1a..e3074eae8f14acf35018fe1f357d42995ecf1066 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html
index eab186f71502d82b1667487b8b6e9c621e887e57..8d32f1c4f9aa78d407540e3872405fd724d9b73e 100644
--- a/doc/src/USER/atc/man_control_thermal.html
+++ b/doc/src/USER/atc/man_control_thermal.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
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 a337a495e0e3eaf2cedb69441267654cdb68316a..d28ec334f5ac84e08570760ddf0bc87896cb4691 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html
index d54a2010342e783243cc0ab90f8010515c23a892..98eedafa6cfc7295ae980e6a8e11268ec75c7a3d 100644
--- a/doc/src/USER/atc/man_decomposition.html
+++ b/doc/src/USER/atc/man_decomposition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html
index ab454c16d271fa0e9ed02e186601f9c2cdc0259e..7cf40f6813e318e57df6fca20dfffc3669839994 100644
--- a/doc/src/USER/atc/man_electron_integration.html
+++ b/doc/src/USER/atc/man_electron_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html
index d01253c4b3e574981cc3d2e32159a4639bd7bcd3..8c81ce5925c0bbb504a9399ef5680f0e78220141 100644
--- a/doc/src/USER/atc/man_equilibrium_start.html
+++ b/doc/src/USER/atc/man_equilibrium_start.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html
index 4f1f5962d9f3956bd1be3bf7a41c6a028769b07e..f4d1b01e880cb17a8ee9174090c68b029156dc5d 100644
--- a/doc/src/USER/atc/man_extrinsic_exchange.html
+++ b/doc/src/USER/atc/man_extrinsic_exchange.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html
index e517dd4855d86a90fe95517bf3bb07a0c99425f1..e39ddd3cec063f57b0e80476dc18b66daadff2b3 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html
index b8ba584816bc2b2fce453df4f12f2a3589378feb..485b8c95a0f24f91fa5c44bc69cfbe9c1676a940 100644
--- a/doc/src/USER/atc/man_fem_mesh.html
+++ b/doc/src/USER/atc/man_fem_mesh.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index 7a871f5c8141c7c8122919f0c2ea8b5abdfa27ca..e2190dea21b38aad2feca6dedd6f684117025a3d 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html
index 2711d128e9f945be4e7c65ad8e18be43b2b78d08..0928139d7dabdd499826726274ce6a5f8a556d91 100644
--- a/doc/src/USER/atc/man_filter_type.html
+++ b/doc/src/USER/atc/man_filter_type.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html
index 7cc6cfea5bad5089cfbddab53036c75ed2fedd0f..f6f7b43a38b7c45d48fb7748e8e46d499ba81119 100644
--- a/doc/src/USER/atc/man_fix_atc.html
+++ b/doc/src/USER/atc/man_fix_atc.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html
index 42815def6bca896ee183505fb869a327908b5853..31bd5619a37ba7aa7db08768f4810a3924cd6524 100644
--- a/doc/src/USER/atc/man_fix_flux.html
+++ b/doc/src/USER/atc/man_fix_flux.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html
index 03cf86eb9220720940f1fae44257a3df93addd12..2245e32607ceb217c23e4cf35642844be2a5aec0 100644
--- a/doc/src/USER/atc/man_fix_nodes.html
+++ b/doc/src/USER/atc/man_fix_nodes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html
index b45b7dfb0101a117ca58cc7faf78b1eec80a3a06..ec2dc3ccb915f280b1370e49b862d0e5988dbecc 100644
--- a/doc/src/USER/atc/man_hardy_computes.html
+++ b/doc/src/USER/atc/man_hardy_computes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html
index 17903aabd0d913d0d0bb78b9998c7c4105df4fba..483e5be6bdf560fb2dfdbc1a28c7069a3b76eda8 100644
--- a/doc/src/USER/atc/man_hardy_fields.html
+++ b/doc/src/USER/atc/man_hardy_fields.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html
index 00935f0ae25968b2c633a068899e03917241edaf..1874ad152e030bbc26afce4f96198bcb26697d98 100644
--- a/doc/src/USER/atc/man_hardy_gradients.html
+++ b/doc/src/USER/atc/man_hardy_gradients.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html
index f97037784c73349cab27f1df5e1145ede359b7ce..620b9b1d365bd5a4ab11ed42885172136561b2a4 100644
--- a/doc/src/USER/atc/man_hardy_kernel.html
+++ b/doc/src/USER/atc/man_hardy_kernel.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html
index 79c1006c973eb515a8416bbfc47399f86e03621e..04d24ff02958ce187c81ba23ff9c1cc488bda786 100644
--- a/doc/src/USER/atc/man_hardy_on_the_fly.html
+++ b/doc/src/USER/atc/man_hardy_on_the_fly.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html
index e51cbc9873a03ed584d3d4fde162cdc738f2b0c9..337a92517eb799c4b9589f9eefa2a51bc8a09acb 100644
--- a/doc/src/USER/atc/man_hardy_rates.html
+++ b/doc/src/USER/atc/man_hardy_rates.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html
index 41ae06eb8c42f7c2afba2ca1362c9ef8361ada52..c8348c45ed7c9ec1a23905059868741c068ac4af 100644
--- a/doc/src/USER/atc/man_initial.html
+++ b/doc/src/USER/atc/man_initial.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html
index dfa19474e5be9e6c314ca23eafa58da8ee50439b..f76607cc914214f73884c0385bb0490c6c0f6818 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html
index 849e8f0671369f9c22f05ccd6190cbddf15e2746..a5d893f2a3095b52d62150990425b13b9fa94937 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html
index 7f10e1707679d2c7027ee0166369aebc4a6654d8..6af543cbaea9991f18986fe46f7c0b979491bb2d 100644
--- a/doc/src/USER/atc/man_internal_quadrature.html
+++ b/doc/src/USER/atc/man_internal_quadrature.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html
index 92db590198a43fc753c5e8becf64e465021f0f59..cb02c05c23c37f9189b1f492582ad5a4b22b7841 100644
--- a/doc/src/USER/atc/man_kernel_function.html
+++ b/doc/src/USER/atc/man_kernel_function.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html
index fd845d0a712f1c6d6d49108d7a8a3fcb174e098b..88442d63a185f4578ef1c9eb6397a35de765df67 100644
--- a/doc/src/USER/atc/man_localized_lambda.html
+++ b/doc/src/USER/atc/man_localized_lambda.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html
index ade780ddee0faf5bc11c18be9b79860db2ce4aa5..89aabebd3c75d62353721f210c54a0699684dee8 100644
--- a/doc/src/USER/atc/man_lumped_lambda_solve.html
+++ b/doc/src/USER/atc/man_lumped_lambda_solve.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html
index 31c18b4f1f961a1d77b321a1775ba4f818f40b59..ea5a6e357ba526125162f3a08668bdc36f13fec3 100644
--- a/doc/src/USER/atc/man_mask_direction.html
+++ b/doc/src/USER/atc/man_mask_direction.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html
index 140b745f09b72e0c208e6d9ce49e084c4f2ea556..fd744e5bbf38572a8b0d05eb9d4fc38f6938027f 100644
--- a/doc/src/USER/atc/man_mass_matrix.html
+++ b/doc/src/USER/atc/man_mass_matrix.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html
index c31ab4938d6c5ad6befe8ae71d6540dce2a7d9b8..1646abc671742d1055e70e04081ff0834f189e11 100644
--- a/doc/src/USER/atc/man_material.html
+++ b/doc/src/USER/atc/man_material.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
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 25a5c2cdae60c930794721d86bd10b933566dfa2..c4976f699d1cc2c7c080d59adfb30e5bd052788c 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html
index a7ee112614fb93652bb14dbf4707907607a84460..98989bd015a754444f63576631163f79f37ca410 100644
--- a/doc/src/USER/atc/man_mesh_create.html
+++ b/doc/src/USER/atc/man_mesh_create.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html
index 2ac383a974bc37de6749eb0b12e1de53c81eda8f..735d462b73cd17422564ac9af160d5a770389b76 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html
index e62a827a783333c6aa596d1e28efdac434c16704..0ae68435e58ff6830a5eac9d674569f1a366162f 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_box.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_box.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_create_faceset_plane.html b/doc/src/USER/atc/man_mesh_create_faceset_plane.html
index b1969cb79dd899194e1b797e25eb56343f319236..cd78816bae757aa604d8abbc474808b1281b12dc 100644
--- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html
+++ b/doc/src/USER/atc/man_mesh_create_faceset_plane.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html
index 39bfffd1198c6715bfa5b9e04e5ca1716519e6a5..0e3624cf8a05225744a8f2e72d2b09c56309b515 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html
index 60a2fe59a1095934762d4c34b845b560e00a3175..e39cc54d416e9c1097a8535e84a65d8775460909 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
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 d05429ebabbf811cd7fe5929aa7fdd3c205fd9ec..66b55a48fb6f0574f12922c584b1df6eba7d1a26 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html
index f768a29c41de56432542fa5febb8cc96782601af..1d2983afff93589b176e15f8a3bc9bb01d7579c7 100644
--- a/doc/src/USER/atc/man_mesh_output.html
+++ b/doc/src/USER/atc/man_mesh_output.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html
index 46487fdce7e7be93fed9d32ca8d09c66c1467298..821e50e4cfc328ce6ab6b2c0a4843675d5ccfec7 100644
--- a/doc/src/USER/atc/man_mesh_quadrature.html
+++ b/doc/src/USER/atc/man_mesh_quadrature.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html
index e0571ccf88eef86cb6dbc8e336591df345d44bf8..315180e1db5096a889f1dffa2791414723249e3d 100644
--- a/doc/src/USER/atc/man_mesh_read.html
+++ b/doc/src/USER/atc/man_mesh_read.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html
index 756cf4992258b507e87a0f199bae5df16407398a..f709c02a8430b6535f5d23722672b308e102cd20 100644
--- a/doc/src/USER/atc/man_mesh_write.html
+++ b/doc/src/USER/atc/man_mesh_write.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html
index 60fbfcd888555ae5fb7c79ea748455c7e8e9704c..ee0505847c9878d79a531c2f1cf30ad9bdeec22a 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html
index aec1d5d55ae33a6713dde6ab621c4c132ad108d4..d0a08fa0da111c62039c6c1726cc58921bc1e928 100644
--- a/doc/src/USER/atc/man_output.html
+++ b/doc/src/USER/atc/man_output.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html
index 54079027c5053a2ebe3d9c2b387b966a1287fa56..18afe0aa973bc5511f5c093a3f124e8662740ed3 100644
--- a/doc/src/USER/atc/man_output_elementset.html
+++ b/doc/src/USER/atc/man_output_elementset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html
index 2fc6e0268169fb3f0f00308ecff8160882f8bba6..7906c5fc52f3fd9f48c34fbd274aa0f2813346ac 100644
--- a/doc/src/USER/atc/man_output_nodeset.html
+++ b/doc/src/USER/atc/man_output_nodeset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html
index 2cb2cb6113383c34effad09f654a8f41d532b1cd..3ec2eecc60504e2c772c49501f381a95e1aa5b62 100644
--- a/doc/src/USER/atc/man_pair_interactions.html
+++ b/doc/src/USER/atc/man_pair_interactions.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html
index b6fabbb27c1613cf8cda041d04560d9c4458b1b3..3e22a51f3e9e4eada56e1fe337018dec72e863d5 100644
--- a/doc/src/USER/atc/man_poisson_solver.html
+++ b/doc/src/USER/atc/man_poisson_solver.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html
index 5fc21282f68860c6726887df2e9916c9b8bfcfff..d13151a12ed3c01ed2d2504f53e2fbd219173a49 100644
--- a/doc/src/USER/atc/man_read_restart.html
+++ b/doc/src/USER/atc/man_read_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html
index e6ad418de6871e7b4dab85dc02eede170bbf048d..54e4e3419fbcf126d22287759c25d45cdb523443 100644
--- a/doc/src/USER/atc/man_remove_molecule.html
+++ b/doc/src/USER/atc/man_remove_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html
index acea7a56074df6c0ed151296fcd1d1048abc1426..c15e0ca46ddcbdb4192d709990f0e3979572e712 100644
--- a/doc/src/USER/atc/man_remove_source.html
+++ b/doc/src/USER/atc/man_remove_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html
index 561364518fe2033590626709f6fd1ac72b512c77..ee063ce57f524120279df2f36071986b33b3a813 100644
--- a/doc/src/USER/atc/man_remove_species.html
+++ b/doc/src/USER/atc/man_remove_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
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 88e6748001c44716880a1b8a71b072d343e33d60..3c438610540faeb48a021a943e1d93628cac7358 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html
index a6429bf6d6c8b040f9171787f779ef49a9333768..9607848e1a490c18addf77da883cb5568f65abae 100644
--- a/doc/src/USER/atc/man_reset_time.html
+++ b/doc/src/USER/atc/man_reset_time.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html
index 4e48c4bb299c854bb86f26adcb83d1a771725a3e..9a9a8e3a02fbeb8d2cbee68a2b057d759f30ff8a 100644
--- a/doc/src/USER/atc/man_sample_frequency.html
+++ b/doc/src/USER/atc/man_sample_frequency.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html
index cf775c9b36d4e9a43abab0d2716c0a6d7c70a29d..55ad8d952b8ae5fb679ba08c0bd83550be7870df 100644
--- a/doc/src/USER/atc/man_set.html
+++ b/doc/src/USER/atc/man_set.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html
index c7239f2c412db0ac97ec56462ce96c93d1726c7e..78fb1652ebc05a9a3296c6faee275c74b3230c3a 100644
--- a/doc/src/USER/atc/man_source.html
+++ b/doc/src/USER/atc/man_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html
index 3f43340af827c5c61162078843dd7b6af7116ff9..3b261b781014715c1346623fb5d6cef6c0b86dee 100644
--- a/doc/src/USER/atc/man_source_integration.html
+++ b/doc/src/USER/atc/man_source_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html
index a07ba29cab6f1780d61dfbc22bd0f5f50f3973b8..c317c06c00cf0aca03cd5eefaf212505cf34a616 100644
--- a/doc/src/USER/atc/man_temperature_definition.html
+++ b/doc/src/USER/atc/man_temperature_definition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html
index fe293138be2a7206963a5c2339be637da3542e6e..830591921e7dbd63cc73d1dc5f4ebb17c65c2d95 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html
index 732eaa3a36114c766118a0ab5aadd541e6284ab5..5000fb079d2a0dc5f7ed1a474a8f516d03a3b5f0 100644
--- a/doc/src/USER/atc/man_time_filter.html
+++ b/doc/src/USER/atc/man_time_filter.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html
index f5410816d75a779a6c6ec38c2e8bad1f64ac262f..2c7cf2615018eaf3a4be95be6ee15d0884c1bfd5 100644
--- a/doc/src/USER/atc/man_track_displacement.html
+++ b/doc/src/USER/atc/man_track_displacement.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html
index 95e1f4be5a85ea44cb7db7b434a0eb053262b9b4..551896431a06dac1dedb2c7b35a2d03351a36fd4 100644
--- a/doc/src/USER/atc/man_unfix_flux.html
+++ b/doc/src/USER/atc/man_unfix_flux.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html
index 78495c928a4751e188868ade7b93cbfb6496b04b..4dfd9b3cfc4c8755eeecfb1b2bffb24868564aae 100644
--- a/doc/src/USER/atc/man_unfix_nodes.html
+++ b/doc/src/USER/atc/man_unfix_nodes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html
index 8a0e5b62a81bb9488e6bf5e9e6f61dbfc929fef3..1722d74f67fa82dbabc61ea535f98553e4adcef8 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 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html
index 6dca57673bbdabe393ad0fa2512f8c566a1f4374..74c6e2d289feac47f5f83f5a8448ee08115a7ad1 100644
--- a/doc/src/USER/atc/man_write_restart.html
+++ b/doc/src/USER/atc/man_write_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 4b4ac3862d102b54ed08cb0b2d8b63f84ec32f89..0f0b241b766c1e5b19b37aedb652b85be57ebbd7 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 7d9e443e7da7455de147ca1531daab58887e65f8..8facb4de63ebfb527e11108ba02e381db6a1425f 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 cda4a36b34d01c83a4977440adc94e747ea090df..46db81eb9e3d366592e3a1a9e254fb3d3f04170a 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 66eecd195da4fb19851d5d84349c72391e51add6..ddc4cc82d30483aa2e5352ed034da9a48bfdb87b 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 669ab9f7ca3ea74e4a3a8a0b5537c0b09cbd814d..7cea62c7b3a4e824de53b234bba0176130447941 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 b3891841b8ce04185b3f0705e877b8c34f87b34f..04f0fd0b82df8a98ac3a11311ba95fe4a7882479 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 192ea0bc9ec96d6c7691214f78f7cf2c080f4ddd..5ba2100fbaa0bb51ab8f2bc112cb22248d745639 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_pair.txt b/doc/src/compute_pair.txt
index a2c25fcc8dc0dbe737e3efb76fd1ef57197dd765..b309019e30fd7927b1c3226612e4f065f397efad 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -27,7 +27,9 @@ compute 1 all pair reax :pre
Define a computation that extracts additional values calculated by a
pair style, and makes them accessible for output or further processing
-by other commands. The group specified for this command is ignored.
+by other commands.
+
+NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index c4c0fc405ff563273c1d9b1ff72c51a638eedf02..72ed0ba5c4003af0a1ca3881baf190a93f6db58d 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 512009093c0e052e8e7b43f44455d1f61d7e6fb8..bc1e3049fadc20b8f98018bcf2cf1fe69426e85f 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 04b38682cc4957ac67459b18652249b1dfb75f14..d11ae9e3bf0ba508a42e46e4cdb8023e33ef21f1 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 9b829a70fcb82a1de7defbafbce6b949ca833f20..67c6209bdf302e471ce2847a1400f4b8ccc799c5 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 92f5923de05f735931aae9908844b197ad127fe3..e9ff2e739b111a8b733fd7aa01f31262834ed45f 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 787ff8cdcfa822ba37c896d464e6c9655d5e543a..e6185a2dd8f88ca2c5c4196f4621e067bb684a8c 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 9a509da4503db6cb3a9e03b0314de6300e28d36b..97e1d6e1ae87ff94166dd20f67518c5dc1d29d92 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 57faf97ad1bf1d213135707989985a1f866a8f8d..a55288e1dbad05e79f32d047355bafd3d65d3caa 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 b29fa82f2d0d16c9b1a252073080aba43332605c..4e336046968ca3b0dc3c7f32db3a341ece4d9c9b 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 98bcbc5e551e85216732c74afebbc6c6b361a663..72f493591677e0e01eefde4f7044898f46966da1 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 dd2b212f0baafc6efd4200c42eb4439e1d6715e3..b5f157cf292cba47d11fc6258b0fdea4ca34cf54 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:
<VMDHOME>/plugins/<VMDARCH>/molfile
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 9c3a1d0349fd097eb9f5572b943872bce1254a4e..ee0d006fe8396fc265a9493a27af86f156b58aea 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 7acc22d702e4b7cfd496df2865fdbdc0844bd276..b7d4e7badfc5496c884c92ae7307d92550007893 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 7317dd26bb3b9d4b563b0266364490fafc39d37c..8e7cb1bdaef8b565a4138bcd5a68cd0d4343a277 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
@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
[Default:]
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
:line
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index be4fbd255b58983cd52ac8a9fbb1e4144b5a2f6c..0c5a4493ae7d7a2507770720bd025c44f157e5bd 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 b30966c2f941de518e42f4c90463f543a21fdad5..4868761d4207675072fc00c1f6fd66c1c7a06629 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 b115aba7dfa38d5a85a0aee82000d2e8bf568fcd..64486a9cc7922efb7a689c09aaba3b98d652671a 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 7bb25e0a687af2c0af3f14a1ccd9d0c9a73e7257..d4836706e2a8577cc3c27b70d9f630aaec1ede51 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 bd61e29dcb66f9c19772345cbe3c19161143474e..c97095bcfc98c015f59c271dc9aa70249351c587 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 1a5239782268f34870cd3ec3faac1b560f7c451a..d9012d8cb396371d3fd4568cbba35b19c5d6e275 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 ddb5f9a4cd4346e6f0d3195a101445c15eaedfde..f50747948a91152948fa1c31e4037ef735d2035a 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 d331d9ad75fbf7c2a203bfe68bb1035abcfd410a..521dfff12b2fe03b0b8c5aa221e1a63abb596676 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 ae403cafd1d8ff7c5ee8f6e7fcc0589dd9437cb6..dc05948de338c24441d5d1849c6f347dc2a8e311 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 a3d1ab702ebd6b28c55215a80d40d548017cc863..f013ebfae1ca4e28fe6b0335237f31fa78d568b4 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 d489762e8022bdfe7f4d82af51a7642fe8fbd286..5d65856735d4125a6b0e62cebfb5b6980914622c 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 644c04eadb9efe7e64d6f51f68893e8d9e59a1e7..774842c7cfe83a47faa17aea140313a81e124fdb 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 ade64d2056e0e23e58e3e762620077d6ada3f1f1..2ee045141a70897ff5bb277f60d19e6bd00afb59 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/lammps.book b/doc/src/lammps.book
index f1ff39d80b0c0806e1e3e4b6928f95b96abeef27..47d05570be4670b27907ac2b22783afbaf50cc69 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -25,6 +25,7 @@ Build_basics.html
Build_settings.html
Build_package.html
Build_extras.html
+Build_windows.html
Run_head.html
Run_basics.html
Run_options.html
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 57e122fdcd53cec635f42746fd23c475f8fca7fc..75d199e0b4cd91e20e1e5e677ac09da52423c7dc 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 8b0581929ff10cffd2661b5268761e61a276e418..65117ba3c3c15d4ec4e4e2dfd5a27a9fe7115c61 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 4c43978fe5a44eae7d15fc21aecf5e2d2c8f780c..d9780e03200bc41976535cc77de8d7edfbc348e5 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 63f85f23d5e480a77ccc5f0c673cdde81d5a2d16..88f95b5b2cb6f62fc2b2ea903093c21509e46c45 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 adaeeb8390e07f080259009962109f909857f56b..8b1ceab85857a0621b8ac6f9ad8b9cbdf8c33e88 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 02d0db7af25e6c86f6ece52e56623bf71825173a..c74028faa91fe9ff80ef42560c13d1bf74b3c685 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 f557e6c731db499de0820bbb39ef9aab1aa0f46a..912fca165750f7f9a63288ef34c8015f23a37a29 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 23da86fc495a6daabdee6048cc4d8dcb72525b6b..e8baf14d2eefb694ff107609d65afad5d8f9b3f4 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 b33897c5aa506cd6be92ef275194ec2ceb83ce44..1441da2b610e26ec5a6be9fb7028fe3189356b13 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 ef899a15b44b153621cc194d317c3a313bd9afac..6aa30d9e634c30f4e0831a431c5e636f5c176bc2 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 0195dce9114f4a3d0bf30a805a1c0f0e31a70be7..79a481746ec8843b20d567a67b1c71a2a234e797 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 391b51fde99e167d813bef98b3a62f96786ed1de..8b217c7b1cc5f60a566ca858354f9c1fdb84ec56 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 7c034f36e0c6d002739c35362afca8440f9358a5..e0fae3909dc771ca15459230886ee5667a1715f2 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 6dd9b56908960bbbe820bcd7f2667a3faf158a73..9defd1314ea9d404ff24aee6e106c2153af9c0dd 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 a57b61664d56e76b28d3aad9f2059bdbb24a9c31..283aad6c2d326b77111ffc94fc01d9bfde888249 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 11460185db56eed8d1b71e71f3b5ec4442c07f09..7b1481ceb9b75da66bbf388fab4d80560b995019 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 6c25c23a793828857f2e41ade334f1af9a75d12b..8d2fa2e57760257a2890fc3be91e49b93c70aa66 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 39ee684a0b078edf4f771d3f52e975bbbf047d20..1eb53c70a29b5becf7c6abd236e3d2312bc00b4e 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 @@
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
{% endif %}
<a href="http://lammps.sandia.gov">Website</a>
- <a href="Section_commands.html#comm">Commands</a>
+ <a href="Commands_all.html">Commands</a>
{% endif %}
</li>
</ul>
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index fb08e4e97e5b19ad0713819f173a78555d0ff42d..febd5c20a02d74a4d588e697cde72da12e7be840 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/python/lammps.py b/python/lammps.py
index 2f4ffb642ef084fbbd1b7567bfc363220288dafc..598e4c506f1bf64d451432305d8c15ae8bd82fdb 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -173,6 +173,9 @@ class lammps(object):
self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
else:
+ if lammps.has_mpi4py:
+ from mpi4py import MPI
+ self.comm = MPI.COMM_WORLD
self.opened = 1
if cmdargs:
cmdargs.insert(0,"lammps.py")
@@ -862,6 +865,10 @@ class PyLammps(object):
def run(self, *args, **kwargs):
output = self.__getattr__('run')(*args, **kwargs)
+
+ if(lammps.has_mpi4py):
+ output = self.lmp.comm.bcast(output, root=0)
+
self.runs += get_thermo_data(output)
return output
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index 9f3221449bb2329923cfa9ed987beb6f26e58e3f..efa2c87296dbd1a78ec7ffba150adb583e39acb2 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/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index c72a1b027bafa28c9e219f1348111c4ec4016f97..5ce1f1147571a024a8037dd2160d369b21cf23c7 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
hang_catch++;
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
- if (hang_catch > atom->nlocal*3) {
- error->all(FLERR,"Excessive iteration of superimpose algorithm");
+ if (hang_catch > atom->nlocal*30) {
+ error->one(FLERR,"Excessive iteration of superimpose algorithm");
}
}
}
@@ -1554,6 +1554,40 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+ // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+ // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (landlocked_atoms[i][myrxn] == 0) {
+ int twomol_atomi = i+1;
+ for (int j = 0; j < twomol->num_bond[i]; j++) {
+ int twomol_atomj = twomol->bond_atom[i][j];
+ if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
+ int onemol_atomi = equivalences[i][1][myrxn];
+ int onemol_batom;
+ for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+ if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ if (newton_bond) {
+ int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+ for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+ if (onemol_batom == equivalences[i][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
for (int i = 0; i < twomol->natoms; i++) {
@@ -2067,7 +2101,7 @@ void FixBondReact::update_everything()
nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
}
- for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+ for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
}
special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 11bf2ae01ed2790cc65b62afe79c7bb2f392ee44..785146a0d6fef2646333d30f6c7f6fd5cfe67f0e 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
diff --git a/src/version.h b/src/version.h
index db73df1ad124b44dd86c4e3f314a9bdcb162255a..2192b25d9147aef94706956d2c16eea09c51e2b9 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Aug 2018"
+#define LAMMPS_VERSION "22 Aug 2018"