Merge remote-tracking branch 'upstream/master'

Conflicts:
	doc/src/compute.txt

doc/src/Build_basics.txt

@@ -49,7 +49,7 @@ make mybox :pre         # uses Makefile.mybox to produce lmp_mybox :pre
 
 Serial build (see src/MAKE/Makefile.serial):
 
-MPI_INC =       -I../STUBS 
+MPI_INC =       -I../STUBS
 MPI_PATH =      -L../STUBS
 MPI_LIB =	-lmpi_stubs :pre
 
@@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
 compilers it is -qopenmp.  If you are using a different compiler,
 please refer to its documentation.
 
+[OpenMP Compiler compatibility info]: :link(default-none-issues)
+
+Some compilers do not fully support the 'default(none)' directive
+and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
+semantics, which are incompatible with the OpenMP 3.1 directives used
+in LAMMPS (for maximal compatibility with compiler versions in use).
+In those case, all 'default(none)' directives (which aid in detecting
+incorrect and unwanted sharing) can be replaced with 'default(shared)'
+while dropping all 'shared()' directives. The script
+'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
+this conversion.
+
 :line
 
 Choice of compiler and compile/link options :h4,link(compile)
@@ -137,9 +149,9 @@ simply loading the appropriate module before building LAMMPS.
 -D CMAKE_C_COMPILER=name              # name of C compiler
 -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
 
--D CMAKE_CXX_FlAGS=string             # flags to use with C++ compiler
--D CMAKE_C_FlAGS=string               # flags to use with C compiler
--D CMAKE_Fortran_FlAGS=string         # flags to use with Fortran compiler :pre
+-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+-D CMAKE_C_FLAGS=string               # flags to use with C compiler
+-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
 
 By default CMake will use a compiler it finds and it will add
 optimization flags appropriate to that compiler and any "accelerator
@@ -172,7 +184,7 @@ want.
 Parallel build (see src/MAKE/Makefile.mpi):
 
 CC =		mpicxx
-CCFLAGS =	-g -O3 
+CCFLAGS =	-g -O3
 LINK =		mpicxx
 LINKFLAGS =	-g -O :pre
 
@@ -292,7 +304,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
 you can browse them locally on your system.  Type "make" from the
 lammps/doc dir to see other options.
 
-NOTE: You can also download a tarball of the documention for the
+NOTE: You can also download a tarball of the documentation for the
 current LAMMPS version (HTML and PDF files), from the website
 "download page"_http://lammps.sandia.gov/download.html.
 

doc/src/Build_cmake.txt

@@ -27,7 +27,7 @@ make command to build LAMMPS, which uses the created
 Makefile(s). Example:
 
 cd lammps                        # change to the LAMMPS distribution directory
-mkdir build; cd build            # create a new directory (folder) for build       
+mkdir build; cd build            # create a new directory (folder) for build
 cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
 make                             # compilation :pre
 
@@ -44,7 +44,7 @@ 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
-library into your system folders (by default under /usr/local) with:
+library into your system folders (by default under $HOME/.local) with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 

doc/src/Build_extras.txt

@@ -36,8 +36,8 @@ This is the list of packages that may require additional steps.
 "OPT"_#opt,
 "POEMS"_#poems,
 "PYTHON"_#python,
-"REAX"_#reax,
 "VORONOI"_#voronoi,
+"USER-ADIOS"_#user-adios,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
@@ -45,6 +45,7 @@ This is the list of packages that may require additional steps.
 "USER-INTEL"_#user-intel,
 "USER-MOLFILE"_#user-molfile,
 "USER-NETCDF"_#user-netcdf,
+"USER-PLUMED"_#user-plumed,
 "USER-OMP"_#user-omp,
 "USER-QMMM"_#user-qmmm,
 "USER-QUIP"_#user-quip,
@@ -63,7 +64,7 @@ available on your system.
 
 If CMake cannot find the library, you can set these variables:
 
--D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
 -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file :pre
 
 [Traditional make]:
@@ -86,22 +87,31 @@ which GPU hardware to build for.
                       # value = double or mixed (default) or single
 -D OCL_TUNE=value     # hardware choice for GPU_API=opencl
                       # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
--D GPU_ARCH=value     # hardware choice for GPU_API=cuda
+-D GPU_ARCH=value     # primary GPU hardware choice for GPU_API=cuda
                       # value = sm_XX, see below
                       # default is Cuda-compiler dependent, but typically sm_20
--D CUDPP_OPT=value    # optimization setting for GPU_API=cudea
+-D CUDPP_OPT=value    # optimization setting for GPU_API=cuda
                       # enables CUDA Performance Primitives Optimizations
                       # yes (default) or no :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
-sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
-sm_30 for Kepler (K10)
-sm_35 for Kepler (K40) or GeForce GTX Titan or similar
-sm_37 for Kepler (dual K80)
-sm_50 for Maxwell
-sm_60 for Pascal (P100)
-sm_70 for Volta :ul
+sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
+sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
+sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
+sm_50 or sm_52 for Maxwell (supported since CUDA 6)
+sm_60 or sm_61 for Pascal (supported since CUDA 8)
+sm_70 for Volta (supported since CUDA 9)
+sm_75 for Turing (supported since CUDA 10) :ul
+
+A more detailed list can be found, for example,
+at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported
+
+CMake can detect which version of the CUDA toolkit is used and thus can
+include support for [all] major GPU architectures supported by this toolkit.
+Thus the GPU_ARCH setting is merely an optimization, to have code for
+the preferred GPU architecture directly included rather than having to wait
+for the JIT compiler of the CUDA driver to translate it.
 
 [Traditional make]:
 
@@ -127,7 +137,7 @@ specified by the "-m" switch.  For your convenience, machine makefiles
 for "mpi" and "serial" are provided, which have the same settings as
 the corresponding machine makefiles in the main LAMMPS source
 folder. In addition you can alter 4 important settings in the
-Makefile.machine you start from via the corresponding -h, -a, -p, -e
+Makefile.machine you start from via the corresponding -c, -a, -p, -e
 switches (as in the examples above), and also save a copy of the new
 Makefile if desired:
 
@@ -136,6 +146,11 @@ CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
 CUDA_PRECISION = precision (double, mixed, single)
 EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
 
+The file Makefile.linux_multi is set up to include support for multiple
+GPU architectures as supported by the CUDA toolkit in use. This is done
+through using the "--gencode " flag, which can be used multiple times and
+thus support all GPU architectures supported by your CUDA compiler.
+
 If the library build is successful, 3 files should be created:
 lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and
 lib/gpu/Makefile.lammps.  The latter has settings that enable LAMMPS
@@ -149,43 +164,38 @@ re-build LAMMPS.  This is because the compilation of files in the GPU
 package uses the library settings from the lib/gpu/Makefile.machine
 used to build the GPU library.
 
+
 :line
- 
+
 KIM package :h4,link(kim)
 
-To build with this package, the KIM library must be downloaded and
-built on your system.  It must include the KIM models that you want to
-use with LAMMPS.
+To build with this package, the KIM library with API v2 must be downloaded
+and built on your system.  It must include the KIM models that you want to
+use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+command, you also need to have libcurl installed with the matching
+development headers and the curl-config tool.
 
 Note that in LAMMPS lingo, a KIM model driver is a pair style
 (e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
 element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that installing the KIM API
-library with all its models, may take around 30 min to build.  Of
-course you only need to do that once.
+specific EAM potential file.  Also note that downloading and installing
+the KIM API library with all its models, may take a long time (10s of
+minutes to hours) to build.  Of course you only need to do that once.
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
+https://openkim.org/browse/models/by-model-drivers
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # KIM library file (only needed if a custom location) 
--D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
-your system (in a location CMake cannot find it), KIM_LIBRARY is the
-filename (plus path) of the KIM library file, not the directory the
-library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
-file is in.
+your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
+environment variable so that libkim-api-v2 can be found.
 
 [Traditional make]:
 
@@ -199,8 +209,8 @@ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
 make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
 make lib-kim args="-b -a everything"     # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
 
 :line
 
@@ -254,7 +264,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables:
 -D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU
                                    # archGPU = GPU from list above
 -D KOKKOS_ENABLE_CUDA=yes
--D KOKKOS_ENABLE_OPENMP=yes 
+-D KOKKOS_ENABLE_OPENMP=yes
 -D CMAKE_CXX_COMPILER=wrapper      # wrapper = full path to Cuda nvcc wrapper :pre
 
 The wrapper value is the Cuda nvcc compiler wrapper provided in the
@@ -296,7 +306,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
 CC =		mpicxx :pre
 
 :line
- 
+
 LATTE package :h4,link(latte)
 
 To build with this package, you must download and build the LATTE
@@ -324,7 +334,7 @@ args:
 make lib-latte                          # print help message
 make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
 make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
+make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
                                         #   copy Makefile.lammps.gfortran to Makefile.lammps
 :pre
 
@@ -335,7 +345,7 @@ also check that the Makefile.lammps file you create is appropriate for
 the compiler you use on your system to build LATTE.
 
 :line
- 
+
 MEAM package :h4,link(meam)
 
 NOTE: the use of the MEAM package is discouraged, as it has been
@@ -378,7 +388,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
 file.
 
 :line
- 
+
 MESSAGE package :h4,link(message)
 
 This package can optionally include support for messaging via sockets,
@@ -407,7 +417,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ
 library if requested in the build.
 
 :line
- 
+
 MSCG package :h4,link(mscg)
 
 To build with this package, you must download and build the MS-CG
@@ -419,7 +429,7 @@ lib/mscg/README and MSCG/Install files for more details.
 [CMake build]:
 
 -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
--D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location) 
+-D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location)
 -D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location) :pre
 
 If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
@@ -464,7 +474,7 @@ line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
 an example.
 
 :line
- 
+
 POEMS package :h4,link(poems)
 
 [CMake build]:
@@ -493,7 +503,7 @@ for your system, which should define an EXTRAMAKE variable to specify
 a corresponding Makefile.lammps.machine file.
 
 :line
- 
+
 PYTHON package :h4,link(python)
 
 Building with the PYTHON package requires you have a Python shared
@@ -519,45 +529,6 @@ process to find Python.  You should only need to create a new
 Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
 build fails.
 
-:line
- 
-REAX package :h4,link(reax)
-
-NOTE: the use of the REAX package and its "pair_style
-reax"_pair_reax.html command is discouraged, as it is no longer
-maintained.  Please use the USER-REAXC package and its "pair_style
-reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
-enabled variant (pair_style reax/c/kk), which has a more robust memory
-management.  See the "pair_style reax/c"_pair_reaxc.html doc page for
-details.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_REAX=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the REAX library in lib/reax.
-You can do this manually if you prefer; follow the instructions in
-lib/reax/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/reax/Install.py script with the specified args:
-
-make lib-reax                    # print help message
-make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library).  Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
 :line
 
 VORONOI package :h4,link(voronoi)
@@ -570,7 +541,7 @@ library"_voro-home.
 [CMake build]:
 
 -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
--D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location) 
+-D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
 -D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location) :pre
 
 If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
@@ -600,14 +571,40 @@ the lib/voronoi/Makefile.lammps file.
 
 :line
 
+USER-ADIOS package :h4,link(user-adios)
+
+The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
+version 2.3.1 or newer. Make sure that you have ADIOS built either with or
+without MPI to match if you build LAMMPS with or without MPI.
+ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
+and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
+installation and the instructions below are followed for the respective build systems.
+
+[CMake build]:
+
+-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+-D PKG_USER-ADIOS=yes     :pre
+
+[Traditional make]:
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+make yes-user-adios                       :pre
+
+otherwise, set ADIOS2_DIR environment variable when turning on the package:
+
+ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre
+
+:line
+
 USER-ATC package :h4,link(user-atc)
 
 The USER-ATC package requires the MANYBODY package also be installed.
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_REAX=yes" and "-D
-PKG_MANYBODY=yes".
+No additional settings are needed besides "-D PKG_USER-ATC=yes"
+and "-D PKG_MANYBODY=yes".
 
 [Traditional make]:
 
@@ -712,6 +709,114 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
+USER-PLUMED package :h4,link(user-plumed)
+
+Before building LAMMPS with this package, you must first build PLUMED.
+PLUMED can be built as part of the LAMMPS build or installed separately
+from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
+:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
+
+PLUMED can be linked into MD codes in three different modes: static,
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
+
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
+
+[CMake build]:
+
+When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
+
+-D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
+-D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
+
+If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG_CONFIG_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
+
+The PLUMED_MODE setting determines the linkage mode for the PLUMED
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
+mode is recommended.
+
+[Traditional make]:
+
+PLUMED needs to be installed before the USER-PLUMED package is installed
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
+
+Download/compilation/configuration of the plumed library can be done
+from the src folder through the following make args:
+
+make lib-plumed                         # print help message
+make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+                                                # /usr/local and use shared linkage mode
+:pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink" are
+created in lib/plumed that point to the location of the PLUMED build to
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
+
+make yes-user-plumed
+make machine :pre
+
+Once this compilation completes you should be able to run LAMMPS in the
+usual way.  For shared linkage mode, libplumed.so must be found by the
+LAMMPS executable, which on many operating systems means, you have to
+set the LD_LIBRARY_PATH environment variable accordingly.
+
+Support for the different linkage modes in LAMMPS varies for different
+operating systems, using the static linkage is expected to be the most
+portable, and thus set to be the default.
+
+If you want to change the linkage mode, you have to re-run "make
+lib-plumed" with the desired settings [and] do a re-install if the
+USER-PLUMED package with "make yes-user-plumed" to update the required
+makefile settings with the changes in the lib/plumed folder.
+
+:line
+
 USER-H5MD package :h4,link(user-h5md)
 
 To build with this package you must have the HDF5 software package
@@ -790,7 +895,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -799,7 +914,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 
@@ -848,7 +967,9 @@ LINKFLAGS: -fopenmp             # for GNU Compilers
 LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre
 
 For other platforms and compilers, please consult the documentation
-about OpenMP support for your compiler.
+about OpenMP support for your compiler. Please see the note about
+how to address compatibility "issues with the 'default(none)'
+directive"_Build_basics.html#default-none-issues of some compilers.
 
 :line
 
@@ -869,7 +990,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version
 [CMake build]:
 
 The CMake build system currently does not support building the full
-QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.  
+QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
 You must use the traditional make build for this package.
 
 [Traditional make]:
@@ -939,7 +1060,7 @@ Coulomb solver library"_scafacos-home
 [CMake build]:
 
 -D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes
--D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location) 
+-D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location)
 -D SCAFACOS_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location) :pre
 
 If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded

doc/src/Build_link.txt

@@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style
 interface.
 
 See the sample codes in examples/COUPLE/simple for examples of C++ and
-C and Fortran codes that invoke LAMMPS thru its library interface.
+C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the "Howto couple"_Howto_couple.html doc page.
 

doc/src/Build_package.txt

@@ -47,8 +47,8 @@ packages:
 "OPT"_Build_extras.html#opt,
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
-"REAX"_Build_extras.html#reax,
 "VORONOI"_Build_extras.html#voronoi,
+"USER-ADIOS"_Build_extras.html#user-adios,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,
 "USER-COLVARS"_Build_extras.html#user-colvars,
@@ -56,6 +56,7 @@ packages:
 "USER-INTEL"_Build_extras.html#user-intel,
 "USER-MOLFILE"_Build_extras.html#user-molfile,
 "USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-PLUMED"_Build_extras.html#user-plumed,
 "USER-OMP"_Build_extras.html#user-omp,
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,

doc/src/Build_settings.txt

@@ -22,7 +22,7 @@ explain how to do this for building both with CMake and make.
 "Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
 
 :line
- 
+
 FFT library :h4,link(fft)
 
 When the KSPACE package is included in a LAMMPS build, the
@@ -73,7 +73,7 @@ FFT_LIB with the appropriate FFT libraries to include in the link.
 The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
 distribution.  It is portable across all platforms.  Depending on the
 size of the FFTs and the number of processors used, the other
-libraries listed here can be faster.  
+libraries listed here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
 per-timestep CPU cost, FFTs are only a portion of long-range
@@ -92,7 +92,7 @@ Building FFTW for your box should be as simple as ./configure; make;
 make install.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
 the "--prefix" option of configure.  Type "./configure --help" to see
-various options. 
+various options.
 
 The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see FFT_LIB setting above).
@@ -139,16 +139,16 @@ adequate.
 [Makefile.machine setting]:
 
 LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
-                               # default is LAMMMPS_SMALLBIG if not specified
+                               # default is LAMMPS_SMALLBIG if not specified
 [CMake and make info]:
 
 The default "smallbig" setting allows for simulations with:
- 
+
 total atom count = 2^63 atoms (about 9e18)
 total timesteps = 2^63 (about 9e18)
 atom IDs = 2^31 (about 2 billion)
 image flags = roll over at 512 :ul
-  
+
 The "bigbig" setting increases the latter two limits.  It allows for:
 
 total atom count = 2^63 atoms (about 9e18)
@@ -209,12 +209,12 @@ Usually these settings are all that is needed.  If CMake cannot find
 the graphics header, library, executable files, you can set these
 variables:
 
--D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file 
--D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file 
--D PNG_INCLUDE_DIR=path     # path to png.h header file 
--D PNG_LIBRARIES=path       # path to libpng.a (.so) file 
--D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
--D ZLIB_LIBRARIES=path      # path to libz.a (.so) file 
+-D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
+-D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
+-D PNG_INCLUDE_DIR=path     # path to png.h header file
+-D PNG_LIBRARIES=path       # path to libpng.a (.so) file
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+-D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
 -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable :pre
 
 [Makefile.machine settings]:

doc/src/Build_windows.txt

@@ -53,20 +53,20 @@ 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.  
+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 
+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. 
+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.
+them as an issue or pull request on the LAMMPS GitHub project.
 
 
 Using a cross-compiler :h4,link(cross)

doc/src/Commands.txt

@@ -42,10 +42,10 @@ END_RST -->
 "Input script structure"_Commands_structure.html
 "Commands by category"_Commands_category.html :all(b)
 
-"All commands"_Commands_all.html 
-"Fix commands"_Commands_fix.html 
-"Compute commands"_Commands_compute.html 
-"Pair commands"_Commands_pair.html 
+"General commands"_Commands_all.html
+"Fix commands"_Commands_fix.html
+"Compute commands"_Commands_compute.html
+"Pair commands"_Commands_pair.html
 "Bond, angle, dihedral, improper commands"_Commands_bond.html
 "KSpace solvers"_Commands_kspace.html  :all(b)
 

doc/src/Commands_all.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 "Improper styles"_Commands_bond.html#improper,
 "KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
 
-All commands :h3
+General commands :h3
 
-An alphabetic list of all LAMMPS commands.
+An alphabetic list of all general LAMMPS commands.
 
 "angle_coeff"_angle_coeff.html,
 "angle_style"_angle_style.html,
@@ -48,23 +48,27 @@ An alphabetic list of all LAMMPS commands.
 "dimension"_dimension.html,
 "displace_atoms"_displace_atoms.html,
 "dump"_dump.html,
+"dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
 "dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
 "fix_modify"_fix_modify.html,
 "group"_group.html,
 "group2ndx"_group2ndx.html,
+"hyper"_hyper.html,
 "if"_if.html,
 "info"_info.html,
 "improper_coeff"_improper_coeff.html,
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
+"kim_query"_kim_query.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -75,6 +79,7 @@ An alphabetic list of all LAMMPS commands.
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
+"min_style spin"_min_spin.html,
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,

doc/src/Commands_bond.txt

@@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -37,6 +37,7 @@ OPT.
 "harmonic (iko)"_bond_harmonic.html,
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"mm3"_bond_mm3.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
 "oxdna/fene"_bond_oxdna.html,
@@ -60,17 +61,19 @@ OPT.
 "charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
 "class2/p6"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
+"cosine (ko)"_angle_cosine.html,
 "cosine/buck6d"_angle_cosine_buck6d.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
 "cosine/shift (o)"_angle_cosine_shift.html,
 "cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
 "cosine/squared (o)"_angle_cosine_squared.html,
+"cross"_angle_cross.html,
 "dipole (o)"_angle_dipole.html,
 "fourier (o)"_angle_fourier.html,
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
+"mm3"_angle_mm3.html,
 "quartic (o)"_angle_quartic.html,
 "sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
@@ -120,8 +123,10 @@ OPT.
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,
 "distance"_improper_distance.html,
+"distharm"_improper_distharm.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
 "inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.html,
+"sqdistharm"_improper_sqdistharm.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_category.txt

@@ -10,10 +10,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Commands by category :h3
 
 This page lists most of the LAMMPS commands, grouped by category.  The
-"Commands all"_Commands_all.html doc page lists all commands
-alphabetically.  It also includes long lists of style options for
-entries that appear in the following categories as a single command
-(fix, compute, pair, etc).
+"General commands"_Commands_all.html doc page lists all general commands
+alphabetically.  Style options for entries like fix, compute, pair etc.
+have their own pages where they are listed alphabetically.
 
 Initialization:
 

doc/src/Commands_compute.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,

doc/src/Commands_fix.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -78,6 +78,8 @@ OPT.
 "grem"_fix_grem.html,
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
+"hyper/global"_fix_hyper_global.html,
+"hyper/local"_fix_hyper_local.html,
 "imd"_fix_imd.html,
 "indent"_fix_indent.html,
 "ipi"_fix_ipi.html,
@@ -94,6 +96,7 @@ OPT.
 "lineforce"_fix_lineforce.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso"_fix_meso.html,
+"meso/move"_fix_meso_move.html,
 "meso/stationary"_fix_meso_stationary.html,
 "momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
@@ -107,7 +110,7 @@ OPT.
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,
 "nph/eff"_fix_nh_eff.html,
-"nph/sphere (ko)"_fix_nph_sphere.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
 "nphug (o)"_fix_nphug.html,
 "npt (iko)"_fix_nh.html,
 "npt/asphere (o)"_fix_npt_asphere.html,
@@ -127,7 +130,7 @@ OPT.
 "nve/line"_fix_nve_line.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/sphere (ko)"_fix_nve_sphere.html,
 "nve/spin"_fix_nve_spin.html,
 "nve/tri"_fix_nve_tri.html,
 "nvk"_fix_nvk.html,
@@ -146,6 +149,7 @@ OPT.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "planeforce"_fix_planeforce.html,
+"plumed"_fix_plumed.html,
 "poems"_fix_poems.html,
 "pour"_fix_pour.html,
 "precession/spin"_fix_precession_spin.html,
@@ -165,13 +169,13 @@ OPT.
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reaxc_bonds.html,
 "reax/c/species (k)"_fix_reaxc_species.html,
 "recenter"_fix_recenter.html,
 "restrain"_fix_restrain.html,
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.html,
+"rigid/meso"_fix_rigid_meso.html,
 "rigid/nph (o)"_fix_rigid.html,
 "rigid/nph/small"_fix_rigid.html,
 "rigid/npt (o)"_fix_rigid.html,
@@ -230,4 +234,4 @@ OPT.
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,
 "wall/region/ees"_fix_wall_ees.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
+"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

doc/src/Commands_kspace.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,

doc/src/Commands_pair.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -63,13 +63,13 @@ OPT.
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
 "coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/dsf (gko)"_pair_coul.html,
 "coul/long (gko)"_pair_coul.html,
 "coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/long/soft (o)"_pair_fep_soft.html,
 "coul/msm (o)"_pair_coul.html,
 "coul/shield"_pair_coul_shield.html,
 "coul/streitz"_pair_coul.html,
@@ -107,38 +107,42 @@ OPT.
 "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lcbop"_pair_lcbop.html,
+"lebedeva/z"_pair_lebedeva_z.html,
 "lennard/mdf"_pair_mdf.html,
 "line/lj"_pair_line_lj.html,
 "list"_pair_list.html,
 "lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/charmm/coul/msm (o)"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/cut/soft"_pair_fep_soft.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/class2/coul/long/soft"_pair_fep_soft.html,
+"lj/class2/soft"_pair_fep_soft.html,
 "lj/cubic (go)"_pair_lj_cubic.html,
 "lj/cut (gikot)"_pair_lj.html,
 "lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/debye (gko)"_pair_lj.html,
 "lj/cut/coul/dsf (gko)"_pair_lj.html,
 "lj/cut/coul/long (gikot)"_pair_lj.html,
 "lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/msm (go)"_pair_lj.html,
 "lj/cut/coul/wolf (o)"_pair_lj.html,
 "lj/cut/dipole/cut (go)"_pair_dipole.html,
 "lj/cut/dipole/long (g)"_pair_dipole.html,
 "lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/thole/long (o)"_pair_thole.html,
 "lj/cut/tip4p/cut (o)"_pair_lj.html,
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/expand/coul/long (g)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
@@ -153,6 +157,7 @@ OPT.
 "lj/sf/dipole/sf (go)"_pair_dipole.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
 "lj96/cut (go)"_pair_lj96.html,
 "lubricate (o)"_pair_lubricate.html,
 "lubricate/poly (o)"_pair_lubricate.html,
@@ -160,8 +165,7 @@ OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "mdpd"_pair_meso.html,
 "mdpd/rhosum"_pair_meso.html,
-"meam"_pair_meam.html,
-"meam/c"_pair_meam.html,
+"meam/c"_pair_meamc.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@@ -169,7 +173,7 @@ OPT.
 "momb"_pair_momb.html,
 "morse (gkot)"_pair_morse.html,
 "morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_morse.html,
+"morse/soft"_pair_fep_soft.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
 "nb3b/harmonic"_pair_nb3b_harmonic.html,
@@ -194,10 +198,10 @@ OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "quip"_pair_quip.html,
-"reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
 "rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/tri_surface"_pair_smd_triangulated_surface.html,
@@ -229,7 +233,7 @@ OPT.
 "thole"_pair_thole.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tip4p/long/soft (o)"_pair_fep_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
 "vashishta (gko)"_pair_vashishta.html,

doc/src/Commands_parse.txt

@@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how
 strings are assigned to variables and evaluated, and how they can be
 used in input script commands.
 
-(4) The line is broken into "words" separated by whitespace (tabs,
+(4) The line is broken into "words" separated by white-space (tabs,
 spaces).  Note that words can thus contain letters, digits,
 underscores, or punctuation characters.
 

doc/src/Developer/.gitignore

@@ -0,0 +1,3 @@
+/developer.aux
+/developer.log
+/developer.toc

doc/src/Eqs/angle_cross.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
+$$
+
+\end{document}

doc/src/Eqs/angle_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
+$$
+
+\end{document}

doc/src/Eqs/bond_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+$$
+
+\end{document}

doc/src/Eqs/improper_distharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d - d_0)^2
+$$
+
+\end{document}

doc/src/Eqs/improper_sqdistharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d^2 - d_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/min_spin_damping.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/min_spin_timestep.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    {\Delta t}_{\rm max} = \frac{2\pi}{\kappa
+    \left|\vec{\omega}_{\rm max} \right|} 
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_coulgauss.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_lj_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+
+\begin{eqnarray*}
+  E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
+% \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_mm3_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+  r_{v,ij} &=& r_{v,i} + r_{v,j} \\ 
+  \epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_switch3.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+\begin{eqnarray*}
+ S_3(r) = \left\lbrace \begin{array}{ll}
+                     1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
+                     3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
+                     0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
+                 \end{array} \right.
+\end{eqnarray*}
+
+\end{document}

doc/src/Errors.txt

@@ -32,7 +32,7 @@ END_RST -->
 
 "Common problems"_Errors_common.html
 "Reporting bugs"_Errors_bugs.html
-"Error messages"_Errors_messages.html 
+"Error messages"_Errors_messages.html
 "Warning messages"_Errors_warnings.html :all(b)
 
 <!-- END_HTML_ONLY -->

doc/src/Errors_common.txt

@@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
 input with an error message (for instance, when an integer is required,
 but a floating-point number 1.0 is provided):
 
-ERROR: Expected integer parameter in input script or data file :pre
+ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
 
 Some commands allow for using variable references in place of numeric
 constants so that the value can be evaluated and may change over the
@@ -85,6 +85,9 @@ reading the input and before parsing commands,
 
 NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
 the documentation of the corresponding command explicitly says it is.
+Otherwise, you will receive an error message of this kind:
+
+ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will

doc/src/Errors_messages.txt

@@ -279,12 +279,6 @@ multibody joint).  The bodies you have defined exceed this limit. :dd
 This is an internal LAMMPS error.  Please report it to the
 developers. :dd
 
-{Atom sorting has bin size = 0.0} :dt
-
-The neighbor cutoff is being used as the bin size, but it is zero.
-Thus you must explicitly list a bin size in the atom_modify sort
-command or turn off sorting. :dd
-
 {Atom style hybrid cannot have hybrid as an argument} :dt
 
 Self-explanatory. :dd
@@ -421,9 +415,9 @@ This is an internal error.  It should normally not occur. :dd
 
 This is an internal error.  It should normally not occur. :dd
 
-{Bad real space Coulomb cutoff in fix tune/kspace} :dt
+{Bad real space Coulombic cutoff in fix tune/kspace} :dt
 
-Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
+Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
 the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd
 
 {Balance command before simulation box is defined} :dt
@@ -460,7 +454,7 @@ compute. :dd
 
 {Big particle in fix srd cannot be point particle} :dt
 
-Big particles must be extended spheriods or ellipsoids. :dd
+Big particles must be extended spheroids or ellipsoids. :dd
 
 {Bigint setting in lmptype.h is invalid} :dt
 
@@ -780,7 +774,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd
 
 Self-explanatory. :dd
 
-{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt
+{Cannot change box z boundary to non-periodic for a 2d simulation} :dt
 
 Self-explanatory. :dd
 
@@ -1288,7 +1282,7 @@ are defined. :dd
 You cannot reset the timestep when a fix that keeps track of elapsed
 time is in place. :dd
 
-{Cannot run 2d simulation with nonperiodic Z dimension} :dt
+{Cannot run 2d simulation with non-periodic Z dimension} :dt
 
 Use the boundary command to make the z dimension periodic in order to
 run a 2d simulation. :dd
@@ -2116,29 +2110,29 @@ Self-explanatory. :dd
 Fix setforce cannot be used in this manner.  Use fix addforce
 instead. :dd
 
-{Cannot use nonperiodic boundares with fix ttm} :dt
+{Cannot use non-periodic boundares with fix ttm} :dt
 
 This fix requires a fully periodic simulation box. :dd
 
-{Cannot use nonperiodic boundaries with Ewald} :dt
+{Cannot use non-periodic boundaries with Ewald} :dt
 
 For kspace style ewald, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with EwaldDisp} :dt
+{Cannot use non-periodic boundaries with EwaldDisp} :dt
 
 For kspace style ewald/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
 slab with a non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPM} :dt
+{Cannot use non-periodic boundaries with PPPM} :dt
 
 For kspace style pppm, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPMDisp} :dt
+{Cannot use non-periodic boundaries with PPPMDisp} :dt
 
 For kspace style pppm/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
@@ -3351,21 +3345,21 @@ probably due to errors in the Python code. :dd
 The default minimum order is 2.  This can be reset by the
 kspace_modify minorder command. :dd
 
-{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt
+{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/coul/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
+{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt
 
-If using a Kspace solver, all Coulomb cutoffs of long pair styles must
+If using a Kspace solver, all Coulombic cutoffs of long pair styles must
 be the same. :dd
 
 {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt
@@ -5938,9 +5932,9 @@ map command will force an atom map to be created. :dd
 
 Self-explanatory. :dd
 
-{Input line quote not followed by whitespace} :dt
+{Input line quote not followed by white-space} :dt
 
-An end quote must be followed by whitespace. :dd
+An end quote must be followed by white-space. :dd
 
 {Insertion region extends outside simulation box} :dt
 
@@ -6923,7 +6917,7 @@ types. :dd
 
 {Invalid use of library file() function} :dt
 
-This function is called thru the library interface.  This
+This function is called through the library interface.  This
 error should not occur.  Contact the developers if it does. :dd
 
 {Invalid value in set command} :dt
@@ -6994,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
-{KIM neighbor iterator exceeded range} :dt
-
-This should not happen.  It likely indicates a bug
-in the KIM implementation of the interatomic potential
-where it is requesting neighbors incorrectly. :dd
-
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -7014,7 +7002,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd
 
 {KSpace accuracy too large to estimate G vector} :dt
 
-Reduce the accuracy request or specify gwald explicitly
+Reduce the accuracy request or specify gewald explicitly
 via the kspace_modify command. :dd
 
 {KSpace accuracy too low} :dt
@@ -8014,7 +8002,7 @@ Self-explanatory. :dd
 
 {Package command after simulation box is defined} :dt
 
-The package command cannot be used afer a read_data, read_restart, or
+The package command cannot be used after a read_data, read_restart, or
 create_box command. :dd
 
 {Package gpu command without GPU package installed} :dt
@@ -9198,7 +9186,7 @@ creates one large file for all processors. :dd
 {Restart file byte ordering is not recognized} :dt
 
 The file does not appear to be a LAMMPS restart file since it doesn't
-contain a recognized byte-orderomg flag at the beginning. :dd
+contain a recognized byte-ordering flag at the beginning. :dd
 
 {Restart file byte ordering is swapped} :dt
 
@@ -9410,7 +9398,7 @@ You may also want to boost the page size. :dd
 
 {Small to big integers are not sized correctly} :dt
 
-This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
+This error occurs when the sizes of smallint, imageint, tagint, bigint,
 as defined in src/lmptype.h are not what is expected.  Contact
 the developers if this occurs. :dd
 
@@ -10191,10 +10179,6 @@ valid. :dd
 
 Self-explanatory. :dd
 
-{Unrecognized virial argument in pair_style command} :dt
-
-Only two options are supported: LAMMPSvirial and KIMvirial :dd
-
 {Unsupported mixing rule in kspace_style ewald/disp} :dt
 
 Only geometric mixing is supported. :dd

doc/src/Errors_warnings.txt

@@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer
 is augmented by an additional energy provided by the fix. Thus the printed
 converged energy may be different from the total potential energy. :dd
 
-{Energy tally does not account for 'zero yes'} :dt
-
-The energy removed by using the 'zero yes' flag is not accounted
-for in the energy tally and thus energy conservation cannot be
-monitored in this case. :dd
-
 {Estimated error in splitting of dispersion coeffs is %g} :dt
 
 Error is greater than 0.0001 percent. :dd
@@ -757,7 +751,7 @@ Self-explanatory. :dd
 
 This may indicate the shell command did not operate as expected. :dd
 
-{Should not allow rigid bodies to bounce off relecting walls} :dt
+{Should not allow rigid bodies to bounce off reflecting walls} :dt
 
 LAMMPS allows this, but their dynamics are not computed correctly. :dd
 
@@ -850,10 +844,10 @@ Most FENE models need this setting for the special_bonds command. :dd
 
 Most FENE models need this setting for the special_bonds command. :dd
 
-{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt
+{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt
 
 This is likely not what you want to do.  The exclusion settings will
-eliminate neighbors in the neighbor list, which the manybody potential
+eliminate neighbors in the neighbor list, which the many-body potential
 needs to calculated its terms correctly. :dd
 
 {Using compute temp/deform with inconsistent fix deform remap option} :dt

doc/src/Examples.txt

@@ -78,7 +78,7 @@ micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:     MSST shock dynamics
-nb3b:     use of nonbonded 3-body harmonic pair style
+nb3b:     use of non-bonded 3-body harmonic pair style
 neb:      nudged elastic band (NEB) calculation for barrier finding
 nemd:     non-equilibrium MD of 2d sheared system
 obstacle: flow around two voids in a 2d channel

doc/src/Howto.txt

@@ -45,7 +45,7 @@ General howto :h3
 <!-- RST
 
 .. toctree::
-   :name: general
+   :name: general_howto
    :maxdepth: 1
 
    Howto_restart

doc/src/Howto_barostat.txt

@@ -19,7 +19,7 @@ barostat attempts to equilibrate the system to the requested T and/or
 P.
 
 Barostatting in LAMMPS is performed by "fixes"_fix.html.  Two
-barosttating methods are currently available: Nose-Hoover (npt and
+barostatting methods are currently available: Nose-Hoover (npt and
 nph) and Berendsen:
 
 "fix npt"_fix_nh.html

doc/src/Howto_bash.txt

@@ -40,7 +40,7 @@ Install Windows Subsystem for Linux :h5
 Next you must ensure that the Window Subsystem for Linux is installed. Again,
 search for "enable windows features" in the Settings dialog. This opens a
 dialog with a list of features you can install. Add a checkmark to Windows
-Subsystem for Linux (Beta) and press OK.   
+Subsystem for Linux (Beta) and press OK.
 
 :image(JPG/bow_tutorial_04_small.png,JPG/bow_tutorial_04.png)
 :image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
@@ -54,12 +54,12 @@ enter. This will then download Ubuntu for Windows.
 
 :image(JPG/bow_tutorial_06.png)
 :image(JPG/bow_tutorial_07.png)
-  
+
 During installation, you will be asked for a new password. This will be used
 for installing new software and running commands with sudo.
 
 :image(JPG/bow_tutorial_08.png)
- 
+
 Type exit to close the command-line window.
 
 Go to the Start menu and type "bash" again. This time you will see a "Bash on

doc/src/Howto_body.txt

@@ -132,7 +132,7 @@ x1 y1 z1
 xN yN zN :pre
 
 where M = 6 + 3*N, and N is the number of sub-particles in the body
-particle.  
+particle.
 
 The integer line has a single value N.  The floating point line(s)
 list 6 moments of inertia followed by the coordinates of the N
@@ -315,7 +315,7 @@ x1 y1 z1
 ...
 xN yN zN
 0 1
-1 2 
+1 2
 2 3
 ...
 0 1 2 -1

doc/src/Howto_chunk.txt

@@ -22,8 +22,8 @@ commands, to calculate various properties of a system:
 "fix ave/chunk"_fix_ave_chunk.html
 any of the "compute */chunk"_compute.html commands :ul
 
-Here, each of the 4 kinds of chunk-related commands is briefly
-overviewed.  Then some examples are given of how to compute different
+Here a brief overview for each of the 4 kinds of chunk-related commands
+is provided.  Then some examples are given of how to compute different
 properties with chunk commands.
 
 Compute chunk/atom command: :h4

doc/src/Howto_client_server.txt

@@ -64,7 +64,7 @@ client or server.
 "server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
 
 The server doc files give details of the message protocols
-for data that is exchanged bewteen the client and server.
+for data that is exchanged between the client and server.
 
 These example directories illustrate how to use LAMMPS as either a
 client or server code:
@@ -75,19 +75,19 @@ examples/COUPLE/lammps_mc
 examples/COUPLE/lammps_vasp :ul
 
 The examples/message dir couples a client instance of LAMMPS to a
-server instance of LAMMPS.  
+server instance of LAMMPS.
 
 The lammps_mc dir shows how to couple LAMMPS as a server to a simple
 Monte Carlo client code as the driver.
 
 The lammps_vasp dir shows how to couple LAMMPS as a client code
 running MD timestepping to VASP acting as a server providing quantum
-DFT forces, thru a Python wrapper script on VASP.
+DFT forces, through a Python wrapper script on VASP.
 
 Here is how to launch a client and server code together for any of the
 4 modes of message exchange that the "message"_message.html command
 and the CSlib support.  Here LAMMPS is used as both the client and
-server code.  Another code could be subsitituted for either.
+server code.  Another code could be substituted for either.
 
 The examples below show launching both codes from the same window (or
 batch script), using the "&" character to launch the first code in the
@@ -106,13 +106,13 @@ together to exchange MPI messages between them.
 
 For message exchange in {file}, {zmq}, or {mpi/two} modes:
 
-% mpirun -np 1 lmp_mpi -log log.client < in.client & 
+% mpirun -np 1 lmp_mpi -log log.client < in.client &
 % mpirun -np 2 lmp_mpi -log log.server < in.server :pre
 
-% mpirun -np 4 lmp_mpi -log log.client < in.client & 
+% mpirun -np 4 lmp_mpi -log log.client < in.client &
 % mpirun -np 1 lmp_mpi -log log.server < in.server :pre
 
-% mpirun -np 2 lmp_mpi -log log.client < in.client & 
+% mpirun -np 2 lmp_mpi -log log.client < in.client &
 % mpirun -np 4 lmp_mpi -log log.server < in.server :pre
 
 For message exchange in {mpi/one} mode:

doc/src/Howto_coreshell.txt

@@ -19,7 +19,7 @@ polarizable"_Howto_polarizable.html doc page for a discussion of all
 the polarizable models available in LAMMPS.
 
 Technically, shells are attached to the cores by a spring force f =
-k*r where k is a parametrized spring constant and r is the distance
+k*r where k is a parameterized spring constant and r is the distance
 between the core and the shell. The charges of the core and the shell
 add up to the ion charge, thus q(ion) = q(core) + q(shell). This
 setup introduces the ion polarizability (alpha) given by
@@ -111,7 +111,7 @@ the core and shell particles corresponds to the polarization,
 hereby an instantaneous relaxation of the shells is approximated
 and a fast core/shell spring frequency ensures a nearly constant
 internal kinetic energy during the simulation.
-Thermostats can alter this polarization behaviour, by scaling the
+Thermostats can alter this polarization behavior, by scaling the
 internal kinetic energy, meaning the shell will not react freely to
 its electrostatic environment.
 Therefore it is typically desirable to decouple the relative motion of
@@ -165,7 +165,7 @@ fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification
 If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
-momentum to the system, which is noticable over long trajectories.
+momentum to the system, which is noticeable over long trajectories.
 Therefore it is recommendable to use the "fix
 momentum"_fix_momentum.html command in combination with "compute
 temp/cs"_compute_temp_cs.html when equilibrating the system to

doc/src/Howto_couple.txt

@@ -50,7 +50,7 @@ In this scenario, the other code can be called as a library, as in
 (1), or it could be a stand-alone code, invoked by a system() call
 made by the command (assuming your parallel machine allows one or more
 processors to start up another program).  In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
+stand-alone code could communicate with LAMMPS through files that the
 command writes and reads.
 
 See the "Modify command"_Modify_command.html doc page for info on how

doc/src/Howto_dispersion.txt

@@ -74,7 +74,7 @@ command.
 A reasonable approach that combines the upsides of both methods is to
 make the first run using the {kspace_modify force/disp/real} and
 {kspace_modify force/disp/kspace} commands, write down the PPPM
-parameters from the outut, and specify these parameters using the
+parameters from the output, and specify these parameters using the
 second approach in subsequent runs (which have the same composition,
 force field, and approximately the same volume).
 

doc/src/Howto_drude.txt

@@ -17,7 +17,7 @@ for a discussion of all the polarizable models available in LAMMPS.
 The Drude model has a number of features aimed at its use in
 molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
 
-Thermostating of the additional degrees of freedom associated with the
+Thermostatting of the additional degrees of freedom associated with the
 induced dipoles at very low temperature, in terms of the reduced
 coordinates of the Drude particles with respect to their cores. This
 makes the trajectory close to that of relaxed induced dipoles. :ulb,l

doc/src/Howto_drude2.txt

@@ -82,7 +82,7 @@ decouple the degrees of freedom associated with the Drude oscillators
 from those of the normal atoms. Thermalizing the Drude dipoles at
 temperatures comparable to the rest of the simulation leads to several
 problems (kinetic energy transfer, very short timestep, etc.), which
-can be remediate by the "cold Drude" technique ("Lamoureux and
+can be remedied by the "cold Drude" technique ("Lamoureux and
 Roux"_#Lamoureux2).
 
 Two closely related models are used to represent polarization through
@@ -213,7 +213,7 @@ of mass of the DC-DP pairs, with relaxation time 100 and with random
 seed 12345.  This fix applies also a Langevin thermostat at temperature
 1. to the relative motion of the DPs around their DCs, with relaxation
 time 20 and random seed 13977.  Only the DCs and non-polarizable
-atoms need to be in this fix's group.  LAMMPS will thermostate the DPs
+atoms need to be in this fix's group.  LAMMPS will thermostat the DPs
 together with their DC.  For this, ghost atoms need to know their
 velocities. Thus you need to add the following command:
 
@@ -360,7 +360,7 @@ fix NPH all nph iso 1. 1. 500 :pre
 It is also possible to use a Nose-Hoover instead of a Langevin
 thermostat.  This requires to use "{fix
 drude/transform}"_fix_drude_transform.html just before and after the
-time intergation fixes.  The {fix drude/transform/direct} converts the
+time integration fixes.  The {fix drude/transform/direct} converts the
 atomic masses, positions, velocities and forces into a reduced
 representation, where the DCs transform into the centers of mass of
 the DC-DP pairs and the DPs transform into their relative position
@@ -396,7 +396,7 @@ global pressure and thus a global temperature whatever the fix group.
 We do want the pressure to correspond to the whole system, but we want
 the temperature to correspond to the fix group only.  We must then use
 the {fix_modify} command for this.  In the end, the block of
-instructions for thermostating and barostating will look like
+instructions for thermostatting and barostatting will look like
 
 compute TATOMS ATOMS temp
 fix DIRECT all drude/transform/direct

doc/src/Howto_elastic.txt

@@ -30,7 +30,7 @@ examples/elastic directory described on the "Examples"_Examples.html
 doc page.
 
 Calculating elastic constants at finite temperature is more
-challenging, because it is necessary to run a simulation that perfoms
+challenging, because it is necessary to run a simulation that performs
 time averages of differential properties. One way to do this is to
 measure the change in average stress tensor in an NVT simulations when
 the cell volume undergoes a finite deformation. In order to balance

doc/src/Howto_github.txt

@@ -96,7 +96,7 @@ machine to a directory with the name you chose. If none is given, it will
 default to "lammps". Typical names are "mylammps" or something similar.
 
 You can use this local clone to make changes and
-test them without interfering with the repository on Github.
+test them without interfering with the repository on GitHub.
 
 To pull changes from upstream into this copy, you can go to the directory
 and use git pull:
@@ -150,7 +150,7 @@ After the commit, the changes can be pushed to the same branch on GitHub:
 $ git push :pre
 
 Git will ask you for your user name and password on GitHub if you have
-not configured anything. If your local branch is not present on Github yet,
+not configured anything. If your local branch is not present on GitHub yet,
 it will ask you to add it by running
 
   $ git push --set-upstream origin github-tutorial-update :pre
@@ -254,20 +254,53 @@ them, or if a developer has requested that something needs to be changed
 before the feature can be accepted into the official LAMMPS version.
 After each push, the automated checks are run again.
 
+[Labels]
+
+LAMMPS developers may add labels to your pull request to assign it to
+categories (mostly for bookkeeping purposes), but a few of them are
+important: needs_work, work_in_progress, test-for-regression, and
+full-regression-test. The first two indicate, that your pull request
+is not considered to be complete. With "needs_work" the burden is on
+exclusively on you; while "work_in_progress" can also mean, that a
+LAMMPS developer may want to add changes. Please watch the comments
+to the pull requests. The two "test" labels are used to trigger
+extended tests before the code is merged. This is sometimes done by
+LAMMPS developers, if they suspect that there may be some subtle
+side effects from your changes. It is not done by default, because
+those tests are very time consuming.
+
+[Reviews]
+
+As of Summer 2018, a pull request needs at least 1 approving review
+from a LAMMPS developer with write access to the repository.
+In case your changes touch code that certain developers are associated
+with, they are auto-requested by the GitHub software.  Those associations
+are set in the file
+".github/CODEOWNERS"_https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS
+Thus if you want to be automatically notified to review when anybody
+changes files or packages, that you have contributed to LAMMPS, you can
+add suitable patterns to that file, or a LAMMPS developer may add you.
+
+Otherwise, you can also manually request reviews from specific developers,
+or LAMMPS developers - in their assessment of your pull request - may
+determine who else should be reviewing your contribution and add that person.
+Through reviews, LAMMPS developers also may request specific changes from you.
+If those are not addressed, your pull requests cannot be merged.
+
 [Assignees]
 
-There is an assignee label for pull requests. If the request has not
+There is an assignee property for pull requests. If the request has not
 been reviewed by any developer yet, it is not assigned to anyone. After
 revision, a developer can choose to assign it to either a) you, b) a
-LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
+LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
 
 Case a) happens if changes are required on your part :ulb,l
 Case b) means that at the moment, it is being tested and reviewed by a
 LAMMPS developer with the expectation that some changes would be required.
 After the review, the developer can choose to implement changes directly
 or suggest them to you. :l
-Case c) means that the pull request has been assigned to the lead
-developer Steve Plimpton and means it is considered ready for merging. :ule,l
+Case c) means that the pull request has been assigned to the developer
+overseeing the merging of pull requests into the master branch. :ule,l
 
 In this case, Axel assigned the tutorial to Steve:
 
@@ -336,7 +369,7 @@ commit and push again:
  $ git commit -m "Merged Axel's suggestions and updated text"
  $ git push git@github.com:Pakketeretet2/lammps :pre
 
-This merge also shows up on the lammps Github page:
+This merge also shows up on the lammps GitHub page:
 
 :c,image(JPG/tutorial_reverse_pull_request7.png)
 
@@ -381,3 +414,6 @@ Furthermore, the naming of the patches now follow the pattern
 "patch_<Day><Month><Year>" to simplify comparisons between releases.
 Finally, all patches and submissions are subject to automatic testing
 and code checks to make sure they at the very least compile.
+
+A discussion of the LAMMPS developer GitHub workflow can be found in the file
+"doc/github-development-workflow.md"_https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md

doc/src/Howto_library.txt

@@ -87,7 +87,7 @@ commands to LAMMPS to execute, the same as if they were coming from an
 input script.
 
 Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
+LAMMPS commands one or multiple at a time and pass it through the library
 interface to setup a problem and then run it in stages.  The caller
 can interleave the command function calls with operations it performs,
 calls to extract information from or set information within LAMMPS, or
@@ -185,7 +185,7 @@ 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).
 For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
-If the count is specified as 1, they are returned 
+If the count is specified as 1, they are returned
 in a packed format with all three image flags stored in a single integer.
 If the count is specified as 3, the values are unpacked into xyz flags
 by the library before returning them.

doc/src/Howto_manifold.txt

@@ -31,8 +31,8 @@ plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with norma
 plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
 sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
 supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R
-spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine
-spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine
+spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendritic spine
+spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendritic spine
 thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
 torus @ R r  @  (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2  @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)
 

doc/src/Howto_nemd.txt

@@ -55,5 +55,5 @@ using the "fix flow/gauss"_fix_flow_gauss.html command.
 :line
 
 :link(Daivis-nemd)
-[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
 Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

doc/src/Howto_polarizable.txt

@@ -45,8 +45,8 @@ high symmetry around each site leads to stable trajectories of the
 core-shell pairs. However, bonded atoms in molecules can be so close
 that a core would interact too strongly or even capture the Drude
 particle of a neighbor. The Drude dipole model is relatively more
-complex in order to remediate this and other issues. Specifically, the
-Drude model includes specific thermostating of the core-Drude pairs
+complex in order to remedy this and other issues. Specifically, the
+Drude model includes specific thermostatting of the core-Drude pairs
 and short-range damping of the induced dipoles.
 
 The three polarization methods can be implemented through a
@@ -77,5 +77,5 @@ motion of the Drude particles with respect to their cores is kept
 approaching the self-consistent regime.  In both models the
 temperature is regulated using the velocities of the center of mass of
 core+shell (or Drude) pairs, but in the Drude model the actual
-relative core-Drude particle motion is thermostated separately as
+relative core-Drude particle motion is thermostatted separately as
 well.

doc/src/Howto_pylammps.txt

@@ -141,16 +141,16 @@ Python code if {L} was a lammps instance:
 L.command("region box block 0 10 0 5 -0.5 0.5") :pre
 
 With the PyLammps interface, any command can be split up into arbitrary parts
-separated by whitespace, passed as individual arguments to a region method.
+separated by white-space, passed as individual arguments to a region method.
 
 L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre
 
 Note that each parameter is set as Python literal floating-point number. In the
 PyLammps interface, each command takes an arbitrary parameter list and transparently
-merges it to a single command string, separating individual parameters by whitespace.
+merges it to a single command string, separating individual parameters by white-space.
 
 The benefit of this approach is avoiding redundant command calls and easier
-parameterization. In the original interface parametrization needed to be done
+parameterization. In the original interface parameterization needed to be done
 manually by creating formatted strings.
 
 L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre
@@ -328,7 +328,7 @@ jupyter notebook :pre
 IPyLammps Examples :h4
 
 Examples of IPython notebooks can be found in the python/examples/pylammps
-subdirectory. To open these notebooks launch {jupyter notebook} inside this
+sub-directory. To open these notebooks launch {jupyter notebook} inside this
 directory and navigate to one of them. If you compiled and installed
 a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
 you should be able to rerun all of these notebooks.

doc/src/Howto_replica.txt

@@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Multi-replica simulations :h3
 
-Several commands in LAMMPS run mutli-replica simulations, meaning
+Several commands in LAMMPS run multi-replica simulations, meaning
 that multiple instances (replicas) of your simulation are run
 simultaneously, with small amounts of data exchanged between replicas
 periodically.

doc/src/Howto_spc.txt

@@ -30,7 +30,7 @@ r0 of OH bond = 1.0
 theta of HOH angle = 109.47 :all(b),p
 
 Note that as originally proposed, the SPC model was run with a 9
-Angstrom cutoff for both LJ and Coulommbic terms.  It can also be used
+Angstrom cutoff for both LJ and Coulombic terms.  It can also be used
 with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
 any of the parameters above, though it becomes a different model in
 that mode of usage.

doc/src/Howto_spherical.txt

@@ -35,7 +35,7 @@ There are several "atom styles"_atom_style.html that allow for
 definition of finite-size particles: sphere, dipole, ellipsoid, line,
 tri, peri, and body.
 
-The sphere style defines particles that are spheriods and each
+The sphere style defines particles that are spheroids and each
 particle can have a unique diameter and mass (or density).  These
 particles store an angular velocity (omega) and can be acted upon by
 torque.  The "set" command can be used to modify the diameter and mass
@@ -236,7 +236,7 @@ particles are point masses.
 Also note that body particles cannot be modeled with the "fix
 rigid"_fix_rigid.html command.  Body particles are treated by LAMMPS
 as single particles, though they can store internal state, such as a
-list of sub-particles.  Individual body partices are typically treated
+list of sub-particles.  Individual body particles are typically treated
 as rigid bodies, and their motion integrated with a command like "fix
 nve/body"_fix_nve_body.html.  Interactions between pairs of body
 particles are computed via a command like "pair_style

doc/src/Howto_spins.txt

@@ -12,48 +12,48 @@ Magnetic spins :h3
 The magnetic spin simulations are enabled by the SPIN package, whose
 implementation is detailed in "Tranchida"_#Tranchida7.
 
-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 
-materials. 
+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
+materials.
 
-The magnetic spins are interacting with each others and with the 
-lattice via pair interactions. Typically, the magnetic exchange 
-interaction can be defined using the 
+The magnetic spins are interacting with each others and with the
+lattice via pair interactions. Typically, the magnetic exchange
+interaction can be defined using the
 "pair/spin/exchange"_pair_spin_exchange.html command. This exchange
 applies a magnetic torque to a given spin, considering the orientation
-of its neighboring spins and their relative distances. 
-It also applies a force on the atoms as a function of the spin 
-orientations and their associated inter-atomic distances. 
- 
+of its neighboring spins and their relative distances.
+It also applies a force on the atoms as a function of the spin
+orientations and their associated inter-atomic distances.
+
 The command "fix precession/spin"_fix_precession_spin.html allows to
 apply a constant magnetic torque on all the spins in the system. This
 torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy. 
+uniaxial magnetic anisotropy.
 
-A Langevin thermostat can be applied to those magnetic spins using 
-"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat 
-can be coupled to another Langevin thermostat applied to the atoms 
-using "fix langevin"_fix_langevin.html in order to simulate 
-thermostated spin-lattice system. 
+A Langevin thermostat can be applied to those magnetic spins using
+"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
+can be coupled to another Langevin thermostat applied to the atoms
+using "fix langevin"_fix_langevin.html in order to simulate
+thermostatted spin-lattice system.
 
-The magnetic Gilbert damping can also be applied using "fix 
-langevin/spin"_fix_langevin_spin.html. It allows to either dissipate 
-the thermal energy of the Langevin thermostat, or to perform a 
+The magnetic Gilbert damping can also be applied using "fix
+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 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 
+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
-the magnetic energy. The second command is "compute 
+the magnetic energy. The second command is "compute
 property/atom"_compute_property_atom.html. It enables to output all the
-per atom magnetic quantities. Typically, the orientation of a given 
+per atom magnetic quantities. Typically, the orientation of a given
 magnetic spin, or the magnetic force acting on this spin.
 
 :line
 
 :link(Tranchida7)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, 
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
 arXiv preprint arXiv:1801.10233, (2018).

doc/src/Howto_thermostat.txt

@@ -96,5 +96,5 @@ temperature compute is used for default thermodynamic output.
 :line
 
 :link(Daivis-thermostat)
-[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
 Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

doc/src/Howto_triclinic.txt

@@ -200,7 +200,7 @@ used with non-orthogonal basis vectors to define a lattice that will
 tile a triclinic simulation box via the
 "create_atoms"_create_atoms.html command.
 
-A second use is to run Parinello-Rahman dynamics via the "fix
+A second use is to run Parrinello-Rahman dynamics via the "fix
 npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
 factors to compensate for off-diagonal components of the pressure
 tensor.  The analog for an "energy minimization"_minimize.html is

doc/src/Howto_viscosity.txt

@@ -140,5 +140,5 @@ with time at sufficiently long times.
 :line
 
 :link(Daivis-viscosity)
-[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
 Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

doc/src/Install_git.txt

@@ -45,18 +45,11 @@ git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre
 where "mylammps" is the name of the directory you wish to create on
 your machine and "unstable" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
-between them at any time using "git checkout <branchname>".)
+between them at any time using "git checkout <branch name>".)
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_linux.txt

@@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
 "Pre-built Fedora Linux executables"_#fedora
 "Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
 "Pre-built OpenSuse Linux executables"_#opensuse
-"Pre-built Gentoo Linux executable"_#gentoo :all(b)
+"Gentoo Linux executable"_#gentoo :all(b)
 
 :line
 
@@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
 lammps-openmpi-devel), the header for compiling programs using
 the C library interface (lammps-headers), and the LAMMPS python
 module for Python 3. All packages can be installed at the same
-time and the name of the LAMMPS executable is {lmp} in all 3 cases.
-By default, {lmp} will refer to the serial executable, unless
-one of the MPI environment modules is loaded 
+time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
+or {lmp_mpich} respectively.  By default, {lmp} will refer to the
+serial executable, unless one of the MPI environment modules is loaded
 ("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
-Then the corresponding parallel LAMMPS executable is used.
+Then the corresponding parallel LAMMPS executable can be used.
 The same mechanism applies when loading the LAMMPS python module.
 
 To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
@@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
 
 :line
 
-Pre-built Gentoo Linux executable :h4,link(gentoo)
+Gentoo Linux executable :h4,link(gentoo)
 
 LAMMPS is part of Gentoo's main package tree and can be installed by
 typing:

doc/src/Install_patch.txt

@@ -17,7 +17,7 @@ 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 
+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

doc/src/Install_svn.txt

@@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on
 your machine.
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_windows.txt

@@ -12,7 +12,7 @@ Download an executable for Windows :h3
 Pre-compiled Windows installers which install LAMMPS executables on a
 Windows system can be downloaded from this site:
 
-"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html
+"http://packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for
@@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
 needed to run in parallel.
 
 The LAMMPS binaries contain all optional packages included in the
-source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
-and USER-QMMM.  The serial version also does not include the MPIIO and
+source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
+The serial version also does not include the MPIIO and
 USER-LB packages.  GPU support is provided for OpenCL.
 
 The installer site also has instructions on how to run LAMMPS under
@@ -42,7 +42,7 @@ environment manipulations.
 
 Note that to update to a newer version of LAMMPS, you should typically
 uninstall the version you currently have, download a new installer,
-and go thru the install procedure described above.  I.e. the same
+and go through the install procedure described above.  I.e. the same
 procedure for installing/updating most Windows programs.  You can
 install multiple versions of LAMMPS (in different directories), but
 only the executable for the last-installed package will be found

doc/src/Intro_authors.txt

@@ -48,7 +48,7 @@ Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
 Mike Parks (Sandia), PERI package for Peridynamics
 Roy Pollock (LLNL), Ewald and PPPM solvers
 Christian Trott (Sandia), USER-CUDA and KOKKOS packages
-Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
+Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
 Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
 
 :line
@@ -58,7 +58,7 @@ page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
 originated as a cooperative project between DOE labs and industrial
 partners.  Folks involved in the design and testing of the original
 version of LAMMPS were the following:
-    
+
 John Carpenter (Mayo Clinic, formerly at Cray Research)
 Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
 Steve Lustig (Dupont)

doc/src/Intro_features.txt

@@ -40,7 +40,7 @@ General features :h4,link(general)
   syntax for defining and using variables and formulas
   syntax for looping over runs and breaking out of loops
   run one or multiple simulations simultaneously (in parallel) from one script
-  build as library, invoke LAMMPS thru library interface or provided Python wrapper
+  build as library, invoke LAMMPS through library interface or provided Python wrapper
   couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
 
 Particle and model types :h4,link(particle)
@@ -68,7 +68,7 @@ commands)
   pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
     Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
   charged pairwise potentials: Coulombic, point-dipole
-  manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
+  many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
     embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
     REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
   long-range interactions for charge, point-dipoles, and LJ dispersion: \
@@ -110,11 +110,11 @@ Atom creation :h4,link(create)
   displace atoms :ul
 
 Ensembles, constraints, and boundary conditions :h4,link(ensemble)
-("fix"_fix.html command) 
+("fix"_fix.html command)
 
   2d or 3d systems
   orthogonal or non-orthogonal (triclinic symmetry) simulation domains
-  constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
+  constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators
   thermostatting options for groups and geometric regions of atoms
   pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
   simulation box deformation (tensile and shear)
@@ -128,7 +128,7 @@ Ensembles, constraints, and boundary conditions :h4,link(ensemble)
   variety of additional boundary conditions and constraints :ul
 
 Integrators :h4,link(integrate)
-("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) 
+("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
 
   velocity-Verlet integrator
   Brownian dynamics
@@ -142,7 +142,7 @@ Diagnostics :h4,link(diag)
   see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
 
 Output :h4,link(output)
-("dump"_dump.html, "restart"_restart.html commands) 
+("dump"_dump.html, "restart"_restart.html commands)
 
   log file of thermodynamic info
   text dump files of atom coords, velocities, other per-atom quantities

doc/src/Intro_nonfeatures.txt

@@ -13,25 +13,29 @@ LAMMPS is designed to be a fast, parallel engine for molecular
 dynamics (MD) simulations.  It provides only a modest amount of
 functionality for setting up simulations and analyzing their output.
 
-Specifically, LAMMPS does not:
+Specifically, LAMMPS was not conceived and designed for:
 
-run thru a GUI
-build molecular systems
+being run through a GUI
+building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
-perform sophisticated analyses of your MD simulation
+perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
 plot your output data :ul
 
+Although over the years these limitations have been somewhat
+reduced through features added to LAMMPS or external tools
+that either closely interface with LAMMPS or extend LAMMPS.
+
 Here are suggestions on how to perform these tasks:
 
-GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
 the library interface is provided.  Thus, GUI interfaces can be
 written in Python (or C or C++ if desired) that run LAMMPS and
 visualize or plot its output.  Examples of this are provided in the
 python directory and described on the "Python"_Python_head.html doc
-page. :ulb,l
+page.  Also, there are several external wrappers or GUI front ends. :ulb,l
 
-Builder: Several pre-processing tools are packaged with LAMMPS.  Some
+[Builder:] Several pre-processing tools are packaged with LAMMPS.  Some
 of them convert input files in formats produced by other MD codes such
 as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them
 are simple programs that will build simple molecular systems, such as
@@ -40,41 +44,54 @@ molecular builder that will generate complex molecular models.  See
 the "Tools"_Tools.html doc page for details on tools packaged with
 LAMMPS.  The "Pre/post processing
 page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
-describes a variety of 3rd party tools for this task. :l
+describes a variety of 3rd party tools for this task.  Furthermore,
+some LAMMPS internal commands allow to reconstruct, or selectively add
+topology information, as well as provide the option to insert molecule
+templates instead of atoms for building bulk molecular systems. :l
 
-Force-field assignment: The conversion tools described in the previous
+[Force-field assignment:] The conversion tools described in the previous
 bullet for CHARMM, AMBER, and Insight will also assign force field
 coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
-or Accelerys force field files. :l
+or BIOVIA (formerly Accelrys) force field files. The tools
+"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
+"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
+powerful and flexible in converting force field and topology data
+between various MD simulation programs.  :l
 
-Simulation analyses: If you want to perform analyses on-the-fly as
+[Simulation analysis:] If you want to perform analysis on-the-fly as
 your simulation runs, see the "compute"_compute.html and
 "fix"_fix.html doc pages, which list commands that can be used in a
 LAMMPS input script.  Also see the "Modify"_Modify.html doc page for
 info on how to add your own analysis code or algorithms to LAMMPS.
 For post-processing, LAMMPS output such as "dump file
 snapshots"_dump.html can be converted into formats used by other MD or
-post-processing codes.  Some post-processing tools packaged with
+post-processing codes.  To some degree, that conversion can be done
+directly inside of LAMMPS by interfacing to the VMD molfile plugins.
+The "rerun"_rerun.html command also allows to do some post-processing
+of existing trajectories, and through being able to read a variety
+of file formats, this can also be used for analyzing trajectories
+from other MD codes.  Some post-processing tools packaged with
 LAMMPS will do these conversions.  Scripts provided in the
 tools/python directory can extract and massage data in dump files to
 make it easier to import into other programs.  See the
 "Tools"_Tools.html doc page for details on these various options. :l
 
-Visualization: LAMMPS can produce JPG or PNG snapshot images
-on-the-fly via its "dump image"_dump_image.html command.  For
-high-quality, interactive visualization there are many excellent and
-free tools available.  See the "Other Codes
+[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
+on-the-fly via its "dump image"_dump_image.html command and pass
+them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
+movies from them.  For high-quality, interactive visualization there are
+many excellent and free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
 visualization packages that can use LAMMPS output data. :l
 
-Plotting: See the next bullet about Pizza.py as well as the
+[Plotting:] See the next bullet about Pizza.py as well as the
 "Python"_Python_head.html doc page for examples of plotting LAMMPS
 output.  Scripts provided with the {python} tool in the tools
 directory will extract and massage data in log and dump files to make
 it easier to analyze and plot.  See the "Tools"_Tools.html doc page
 for more discussion of the various tools. :l
 
-Pizza.py: Our group has also written a separate toolkit called
+[Pizza.py:] Our group has also written a separate toolkit called
 "Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
 setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
 simulations.  It thus provides some functionality for several of the

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="24 Oct 2018 version">
+<META NAME="docnumber" CONTENT="28 Feb 2019 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
-24 Oct 2018 version :c,h2
+28 Feb 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 
@@ -37,27 +37,21 @@ LAMMPS is an open-source code, distributed freely under the terms of
 the GNU Public License (GPL).
 
 The "LAMMPS website"_lws has a variety of information about the code.
-It includes links to an on-line version of this manual, a "mail
+It includes links to an on-line version of this manual, a "mailing
 list"_http://lammps.sandia.gov/mail.html where users can post
-questions, and a "GitHub site"https://github.com/lammps/lammps where
+questions, and a "GitHub site"_https://github.com/lammps/lammps where
 all LAMMPS development is coordinated.
 
 :line
 
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
-
 The content for this manual is part of the LAMMPS distribution.  You
 can build a local copy of the Manual as HTML pages or a PDF file, by
 following the steps on the "Manual build"_Manual_build.html doc page.
-
 There is also a "Developer.pdf"_Developer.pdf document which gives
 a brief description of the basic code structure of LAMMPS.
 
 :line
 
-This manual is organized into the following sections.
-
 Once you are familiar with LAMMPS, you may want to bookmark "this
 page"_Commands.html since it gives quick access to a doc page for
 every LAMMPS command.

doc/src/Manual_build.txt

@@ -61,10 +61,12 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 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 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
+make anchor_check # check for duplicate anchor labels
+make spelling     # spell-check the manual
 
 :line
 
@@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
+Building the PDF manual requires a working C++ compiler (to
+compile the txt2html tool and a working installation of
+"HTMLDOC"_https://www.msweet.org/htmldoc/
+HTMLDOC has its own list of prerequisites, but in most cases
+you can install a binary package of it either through your
+Linux package manager or MacOS (dmg) and Windows installer
+(msi) packages from its
+"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
 
 :line
 

doc/src/Modify_contribute.txt

@@ -33,11 +33,11 @@ how much effort it will cause to integrate and test it, how much it
 requires changes to the core codebase, and of how much interest it is
 to the larger LAMMPS community.  Please see below for a checklist of
 typical requirements. Once you have prepared everything, see the
-"Howto github"_Howto_github.html doc page for instructions on how to
+"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to
 submit your changes or new files through a GitHub pull request. If you
 prefer to submit patches or full files, you should first make certain,
 that your code works correctly with the latest patch-level version of
-LAMMPS and contains all bugfixes from it. Then create a gzipped tar
+LAMMPS and contains all bug fixes from it. Then create a gzipped tar
 file of all changed or added files or a corresponding patch file using
 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
 compression, as this works well on all platforms.
@@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its
 standard packages, it needs to be written in a style compatible with
 other LAMMPS source files. This means: 2-character indentation per
 level, [no tabs], no lines over 80 characters. I/O is done via
-the C-style stdio library, class header files should not import any
-system headers outside <stdio.h>, STL containers should be avoided
-in headers, and forward declarations used where possible or needed.
+the C-style stdio library (mixing of stdio and iostreams is generally
+discouraged), class header files should not import any system headers
+outside of <cstdio>, STL containers should be avoided in headers,
+system header from the C library should use the C++-style names
+(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
+<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
+used where possible or needed to avoid including headers.
 All added code should be placed into the LAMMPS_NS namespace or a
 sub-namespace; global or static variables should be avoided, as they
 conflict with the modular nature of LAMMPS and the C++ class structure.

doc/src/Modify_pair.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Pair styles :h3
 
 Classes that compute pairwise interactions are derived from the Pair
-class.  In LAMMPS, pairwise calculation include manybody potentials
+class.  In LAMMPS, pairwise calculation include many-body potentials
 such as EAM or Tersoff where particles interact without a static bond
 topology.  New styles can be created to add new pair potentials to
 LAMMPS.

doc/src/Modify_region.txt

@@ -20,6 +20,6 @@ Here is a brief description of methods you define in your new derived
 class.  See region.h for details.
 
 inside: determine whether a point is in the region
-surface_interior: determine if a point is within a cutoff distance inside of surc
-surface_exterior: determine if a point is within a cutoff distance outside of surf
+surface_interior: determine if a point is within a cutoff distance inside of surface
+surface_exterior: determine if a point is within a cutoff distance outside of surface
 shape_update : change region shape if set by time-dependent variable :tb(s=:)

doc/src/Packages_details.txt

@@ -45,7 +45,6 @@ as contained in the file name.
 "LATTE"_#PKG-LATTE,
 "MANYBODY"_#PKG-MANYBODY,
 "MC"_#PKG-MC,
-"MEAM"_#PKG-MEAM,
 "MESSAGE"_#PKG-MESSAGE,
 "MISC"_#PKG-MISC,
 "MOLECULE"_#PKG-MOLECULE,
@@ -56,7 +55,6 @@ as contained in the file name.
 "POEMS"_#PKG-POEMS,
 "PYTHON"_#PKG-PYTHON,
 "QEQ"_#PKG-QEQ,
-"REAX"_#PKG-REAX,
 "REPLICA"_#PKG-REPLICA2,
 "RIGID"_#PKG-RIGID,
 "SHOCK"_#PKG-SHOCK,
@@ -65,6 +63,7 @@ as contained in the file name.
 "SRD"_#PKG-SRD,
 "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
 
+"USER-ADIOS"_#PKG-USER-ADIOS,
 "USER-ATC"_#PKG-USER-ATC,
 "USER-AWPMD"_#PKG-USER-AWPMD,
 "USER-BOCS"_#PKG-USER-BOCS,
@@ -89,18 +88,21 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"USER-PLUMED"_#PKG-USER-PLUMED,
 "USER-PTM"_#PKG-USER-PTM,
 "USER-QMMM"_#PKG-USER-QMMM,
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
 "USER-REAXC"_#PKG-USER-REAXC,
 "USER-SCAFACOS"_#PKG-USER-SCAFACOS,
+"USER-SDPD"_#PKG-USER-SDPD,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
 "USER-TALLY"_#PKG-USER-TALLY,
 "USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+"USER-VTK"_#PKG-USER-VTK,
+"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
 
 :line
 
@@ -203,7 +205,7 @@ available on your system.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -284,7 +286,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
 [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
 (Northwestern U) while at ORNL.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -339,20 +341,21 @@ KIM package :link(PKG-KIM),h4
 A "pair_style kim"_pair_kim.html command which is a wrapper on the
 Knowledge Base for Interatomic Models (KIM) repository of interatomic
 potentials, enabling any of them to be used in LAMMPS simulations.
+Also a "kim_query"_kim_query.html command, which allows to query
+the OpenKIM database for stored properties.
 
 To use this package you must have the KIM library available on your
 system.
 
 Information about the KIM project can be found at its website:
 https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota) and James Sethna (Cornell U).
+Elliott (U Minnesota).
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
 API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style in collaboration with Valeriu Smirichinski (U
-Minnesota).
+developed the pair style.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -398,7 +401,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
 Sandia, and which is included in the LAMMPS distribution in
 lib/kokkos.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -492,7 +495,7 @@ MANYBODY package :link(PKG-MANYBODY),h4
 
 [Contents:]
 
-A variety of manybody and bond-order potentials.  These include
+A variety of many-body and bond-order potentials.  These include
 (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
 
 [Supporting info:]
@@ -516,7 +519,7 @@ MC package :link(PKG-MC),h4
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjuction with dynamics.
+(GCMC) in conjunction with dynamics.
 
 [Supporting info:]
 
@@ -531,37 +534,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
 
 :line
 
-MEAM package :link(PKG-MEAM),h4
-
-[Contents:]
-
-A pair style for the modified embedded atom (MEAM) potential.
-
-Please note that the use of the MEAM package is discouraged as
-it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
-which is a direct translation of the MEAM package to C++.
-USER-MEAMC contains additional optimizations making it run faster
-than MEAM on most machines, while providing the identical features
-and user interface.
-
-[Author:] Greg Wagner (Northwestern U) while at Sandia.
-
-[Install:] 
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MEAM: filenames -> commands
-src/meam/README
-lib/meam/README
-"pair_style meam"_pair_meam.html
-examples/meam :ul
-
-:line
-
 MESSAGE package :link(PKG-MESSAGE),h4
 
 [Contents:]
@@ -679,7 +651,7 @@ system.
 library was developed by Jacob Wagner in Greg Voth's group at the
 University of Chicago.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -711,7 +683,7 @@ have styles optimized for CPU performance.
 [Authors:] James Fischer (High Performance Technologies), David Richie,
 and Vincent Natoli (Stone Ridge Technolgy).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -768,7 +740,7 @@ connections at hinge points.
 
 [Author:] Rudra Mukherjee (JPL) while at RPI.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -800,7 +772,7 @@ shared library available on your system, which needs to be a Python 2
 version, 2.6 or later.  Python 3 is not yet supported.  See the
 lib/python/README for more details.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -832,38 +804,6 @@ examples/streitz :ul
 
 :line
 
-REAX package :link(PKG-REAX),h4
-
-[Contents:]
-
-NOTE: the use of the REAX package is discouraged, as it is no longer
-maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
-and possibly the KOKKOS enabled variant of that, which has a more robust
-memory management.
-
-A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field.  Also included is
-a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
-as bonds are created and destroyed.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Install:] 
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/REAX: filenames -> commands
-lib/reax/README
-"pair_style reax"_pair_reax.html
-"fix reax/bonds"_fix_reax_bonds.html
-examples/reax :ul
-
-:line
-
 REPLICA package :link(PKG-REPLICA2),h4
 
 [Contents:]
@@ -1021,7 +961,7 @@ system.
 library was written by Chris Rycroft (Harvard U) while at UC Berkeley
 and LBNL.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1037,6 +977,31 @@ examples/voronoi :ul
 
 :line
 
+USER-ADIOS package :link(PKG-USER-ADIOS),h4
+
+[Contents:]
+
+ADIOS is a high-performance I/O library. This package implements the 
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library. 
+
+[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-adios on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ADIOS: filenames -> commands
+src/USER-ADIOS/README
+examples/USER/adios
+https://github.com/ornladios/ADIOS2 :ul
+
+:line
+
 USER-ATC package :link(PKG-USER-ATC),h4
 
 [Contents:]
@@ -1048,7 +1013,7 @@ atomic information to continuum fields.
 
 [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1075,7 +1040,7 @@ model.
 
 [Author:] Ilya Valuev (JIHT, Russia).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1098,7 +1063,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
 of "fix npt"_fix_nh.html which includes the pressure correction to
 the barostat as outlined in:
 
-N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
 molecular liquids," J. Chem. Phys. 143, 243148 (2015).
 
@@ -1183,10 +1148,10 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
 the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
 (Temple U) provided the interface to LAMMPS.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-colvars on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1200,6 +1165,36 @@ examples/USER/colvars :ul
 
 :line
 
+USER-PLUMED package :link(PKG-USER-PLUMED),h4
+
+[Contents:]
+
+The fix plumed command allows you to use the PLUMED free energy plugin
+for molecular dynamics to analyze and bias your LAMMPS trajectory on
+the fly.  The PLUMED library is called from within the LAMMPS input
+script by using the "fix plumed _fix_plumed.html command.
+
+[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
+Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
+Tribello.
+
+:link(PLUMED,http://www.plumed.org)
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-PLUMED/README
+lib/plumed/README
+"fix plumed"_fix_plumed.html
+examples/USER/plumed :ul
+
+:line
+
 USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
 
 [Contents:]
@@ -1338,7 +1333,7 @@ src/USER-FEP: filenames -> commands
 src/USER-FEP/README
 "fix adapt/fep"_fix_adapt_fep.html
 "compute fep"_compute_fep.html
-"pair_style */soft"_pair_lj_soft.html
+"pair_style */soft"_pair_fep_soft.html
 examples/USER/fep
 tools/fep/README
 tools/fep :ul
@@ -1363,7 +1358,7 @@ system.
 [Author:] Pierre de Buyl (KU Leuven) created both the package and the
 H5MD format.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1401,7 +1396,7 @@ NOTE: the USER-INTEL package contains styles that require using the
 
 [Author:] Mike Brown (Intel).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1520,10 +1515,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
 [Contents:]
 
 A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_#PKG-MEAM package
-to plain C++. In contrast to the MEAM package, no library
-needs to be compiled and the pair style can be instantiated
-multiple times.
+translated from the Fortran version in the (obsolete) "MEAM" package
+to plain C++. The USER-MEAMC fully replaces the MEAM package, which
+has been removed from LAMMPS after the 12 December 2018 version.
 
 [Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
 based on the Fortran version of Greg Wagner (Northwestern U) while at
@@ -1533,8 +1527,8 @@ Sandia.
 
 src/USER-MEAMC: filenames -> commands
 src/USER-MEAMC/README
-"pair_style meam/c"_pair_meam.html
-examples/meam :ul
+"pair_style meam/c"_pair_meamc.html
+examples/meamc :ul
 
 :line
 
@@ -1571,17 +1565,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
 [Contents:]
 
 Pair, angle and improper styles needed to employ the MOF-FF
-force field by Schmid and coworkers with LAMMPS. 
+force field by Schmid and coworkers with LAMMPS.
 MOF-FF is a first principles derived force field with the primary aim
-to simulate MOFs and related porous framework materials, using spherical 
+to simulate MOFs and related porous framework materials, using spherical
 Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
 2013, 250, 1128-1141.
-For the usage of MOF-FF see the example in the example directory as 
+For the usage of MOF-FF see the example in the example directory as
 well as the "MOF+"_MOFplus website.
 
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
 
-[Author:] Hendrik Heenen (Technical U of Munich), 
+[Author:] Hendrik Heenen (Technical U of Munich),
 Rochus Schmid (Ruhr-University Bochum).
 
 [Supporting info:]
@@ -1622,7 +1616,7 @@ at
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1662,7 +1656,7 @@ tools:
 
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1706,7 +1700,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1733,14 +1727,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
+And a "dynamical_matrix" command to compute the dynamical matrix
+from finite differences.
+
+[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
+and Charlie Sievers (UC Davis) for "dynamical_matrix"
 
-[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
+"dynamical_matrix"_dynamical_matrix.html
 examples/USER/phonon :ul
 
 :line
@@ -1785,7 +1784,7 @@ without changes to LAMMPS itself.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1843,7 +1842,7 @@ on your system.
 
 [Author:] Albert Bartok (Cambridge University)
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1862,9 +1861,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
 
 [Contents:]
 
-A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#PKG-REAX and its Fortran library).  ReaxFF
-is universal reactive force field.  See the src/USER-REAXC/README file
+A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
+is a universal reactive force field.  See the src/USER-REAXC/README file
 for more info on differences between the two packages.  Also two fixes
 for monitoring molecules as bonds are created and destroyed.
 
@@ -1875,7 +1873,7 @@ for monitoring molecules as bonds are created and destroyed.
 src/USER-REAXC: filenames -> commands
 src/USER-REAXC/README
 "pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/bonds"_fix_reaxc_bonds.html
 "fix reax/c/species"_fix_reaxc_species.html
 examples/reax :ul
 
@@ -1916,6 +1914,31 @@ examples/USER/scafacos :ul
 
 :line
 
+USER-SDPD package :link(PKG-USER-SDPD),h4
+
+[Contents:]
+
+A pair style for smoothed dissipative particle dynamics (SDPD), which
+is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
+where thermal fluctuations are important (see the
+"USER-SPH package"_#PKG-USER-SPH).
+Also two fixes for moving and rigid body integration of SPH/SDPD particles
+(particles of atom_style meso).
+
+[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
+Sciences, Iran).
+
+[Supporting info:]
+
+src/USER-SDPD: filenames -> commands
+src/USER-SDPD/README
+"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
+"fix meso/move"_fix_meso_move.html
+"fix rigid/meso"_fix_rigid_meso.html
+examples/USER/sdpd :ul
+
+:line
+
 USER-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]
@@ -1937,7 +1960,7 @@ specified as surface geometries from *.STL files.
 [Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
 Dynamics, Ernst Mach Institute, Germany).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -2063,7 +2086,7 @@ system.
 
 [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -2077,3 +2100,37 @@ lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
 
 
+:line
+
+USER-YAFF package :link(PKG-USER-YAFF),h4
+
+[Contents:]
+
+Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
+The expressions and their use are discussed in the following papers
+
+Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
+Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
+
+which discuss the "QuickFF"_quickff methodology.
+
+
+:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
+:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
+:link(quickff,http://molmod.github.io/QuickFF)
+:link(yaff,https://github.com/molmod/yaff)
+
+
+[Author:] Steven Vandenbrande.
+
+[Supporting info:]
+
+src/USER-YAFF/README
+"angle_style cross"_angle_cross.html
+"angle_style mm3"_angle_mm3.html
+"bond_style mm3"_bond_mm3.html
+"improper_style distharm"_improper_distharm.html
+"improper_style sqdistharm"_improper_sqdistharm.html
+"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
+"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
+examples/USER/yaff :ul

doc/src/Packages_standard.txt

@@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
 "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
 "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
 "MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
 "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
@@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
 "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
-"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
 "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
 "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
 "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no

doc/src/Packages_user.txt

@@ -38,8 +38,9 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
-"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
-"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
+"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
+"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
 "USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
 "USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
@@ -53,7 +54,7 @@ Package, Description, Doc page, Example, Library
 "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
 "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
 "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
 "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
@@ -62,16 +63,21 @@ Package, Description, Doc page, Example, Library
 "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
+"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext
 "USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
 "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
 "USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
+"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, USER/sdpd, no
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
 "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
 "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
 "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext
+"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l)
+
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
+:link(PLUMED,http://www.plumed.org)

doc/src/Python_call.txt

@@ -79,7 +79,7 @@ of Python and your machine to successfully build LAMMPS.  See the
 lib/python/README file for more info.
 
 If you want to write Python code with callbacks to LAMMPS, then you
-must also follow the steps overviewed in the "Python
+must also follow the steps summarized in the "Python
 run"_Python_run.html doc page.  I.e. you must build LAMMPS as a shared
 library and insure that Python can find the python/lammps.py file and
 the shared library.

doc/src/Python_examples.txt

@@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS.  If you create your
 own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 
-trivial.py, read/run a LAMMPS input script thru Python,
+trivial.py, read/run a LAMMPS input script through Python,
 demo.py, invoke various LAMMPS library interface routines,
 simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
 split.py, same as simple.py but running in parallel on a subset of procs,
@@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
 :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
 :link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
 
-The latter link is to AtomEye 3 which has the scriping
+The latter link is to AtomEye 3 which has the scripting
 capability needed by these Python scripts.
 
 Note that for PyMol, you need to have built and installed the

doc/src/Python_run.txt

@@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid
 development and debugging.  If you use it to mostly invoke costly
 operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
-LAMMPS thru Python will be negligible.
+LAMMPS through Python will be negligible.
 
 The Python wrapper for LAMMPS uses the "ctypes" package in Python,
 which auto-generates the interface code needed between Python and a

doc/src/Python_test.txt

@@ -32,7 +32,7 @@ first importing from the lammps.py file:
 >>> from ctypes import CDLL
 >>> CDLL("liblammps.so") :pre
 
-If an error occurs, carefully go thru the steps on the
+If an error occurs, carefully go through the steps on the
 "Build_basics"_Build_basics.html doc page about building a shared
 library and the "Python_install"_Python_install.html doc page about
 insuring Python can find the necessary two files it needs.

doc/src/Run_options.txt

@@ -354,29 +354,31 @@ the LAMMPS simulation domain.
 
 :line
 
-[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
+[-restart2data restartfile \[remap\] datafile keyword value ...]
+:link(restart2data)
 
 Convert the restart file into a data file and immediately exit.  This
 is the same operation as if the following 2-line input script were
 run:
 
-read_restart restartfile (remap)
+read_restart restartfile \[remap\]
 write_data datafile keyword value ... :pre
 
-Note that the specified restartfile and/or datafile can have the
-wild-card character "*".  The restartfile can also have the wild-card
+The specified restartfile and/or datafile name may contain the wild-card
+character "*".  The restartfile name may also contain the wild-card
 character "%".  The meaning of these characters is explained on the
 "read_restart"_read_restart.html and "write_data"_write_data.html doc
 pages.  The use of "%" means that a parallel restart file can be read.
-Note that a filename such as file.* will need to be enclosed in quotes
-to avoid shell expansion of the "*" character.
+Note that a filename such as file.* may need to be enclosed in quotes or
+the "*" character prefixed with a backslash ("\") to avoid shell
+expansion of the "*" character.
 
-Note that following restartfile, the optional word "remap" can be
-used.  This has the effect of adding it to the
-"read_restart"_read_restart.html command, as explained on its doc
-page.  This is useful if reading the restart file triggers an error
-that atoms have been lost.  In that case, use of the remap flag should
-allow the data file to still be produced.
+Following restartfile argument, the optional word "remap" may be used.
+This has the same effect like adding it to a
+"read_restart"_read_restart.html command, and operates as explained on
+its doc page.  This is useful if reading the restart file triggers an
+error that atoms have been lost.  In that case, use of the remap flag
+should allow the data file to still be produced.
 
 The syntax following restartfile (or remap), namely
 
@@ -388,29 +390,30 @@ optional keyword/value settings.
 
 :line
 
-[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
+[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
 
 Convert the restart file into a dump file and immediately exit.  This
 is the same operation as if the following 2-line input script were
 run:
 
-read_restart restartfile (remap)
+read_restart restartfile \[remap\]
 write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
 
-Note that the specified restartfile and dumpfile can have wild-card
-characters ("*","%") as explained on the
+Note that the specified restartfile and dumpfile names may contain
+wild-card characters ("*","%") as explained on the
 "read_restart"_read_restart.html and "write_dump"_write_dump.html doc
 pages.  The use of "%" means that a parallel restart file and/or
 parallel dump file can be read and/or written.  Note that a filename
-such as file.* will need to be enclosed in quotes to avoid shell
-expansion of the "*" character.
+such as file.* may need to be enclosed in quotes or the "*" character
+prefixed with a backslash ("\") to avoid shell expansion of the "*"
+character.
 
-Note that following restartfile, the optional word "remap" can be
-used.  This has the effect as adding it to the
-"read_restart"_read_restart.html command, as explained on its doc
-page.  This is useful if reading the restart file triggers an error
-that atoms have been lost.  In that case, use of the remap flag should
-allow the dump file to still be produced.
+Note that following the restartfile argument, the optional word "remap"
+can be used.  This has the effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc page.
+This is useful if reading the restart file triggers an error that atoms
+have been lost.  In that case, use of the remap flag should allow the
+dump file to still be produced.
 
 The syntax following restartfile (or remap), namely
 
@@ -524,7 +527,7 @@ option is equivalent to putting the line "variable name index value1
 value2 ..."  at the beginning of the input script.  Defining an index
 variable as a command-line argument overrides any setting for the same
 index variable in the input script, since index variables cannot be
-re-defined.  
+re-defined.
 
 See the "variable"_variable.html command for more info on defining
 index and other kinds of variables and the "Commands

doc/src/Run_windows.txt

@@ -41,7 +41,7 @@ path for the default location of this MPI package. After the
 installation of the MPICH2 software, it needs to be integrated into
 the system.  For this you need to start a Command Prompt in
 {Administrator Mode} (right click on the icon and select it). Change
-into the MPICH2 installation directory, then into the subdirectory
+into the MPICH2 installation directory, then into the sub-directory
 [bin] and execute [smpd.exe -install]. Exit the command window.
 
 Get a new, regular command prompt by going to Start->Run... ,

doc/src/Speed.txt

@@ -19,7 +19,7 @@ using code options that implement alternate algorithms that can
 speed-up a simulation.  The second is to use one of the several
 accelerator packages provided with LAMMPS that contain code optimized
 for certain kinds of hardware, including multi-core CPUs, GPUs, and
-Intel Xeon Phi coprocessors.
+Intel Xeon Phi co-processors.
 
 The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
 web site gives performance results for the various accelerator