Merge pull request #1307 from akohlmey/next-patch-release

Patch release 1 February 2019

.github/CODEOWNERS

@@ -126,3 +126,6 @@ python/*              @rbberger
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.gitignore

@@ -22,6 +22,7 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*

cmake/CMakeLists.txt

@@ -171,14 +171,14 @@ set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+  KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
   SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
   USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
   USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
   USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
   USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM)
+  USER-QUIP USER-QMMM USER-YAFF)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -191,11 +191,11 @@ endforeach()
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
   enable_language(Fortran)
 endif()
 
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
   enable_language(C)
 endif()
 
@@ -221,7 +221,7 @@ else()
 endif()
 
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
@@ -354,7 +354,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -559,17 +559,22 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
-      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
+      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
       BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                                --enable-modules=all
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+    )
     ExternalProject_get_property(plumed_build INSTALL_DIR)
     set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
-        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})
+        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
@@ -614,8 +619,8 @@ if(PKG_USER-SMD)
     message(STATUS "Eigen3 download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(Eigen3_build
-      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
-      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
       CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     )
     ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@@ -756,7 +761,7 @@ endif()
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
 include(CheckIncludeFileCXX)
-foreach(HEADER math.h)
+foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")
@@ -826,7 +831,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   USER-QMMM)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
@@ -856,6 +861,9 @@ if(PKG_USER-AWPMD)
 endif()
 
 if(PKG_USER-ATC)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
@@ -1322,7 +1330,7 @@ if(BUILD_LIB)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
 else()
   list(APPEND LMP_SOURCES ${LIB_SOURCES})
 endif()

cmake/README.md

@@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Build directory vs. Source Directory](#build-directory-vs-source-directory)
    * [Defining and using presets](#defining-and-using-presets)
    * [Reference](#reference)
-      * [Common CMAKE Configuration Options](#common-cmake-configuration-options)
+      * [Common CMake Configuration Options](#common-cmake-configuration-options)
       * [LAMMPS Configuration Options](#lammps-configuration-options)
       * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
       * [Default Packages](#default-packages)
@@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
 
 # Reference
 
-## Common CMAKE Configuration Options
+## Common CMake Configuration Options
 
 
 <table>
@@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
   value of `FC` environment variable at first `cmake` run
   </td>
 </tr>
+<tr>
+  <td><code>CXX_COMPILER_LAUNCHER</code></td>
+  <td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
+  <td>
+  (empty)
+  </td>
+</tr>
 </tbody>
 </table>
 

doc/Makefile

@@ -1,7 +1,7 @@
 # Makefile for LAMMPS documentation
 
-SHELL 	      = /bin/bash
-SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+SHELL         = /bin/bash
+SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
@@ -48,6 +48,7 @@ help:
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
 

doc/github-development-workflow.md

@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2018-11-15.
+adapt accordingly. Last change 2018-12-19.
 
 ## Table of Contents
 
@@ -50,8 +50,8 @@ This is indicated by who the pull request is assigned to. LAMMPS core
 developers can self-assign or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine what this might be needed or not, and may either implement the
-required changes or ask the submitter of the pull request to implement
+determine whether this might be needed or not, and may either implement
+the required changes or ask the submitter of the pull request to implement
 them.  Even though, all LAMMPS developers may have write access to pull
 requests (if enabled by the submitter, which is the default), only the
 submitter or the assignee of a pull request may do so.  During this
@@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways:
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least one review from a LAMMPS developer with write access is required
-before merging in addition to the automated compilation tests.  The
-feature, that reviews from code owners are "hard" reviews (i.e. they
-must all be approved before merging is allowed), is currently disabled
-and it is in the discretion of the merge maintainer to assess when
-a sufficient degree of approval has been reached.  Reviews may be
+least two approvals from LAMMPS developers with write access are required
+before merging in addition to the automated compilation tests.
+Merging counts as implicit approval, so does submission of a pull request
+(by a LAMMPS developer). So the person doing the merge may not also submit
+an approving review. The feature, that reviews from code owners are "hard"
+reviews (i.e. they must all be approved before merging is allowed), is
+currently disabled and it is in the discretion of the merge maintainer to
+assess when a sufficient degree of approval, especially from external
+contributors, has been reached in these cases.  Reviews may be
 (automatically) dismissed, when the reviewed code has been changed,
 and then approval is required a second time.
 
@@ -129,16 +132,17 @@ Here are some items to check:
     * stdlib.h -> cstdlib
     * string.h -> cstring
     * time.h -> ctime
-  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
+    * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
-  * indentation is two spaces per level
-  * there should be no tabs and no trailing whitespace
+  * indentation is 2 spaces per level
+  * there should be NO tabs and no trailing whitespace
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.
   * iostreams should be avoided. LAMMPS uses stdio from the C-library.
   * use of STL in headers and class definitions should be avoided.
+  * there MUST NOT be any "using namespace XXX;" statements in headers.
   * static class members should be avoided at all cost.
   * anything storing atom IDs should be using `tagint` and not `int`.
   This can be flagged by the compiler only for pointers and only when

doc/src/Build_extras.txt

@@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
 "OPT"_#opt,
 "POEMS"_#poems,
 "PYTHON"_#python,
-"REAX"_#reax,
 "VORONOI"_#voronoi,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
@@ -96,6 +95,7 @@ which GPU hardware to build for.
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
+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)
@@ -136,7 +136,7 @@ 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:
 
@@ -536,45 +536,6 @@ 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)
 
 To build with this package, you must download and build the "Voro++
@@ -621,8 +582,8 @@ 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]:
 
@@ -735,58 +696,69 @@ 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 required PLUMED code
-is linked statically into the MD code. The MD code is then fully
-independent from the PLUMED installation, but also you have to
-rebuild/relink the MD code to update the PLUMED code inside it.  With
-"shared" linkage mode, the MD code is linked to a shared library
-containing the PLUMED code, preferably after it was installed in a
-globally accessible location. This way the same installed PLUMED code
-can be shared across multiple MD packages and can be updated, for as
-long as the shared PLUMED library is ABI-compatible. The third linkage
-mode is "runtime" which allows to switch the PLUMED kernel at runtime
-between different variants through setting the PLUMED_KERNEL environment
-variable, which has to point to the location of the libplumedKernel.so
-dynamical shared object, which is then loaded at runtime. This is
-particularly convenient for doing PLUMED development and comparing
-multiple PLUMED versions without having to recompile 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 most portable, 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, or switch to a different build system, or consider
-a global PLUMED installation or downloading it during building LAMMPS.
+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 that 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 an installed version of PLUMED and link to
-that. 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.
+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 of the PLUMED
-library.  Allowed values are "static" (default), "shared", or "runtime".
-For a discussion of PLUMED linkage modes, please see above.  When
-enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.
+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]:
 
-Before installing the USER-PLUMED package, first the PLUMED library
-needs to be configured so that LAMMPS can find the right settings when
-compiling and linking the LAMMPS executable itself. 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.
+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:
@@ -799,11 +771,11 @@ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installati
 :pre
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink" are
-created in lib/plumed to point into the location of the PLUMED build to
-use and also a new file lib/plumed/Makefile.lammps is created with
-settings suitable for LAMMPS to compile and link PLUMED in the desired
-linkage mode. After this step is completed, you can install the
-USER-PLUMED package and compile LAMMPS in the usual manner:
+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

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

@@ -47,7 +47,6 @@ 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-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,

doc/src/Commands_bond.txt

@@ -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,
@@ -67,10 +68,12 @@ OPT.
 "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_fix.txt

@@ -169,8 +169,7 @@ 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,

doc/src/Commands_pair.txt

@@ -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,
@@ -194,7 +198,6 @@ 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,
@@ -230,7 +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/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/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_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
@@ -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

doc/src/Howto_client_server.txt

@@ -82,7 +82,7 @@ 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

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_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

doc/src/Install_git.txt

@@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above.
 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_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

@@ -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_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)

doc/src/Intro_nonfeatures.txt

@@ -15,8 +15,8 @@ functionality for setting up simulations and analyzing their output.
 
 Specifically, LAMMPS was not conceived and designed for:
 
-being run thru a GUI
-build molecular systems, or building molecular topologies
+being run through a GUI
+building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
@@ -24,18 +24,18 @@ 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 interface with LAMMPS or extend LAMMPS.
+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.  Also, there are several external wrappers or GUI front ends.: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
@@ -45,15 +45,20 @@ 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.  Furthermore,
-some LAMMPS internal commands to reconstruct topology, as well as
-the option to insert molecule templates instead of atoms.:l
+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 BIOVIA (formerly Accelrys) 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 analysis: If you want to perform analysis 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
@@ -71,22 +76,22 @@ 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
+[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 to generate movies from them.  For
-high-quality, interactive visualization there are many excellent and
-free tools available.  See the "Other Codes
+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="27 Nov 2018 version">
+<META NAME="docnumber" CONTENT="1 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
-27 Nov 2018 version :c,h2
+1 Feb 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Manual_build.txt

@@ -65,6 +65,8 @@ 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

@@ -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/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,
@@ -102,7 +100,8 @@ as contained in the file name.
 "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
 
@@ -533,37 +532,6 @@ 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:]
@@ -834,38 +802,6 @@ 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:]
@@ -1370,7 +1306,7 @@ 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
@@ -1552,10 +1488,9 @@ 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
@@ -1565,8 +1500,8 @@ 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
 
@@ -1894,9 +1829,8 @@ 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.
 
@@ -1907,7 +1841,7 @@ 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
 
@@ -2134,3 +2068,39 @@ 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

@@ -53,7 +53,7 @@ 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
@@ -75,7 +75,8 @@ Package, Description, Doc page, Example, Library
 "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_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,

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/Tools.txt

@@ -391,15 +391,16 @@ definition file.  This tool was used to create the system for the
 
 moltemplate tool :h4,link(moltemplate)
 
-The moltemplate sub-directory contains a Python-based tool for
-building molecular systems based on a text-file description, and
-creating LAMMPS data files that encode their molecular topology as
-lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
-more information.
+The moltemplate sub-directory contains instructions for installing
+moltemplate, a Python-based tool for building molecular systems based
+on a text-file description, and creating LAMMPS data files that encode
+their molecular topology as lists of bonds, angles, dihedrals, etc.
+See the README.txt file for more information.
 
 This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
 supports it.  It has its own WWW page at
 "http://moltemplate.org"_http://moltemplate.org.
+The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases
 
 :line
 
@@ -485,9 +486,9 @@ README for more info on Pizza.py and how to use these scripts.
 
 reax tool :h4,link(reax_tool)
 
-The reax sub-directory contains stand-alond codes that can
-post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html.  See
+The reax sub-directory contains stand-alone codes that can
+post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
+command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html.  See
 the README.txt file for more info.
 
 These tools were written by Aidan Thompson at Sandia.

doc/src/angle_cross.txt

@@ -0,0 +1,62 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+angle_style cross command :h3
+
+[Syntax:]
+
+angle_style cross :pre
+
+[Examples:]
+
+angle_style cross
+angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
+
+[Description:]
+
+The {cross} angle style uses a potential that couples the bond stretches of
+a bend with the angle stretch of that bend:
+
+:c,image(Eqs/angle_cross.jpg)
+
+where r12,0 is the rest value of the bond length between atom 1 and 2,
+r32,0 is the rest value of the bond length between atom 2 and 2,
+and theta0 is the rest value of the angle. KSS is the force constant of
+the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
+of the bond stretch-angle stretch terms.
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+KSS (energy/distance^2)
+KBS0 (energy/distance/rad)
+KBS1 (energy/distance/rad)
+r12,0 (distance)
+r32,0 (distance)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+
+

doc/src/angle_mm3.txt

@@ -0,0 +1,55 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+angle_style mm3 command :h3
+
+[Syntax:]
+
+angle_style mm3 :pre
+
+[Examples:]
+
+angle_style mm3
+angle_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} angle style uses the potential that is anharmonic in the angle
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/angle_mm3.jpg)
+
+where theta0 is the equilibrium value of the angle, and K is a
+prefactor. The anharmonic prefactors have units deg^(-n), for example
+-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/radian^2)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+

doc/src/angle_style.txt

@@ -81,10 +81,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
 "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
 "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
+"cross"_angle_cross.html - cross term coupling angle and bond lengths
 "dipole"_angle_dipole.html - angle that controls orientation of a point dipole
 "fourier"_angle_fourier.html - angle with multiple cosine terms
 "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
 "harmonic"_angle_harmonic.html - harmonic angle
+"mm3"_angle_mm3.html - anharmonic angle
 "quartic"_angle_quartic.html - angle with cubic and quartic terms
 "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
 "table"_angle_table.html - tabulated by angle :ul

doc/src/angles.txt

@@ -14,11 +14,13 @@ Angle Styles :h1
    angle_cosine_shift
    angle_cosine_shift_exp
    angle_cosine_squared
+   angle_cross
    angle_dipole
    angle_fourier
    angle_fourier_simple
    angle_harmonic
    angle_hybrid
+   angle_mm3
    angle_none
    angle_quartic
    angle_sdk

doc/src/atom_modify.txt

@@ -166,7 +166,8 @@ info), a map is used.  The default map style is array if no atom ID is
 larger than 1 million, otherwise the default is hash.  By default, a
 "first" group is not defined.  By default, sorting is enabled with a
 frequency of 1000 and a binsize of 0.0, which means the neighbor
-cutoff will be used to set the bin size.
+cutoff will be used to set the bin size. If no neighbor cutoff is
+defined, sorting will be turned off.
 
 :line
 

doc/src/bond_mm3.txt

@@ -0,0 +1,58 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+bond_style mm3 command :h3
+
+[Syntax:]
+
+bond_style mm3 :pre
+
+[Examples:]
+
+bond_style mm3
+bond_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} bond style uses the potential that is anharmonic in the bond
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/bond_mm3.jpg)
+
+where r0 is the equilibrium value of the bond, and K is a
+prefactor. The anharmonic prefactors have units angstrom^(-n):
+-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
+care of the necessary unit conversion for these factors internally.
+Note that the MM3 papers contains an error in Eq (1):
+(7/12)2.55 should be replaced with (7/12)2.55^2
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^2)
+r0 (distance) :ul
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html
+
+[Default:] none
+
+:line
+
+:link(mm3-allinger1989)
+[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
+(1989),

doc/src/bond_style.txt

@@ -86,6 +86,7 @@ accelerated styles exist.
 "harmonic"_bond_harmonic.html - harmonic bond
 "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
 "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
+"mm3"_bond_mm3.html - MM3 anharmonic bond
 "morse"_bond_morse.html - Morse bond
 "nonlinear"_bond_nonlinear.html - nonlinear bond
 "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling

doc/src/bonds.txt

@@ -13,6 +13,7 @@ Bond Styles :h1
    bond_harmonic_shift
    bond_harmonic_shift_cut
    bond_hybrid
+   bond_mm3
    bond_morse
    bond_none
    bond_nonlinear

doc/src/compute_angmom_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the angular momentum
 vector for each chunk, due to the velocity/momentum of the individual
 atoms in the chunk around the center-of-mass of the chunk.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_com.txt

@@ -22,7 +22,7 @@ compute 1 all com :pre
 [Description:]
 
 Define a computation that calculates the center-of-mass of the group
-of atoms, including all effects due to atoms passing thru periodic
+of atoms, including all effects due to atoms passing through periodic
 boundaries.
 
 A vector of three quantities is calculated by this compute, which

doc/src/compute_com_chunk.txt

@@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the center-of-mass
-for each chunk, which includes all effects due to atoms passing thru
+for each chunk, which includes all effects due to atoms passing through
 periodic boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_dipole_chunk.txt

@@ -38,7 +38,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the dipole vector
 and the total dipole moment for each chunk, which includes all effects
-due to atoms passing thru periodic boundaries. For chunks with a net
+due to atoms passing through periodic boundaries. For chunks with a net
 charge the resulting dipole is made position independent by subtracting
 the position vector of the center of mass or geometric center times the
 net charge from the computed dipole vector.

doc/src/compute_displace_atom.txt

@@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre
 
 Define a computation that calculates the current displacement of each
 atom in the group from its original (reference) coordinates, including
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.

doc/src/compute_fep.txt

@@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it.
 
 The {pstyle} argument is the name of the pair style. For example,
 {pstyle} could be specified as "lj/cut".  The {pparam} argument is the
-name of the parameter to change.  This is a (non-exclusive) list of
+name of the parameter to change.  This is a list of
 pair styles and parameters that can be used with this compute.  See
 the doc pages for individual pair styles and their energy formulas for
 the meaning of these parameters:
 
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
-"coul/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
 "born"_pair_born.html: a,b,c: type pairs:
-"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:)
+"buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
+"coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
+"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 Note that it is easy to add new potentials and their parameters to
 this list.  All it typically takes is adding an extract() method to
@@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info.
 [Related commands:]
 
 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_style lj/soft/coul/soft"_pair_lj_soft.html
+"pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/compute_gyration.txt

@@ -22,7 +22,7 @@ compute 1 molecule gyration :pre
 [Description:]
 
 Define a computation that calculates the radius of gyration Rg of the
-group of atoms, including all effects due to atoms passing thru
+group of atoms, including all effects due to atoms passing through
 periodic boundaries.
 
 Rg is a measure of the size of the group of atoms, and is computed as

doc/src/compute_gyration_chunk.txt

@@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the radius of gyration Rg for each chunk,
-which includes all effects due to atoms passing thru periodic
+which includes all effects due to atoms passing through periodic
 boundaries.
 
 Rg is a measure of the size of a chunk, and is computed by this

doc/src/compute_inertia_chunk.txt

@@ -36,7 +36,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the 6 components of the symmetric inertia
 tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd.txt

@@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) of the group of atoms, including all effects due to atoms
-passing thru periodic boundaries.  For computation of the non-Gaussian
+passing through periodic boundaries.  For computation of the non-Gaussian
 parameter of mean-squared displacement, see the "compute
 msd/nongauss"_compute_msd_nongauss.html command.
 

doc/src/compute_msd_chunk.txt

@@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
 center-of-mass.  The 4th component is the total squared displacement,
 i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These
-calculations include all effects due to atoms passing thru periodic
+calculations include all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd_nongauss.txt

@@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) and non-Gaussian parameter (NGP) of the group of atoms,
-including all effects due to atoms passing thru periodic boundaries.
+including all effects due to atoms passing through periodic boundaries.
 
 A vector of three quantities is calculated by this compute.  The first
 element of the vector is the total squared dx,dy,dz displacements

doc/src/compute_omega_chunk.txt

@@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity
 vector for each chunk, via the formula L = Iw where L is the angular
 momentum vector of the chunk, I is its moment of inertia tensor, and w
 is omega = angular velocity of the chunk.  The calculation includes
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/compute_pair.txt

@@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
 compute 1 all pair gauss
 compute 1 all pair lj/cut/coul/cut ecoul
 compute 1 all pair tersoff 2 epair
-compute 1 all pair reax :pre
+compute 1 all pair reax/c :pre
 
 [Description:]
 
@@ -60,8 +60,8 @@ corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.
 
 Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html command.  These values (1 or more)
+potential energy into 14 components is tallied by the "pair_style
+reax/c"_pair_reaxc.html command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 "individual pair styles"_pair_style.html for info on these values.
 

doc/src/compute_rigid_local.txt

@@ -107,7 +107,7 @@ mass (COM) of the body.  The {x}, {y}, {z} attributes write the COM
 "unscaled", in the appropriate distance "units"_units.html (Angstroms,
 sigma, etc).  Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
-COM has passed thru a periodic boundary one or more times, the value
+COM has passed through a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been
 wrapped back into the periodic box.
 

doc/src/compute_sna_atom.txt

@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
   {diagonal} value = {0} or {1} or {2} or {3}
      {0} = all j1, j2, j <= twojmax, j2 <= j1
      {1} = subset satisfying j1 == j2

doc/src/compute_torque_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the torque vector for eqch
 chunk, due to the forces on the individual atoms in the chunk around
 the center-of-mass of the chunk.  The calculation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/displace_atoms.txt

@@ -83,7 +83,7 @@ used in such a way that the displacement of a particular atom is the
 same, regardless of how many processors are being used.
 
 The {rotate} style rotates each atom in the group by the angle {theta}
-around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
+around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} =
 (Px,Py,Pz).  The direction of rotation for the atoms around the
 rotation axis is consistent with the right-hand rule: if your
 right-hand thumb points along {R}, then your fingers wrap around the

doc/src/dump.txt

@@ -312,7 +312,7 @@ so that any machine which supports XDR should be able to read them.
 The number of atoms per snapshot cannot change with the {xtc} style.
 The {unwrap} option of the "dump_modify"_dump_modify.html command allows
 XTC coordinates to be written "unwrapped" by the image flags for each
-atom.  Unwrapped means that if the atom has passed thru a periodic
+atom.  Unwrapped means that if the atom has passed through a periodic
 boundary one or more times, the value is printed for what the
 coordinate would be if it had not been wrapped back into the periodic
 box.  Note that these coordinates may thus be far outside the box size
@@ -534,7 +534,7 @@ on the "Howto triclinic"_Howto_triclinic.html doc page.
 
 Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
 image flags for each atom.  Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
+passed through a periodic boundary one or more times, the value is
 printed for what the coordinate would be if it had not been wrapped
 back into the periodic box.  Note that using {xu}, {yu}, {zu} means
 that the coordinate values may be far outside the box bounds printed

doc/src/dump_modify.txt

@@ -344,7 +344,7 @@ The {image} keyword applies only to the dump {atom} style.  If the
 image value is {yes}, 3 flags are appended to each atom's coords which
 are the absolute box image of the atom in each dimension.  For
 example, an x image flag of -2 with a normalized coord of 0.5 means
-the atom is in the center of the box, but has passed thru the box
+the atom is in the center of the box, but has passed through the box
 boundary 2 times and is really 2 box lengths to the left of its
 current coordinate.  Note that for dump style {custom} these various
 values can be printed in the dump file by using the appropriate atom
@@ -461,10 +461,10 @@ last snapshot.  This can be accomplished with something the following
 commands:
 
 variable        Dhop equal 0.6
-variable        check atom "c_dsp[4] > v_Dhop"
+variable        check atom "c_dsp\[4\] > v_Dhop"
 compute         dsp all displace/atom refresh check
 dump            1 all custom 20 tmp.dump id type x y z
-dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
+dump_modify     1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre
 
 The "compute displace/atom"_compute_displace_atom.html command
 calculates the displacement of each atom from its reference position.
@@ -622,7 +622,7 @@ threshold criterion is met.  Otherwise it is not met.
 
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
-flags for each atom.  Unwrapped means that if the atom has passed thru
+flags for each atom.  Unwrapped means that if the atom has passed through
 a periodic boundary one or more times, the value is printed for what
 the coordinate would be if it had not been wrapped back into the
 periodic box.  Note that these coordinates may thus be far outside the

doc/src/fix.txt

@@ -312,9 +312,8 @@ accelerated styles exist.
 "qmmm"_fix_qmmm.html -
 "qtb"_fix_qtb.html -
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
-"reax/c/bonds"_fix_reax_bonds.html -
-"reax/c/species"_fix_reaxc_species.html -
+"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
+"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
 "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
 "rhok"_fix_rhok.html -

doc/src/fix_adapt.txt

@@ -112,17 +112,43 @@ pages for individual pair styles and their energy formulas for the
 meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
+"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
 "coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
+"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:
+"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs:
 "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: A,B: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs:
 "lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs:
+"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:
+"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
 "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
 "lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
 "lubricate"_pair_lubricate.html: mu: global:
-"gauss"_pair_gauss.html: a: type pairs:
-"morse"_pair_morse.html: d0,r0,alpha: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs:
+"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:
+"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:
+"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:
+"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:
+"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:
+"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
+"table"_pair_table.html: table_cutoff: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
 "soft"_pair_soft.html: a: type pairs:
 "kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
 
@@ -217,6 +243,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are
 
+"gromos"_bond_gromos.html: k, r0: type bonds:
 "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
 
 :line

doc/src/fix_adapt_fep.txt

@@ -114,24 +114,37 @@ styles and their energy formulas for the meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
-"coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
-"lubricate"_pair_lubricate.html: mu: global:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
 "gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
 "soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 NOTE: It is easy to add new potentials and their parameters to this
 list.  All it typically takes is adding an extract() method to the
 pair_*.cpp file associated with the potential.
 
-Some parameters are global settings for the pair style, e.g. the
-viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
-Other parameters apply to atom type pairs within the pair style,
-e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
-
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
 potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
@@ -253,7 +266,7 @@ minimization"_minimize.html.
 [Related commands:]
 
 "compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute
-ti"_compute_ti.html
+ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/fix_ave_histo.txt

@@ -241,7 +241,7 @@ first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
 values > {hi} are counted in the last bin (Nbins+1).  Values between
-{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1.  The
+{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
 

doc/src/fix_bond_react.txt

@@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
   template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
   map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
   zero or more individual keyword/value pairs may be appended to each react argument :l
-  individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
+  individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
     {prob} values = fraction seed
       fraction = initiate reaction with this probability if otherwise eligible
       seed = random number seed (positive integer)
+    {max_rxn} value = N
+      N = maximum number of reactions allowed to occur
     {stabilize_steps} value = timesteps
       timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
     {update_edges} value = {none} or {charges} or {custom}
@@ -69,8 +71,9 @@ Initiate complex covalent bonding (topology) changes. These topology
 changes will be referred to as 'reactions' throughout this
 documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
-angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
-atom-types, or atomic charges.
+angles, dihedrals, impropers, bond types, angle types, dihedral types,
+atom types, or atomic charges. In addition, reaction by-products or
+other molecules can be identified and deleted.
 
 Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
 pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@@ -141,7 +144,7 @@ modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms I,J within the specified react-group-ID of type
-itype and jtype must separated by a distance between {Rmin} and
+itype and jtype must be separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
 identified: if the bonding atoms in the pre-reacted template are not
 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
@@ -203,15 +206,17 @@ A discussion of correctly handling this is also provided on the
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and two optional keywords. The
+contains one mandatory keyword and three optional keywords. The
 mandatory keyword is 'equivalences' and the optional keywords are
-'edgeIDs' and 'customIDs':
+'edgeIDs' and 'deleteIDs' and 'customIDs':
 
 N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
-N {customIDs} = # of atoms N that are specified for a custom update :pre
+N {deleteIDs} = # of atoms N that are specified for deletion
+N {customIDs} = # of atoms N that are specified for a custom update
+N {constraints} = # of specified reaction constraints N :pre
 
-The body of the map file contains two mandatory sections and two
+The body of the map file contains two mandatory sections and four
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -222,11 +227,16 @@ second column is the corresponding atom ID of the post-reacted
 molecule template. The first optional section begins with the keyword
 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
 molecule template. The second optional section begins with the keyword
-'Custom Edges' and allows for forcing the update of a specific atom's
-atomic charge. The first column is the ID of an atom near the edge of
-the pre-reacted molecule template, and the value of the second column
-is either 'none' or 'charges.' Further details are provided in the
-discussion of the 'update_edges' keyword.
+'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
+delete. The third optional section begins with the keyword 'Custom
+Edges' and allows for forcing the update of a specific atom's atomic
+charge. The first column is the ID of an atom near the edge of the
+pre-reacted molecule template, and the value of the second column is
+either 'none' or 'charges.' Further details are provided in the
+discussion of the 'update_edges' keyword. The fourth optional section
+begins with the keyword 'Constraints' and lists additional criteria
+that must be satisfied in order for the reaction to occur. Currently,
+there is one type of constraint available, as discussed below.
 
 A sample map file is given below:
 
@@ -259,6 +269,18 @@ Equivalences :pre
 
 :line
 
+Any number of additional constraints may be specified in the
+Constraints section of the map file. Currently there is one type of
+additional constraint, of type 'distance', whose syntax is as follows:
+
+distance {ID1} {ID2} {rmin} {rmax} :pre
+
+where 'distance' is the required keyword, {ID1} and {ID2} are
+pre-reaction atom IDs, and these two atoms must be separated by a
+distance between {rmin} and {rmax} for the reaction to occur. This
+constraint can be used to enforce a certain orientation between
+reacting molecules.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -281,7 +303,8 @@ The {prob} keyword can affect whether an eligible reaction actually
 occurs. The fraction setting must be a value between 0.0 and 1.0. A
 uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
-fraction.
+fraction. Up to N reactions are permitted to occur, as optionally
+specified by the {max_rxn} keyword.
 
 The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the
@@ -309,7 +332,16 @@ edge are unaffected by this setting.
 
 A few other considerations:
 
-It may be beneficial to ensure reacting atoms are at a certain
+Many reactions result in one or more atoms that are considered
+unwanted by-products. Therefore, bond/react provides the option to
+delete a user-specified set of atoms. These pre-reaction atoms are
+identified in the map file. A deleted atom must still be included in
+the post-reaction molecule template, in which it cannot be bonded to
+an atom that is not deleted. In addition to deleting unwanted reaction
+by-products, this feature can be used to remove specific topologies,
+such as small rings, that may be otherwise indistinguishable.
+
+Also, it may be beneficial to ensure reacting atoms are at a certain
 temperature before being released to the overall thermostat. For this,
 you can use the internally-created dynamic group named
 "bond_react_MASTER_group." For example, adding the following command

doc/src/fix_meso_move.txt

@@ -56,7 +56,7 @@ by other fixes (e.g. "fix meso"_fix_meso.html, "fix
 meso/stationary"_fix_meso_stationary.html), since that will change their
 positions and velocities twice.
 
-NOTE: As particles move due to this fix, they will pass thru periodic
+NOTE: As particles move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 meso"_fix_meso.html command).  It is up to you to decide whether periodic
@@ -126,7 +126,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates particles around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 particles around the rotation axis is consistent with the right-hand
 rule: if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_move.txt

@@ -51,7 +51,7 @@ integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
 nvt"_fix_nh.html), since that will change their positions and
 velocities twice.
 
-NOTE: As atoms move due to this fix, they will pass thru periodic
+NOTE: As atoms move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 nve"_fix_nve.html command).  It is up to you to decide whether
@@ -121,7 +121,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates atoms around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 atoms around the rotation axis is consistent with the right-hand rule:
 if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_nh.txt

@@ -626,10 +626,10 @@ over time or the atom count becomes very small.
 
 [Default:]
 
-The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
 ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
-scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
-not coupled to barostat, otherwise no.
+flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
+dimension and not coupled to barostat, otherwise no.
 
 :line
 

doc/src/fix_plumed.txt

@@ -32,11 +32,10 @@ enhance the sampling of phase space.
 
 The documentation included here only describes the fix plumed command
 itself.  This command is LAMMPS specific, whereas most of the
-functionality implemented in PLUMED, however, will work with a range of
-MD codes, and when PLUMED is used as a stand alone code for analysis.
-The full "documentation for PLUMED"_plumeddocs is available online and
-included in the PLUMED source code.  The PLUMED library development is
-hosted at
+functionality implemented in PLUMED will work with a range of MD codes,
+and when PLUMED is used as a stand alone code for analysis.  The full
+"documentation for PLUMED"_plumeddocs is available online and included
+in the PLUMED source code.  The PLUMED library development is hosted at
 "https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
 A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
 
@@ -54,11 +53,12 @@ have been set.
 
 The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
 to PLUMED and there can only be one instance of the plumed fix at a
-time. The plumed fix communicates the minimum amount of information
-required and the PLUMED supports multiple, completely independent
-collective variables, multiple independent biases and multiple
-independent forms of analysis.  There is thus really no restriction in
-functionality by only allowing only one plumed fix in the LAMMPS input.
+time. The way the plumed fix is implemented ensures that the minimum
+amount of information required is communicated.  Furthermore, PLUMED
+supports multiple, completely independent collective variables, multiple
+independent biases and multiple independent forms of analysis.  There is
+thus really no restriction in functionality by only allowing only one
+plumed fix in the LAMMPS input.
 
 The {plumedfile} keyword allows the user to specify the name of the
 PLUMED input file.  Instructions as to what should be included in a

doc/src/fix_qeq.txt

@@ -22,7 +22,7 @@ Nevery = perform charge equilibration every this many steps :l
 cutoff = global cutoff for charge-charge interactions (distance unit) :l
 tolerance = precision to which charges will be equilibrated :l
 maxiter = maximum iterations to perform charge equilibration :l
-qfile = a filename with QEq parameters :l
+qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l
 
 zero or more keyword/value pairs may be appended :l
 keyword = {alpha} or {qdamp} or {qstep} :l
@@ -122,7 +122,9 @@ field"_#vanDuin paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
 as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
 reax/c"_pair_reaxc.html.  Only the {chi}, {eta}, and {gamma}
-parameters from the {qfile} file are used.  This style solves partial
+parameters from the {qfile} file are used. When using the string
+{reax/c} as filename, these parameters are extracted directly from
+an active {reax/c} pair style.  This style solves partial
 charges on atoms via the matrix inversion method.  A tolerance of
 1.0e-6 is usually a good number.
 
@@ -132,7 +134,9 @@ that the interaction between a pair of charged particles is the
 product of two Slater 1{s} orbitals.  The expression for the Slater
 1{s} orbital is given under equation (6) of the
 "Streitz-Mintmire"_#Streitz1 paper.  Only the {chi}, {eta}, {zeta}, and
-{qcore} parameters from the {qfile} file are used.  This style solves
+{qcore} parameters from the {qfile} file are used. When using the string
+{coul/streitz} as filename, these parameters are extracted directly from
+an active {coul/streitz} pair style.  This style solves
 partial charges on atoms via the matrix inversion method.  A tolerance
 of 1.0e-6 is usually a good number.  Keyword {alpha} can be used to
 change the Slater type orbital exponent.

doc/src/fix_reaxc_bonds.txt

@@ -6,13 +6,12 @@
 
 :line
 
-fix reax/bonds command :h3
 fix reax/c/bonds command :h3
 fix reax/c/bonds/kk command :h3
 
 [Syntax:]
 
-fix ID group-ID reax/bonds Nevery filename :pre
+fix ID group-ID reaxc/bonds Nevery filename :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 reax/bonds = style name of this fix command
@@ -21,16 +20,14 @@ filename = name of output file :ul
 
 [Examples:]
 
-fix 1 all reax/bonds 100 bonds.tatb
 fix 1 all reax/c/bonds 100 bonds.reaxc :pre
 
 [Description:]
 
-Write out the bond information computed by the ReaxFF potential
-specified by "pair_style reax"_pair_reax.html or "pair_style
-reax/c"_pair_reaxc.html in the exact same format as the original
-stand-alone ReaxFF code of Adri van Duin.  The bond information is
-written to {filename} on timesteps that are multiples of {Nevery},
+Write out the bond information computed by the ReaxFF potential specified
+by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
+original stand-alone ReaxFF code of Adri van Duin.  The bond information
+is written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
 please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
 
@@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restrictions:]
 
-The fix reax/bonds command requires that the "pair_style
-reax"_pair_reax.html be invoked.  This fix is part of the REAX
-package.  It is only enabled if LAMMPS was built with that package,
-which also requires the REAX library be built and linked with LAMMPS.
 The fix reax/c/bonds command requires that the "pair_style
-reax/c"_pair_reaxc.html be invoked.  This fix is part of the
+reax/c"_pair_reaxc.html is invoked.  This fix is part of the
 USER-REAXC package.  It is only enabled if LAMMPS was built with that
 package.  See the "Build package"_Build_package.html doc page for more
 info.
@@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
 
 [Related commands:]
 
-"pair_style reax"_pair_reax.html, "pair_style
-reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
 
 [Default:] none

doc/src/fix_reaxc_species.txt

@@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restrictions:]
 
-The fix species currently only works with "pair_style
+The "fix reax/c/species" currently only works with "pair_style
 reax/c"_pair_reaxc.html and it requires that the "pair_style
 reax/c"_pair_reaxc.html be invoked.  This fix is part of the
 USER-REAXC package.  It is only enabled if LAMMPS was built with that
@@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
 
 [Related commands:]
 
-"pair_style reax/c"_pair_reaxc.html, "fix
-reax/bonds"_fix_reax_bonds.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
 
 [Default:]
 

doc/src/fix_rigid_meso.txt

@@ -160,7 +160,7 @@ unaffected by interactions with other particles.  Note that if you
 expect a rigid body not to move or rotate by using these keywords, you
 must insure its initial center-of-mass translational or angular
 velocity is 0.0. Otherwise the initial translational or angular
-momentum the body has will persist.
+momentum, the body has, will persist.
 
 An xflag, yflag, or zflag set to {off} means turn off the component of
 force or torque in that dimension.  A setting of {on} means turn on
@@ -287,9 +287,10 @@ bodies.  The number of columns is 28.  Thus for each rigid body, 28
 values are stored: the xyz coords of the center of mass (COM), the xyz
 components of the COM velocity, the xyz components of the force acting
 on the COM, the components of the 4-vector quaternion representing the
-orientation of the rigid body, the xyz components of the angular momentum
+orientation of the rigid body, the xyz components of the angular velocity
 of the body around its COM, the xyz components of the torque acting on the
-COM, the 3 principal components of the moment of inertia and the xyz image
+COM, the 3 principal components of the moment of inertia, the xyz components
+of the angular momentum of the body around its COM, and the xyz image
 flags of the COM.
 
 The center of mass (COM) for each body is similar to unwrapped

doc/src/fix_srd.txt

@@ -117,7 +117,7 @@ Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
 SRD particles are bounded by Vmax, which is set so that an SRD
 particle will not advect further than Dmax = 4*lamda in dt_SRD.  This
 means that roughly speaking, Dmax should not be larger than a big
-particle diameter, else SRDs may pass thru big particles without
+particle diameter, else SRDs may pass through big particles without
 colliding.  A warning is generated if this is the case.
 
 Collisions between SRD particles and big particles or walls are

doc/src/fix_tune_kspace.txt

@@ -86,6 +86,9 @@ package"_Build_package.html doc page for more info.
 Do not set "neigh_modify once yes" or else this fix will never be
 called.  Reneighboring is required.
 
+This fix is not compatible with a hybrid pair style, long-range dispersion,
+TIP4P water support, or long-range point dipole support.
+
 [Related commands:]
 
 "kspace_style"_kspace_style.html, "boundary"_boundary.html

doc/src/fix_wall_reflect.txt

@@ -41,7 +41,7 @@ fix top all wall/reflect zhi v_pressdown :pre
 [Description:]
 
 Bound the simulation with one or more walls which reflect particles
-in the specified group when they attempt to move thru them.
+in the specified group when they attempt to move through them.
 
 Reflection means that if an atom moves outside the wall on a timestep
 by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is