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

Patch release 1 February 2019

.github/CODEOWNERS

@@ -29,6 +29,7 @@ src/USER-MEAMC/*      @martok
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
+src/USER-PLUMED/*     @gtribello
 src/USER-PHONON/*     @lingtikong
 src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey
@@ -125,3 +126,6 @@ python/*              @rbberger
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.github/CONTRIBUTING.md

@@ -6,7 +6,7 @@ The following is a set of guidelines as well as explanations of policies and wor
 
 Thus please also have a look at:
 * [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15)
-* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html)
+* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 ## Table of Contents
 
@@ -62,7 +62,7 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
 
-How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html)
+How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/Howto_github.html)
  for instructions on how to submit your changes or new files through a GitHub pull request
 
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
@@ -102,11 +102,11 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 
 ### Pull Requests
 
-For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.
+For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
 Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
 Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that.
 You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
-If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.
-Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.
+If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.
+Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.
 

.gitignore

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

cmake/CMakeLists.txt

@@ -11,6 +11,10 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
 
+# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
+if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+endif()
 
 # To avoid conflicts with the conventional Makefile build system, we build everything here
 file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
@@ -69,10 +73,13 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+include(PreventInSourceBuilds)
+
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   #release comes with -O3 by default
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 
 # check for files auto-generated by make-based buildsystem
 # this is fast, so check for it all the time
@@ -164,13 +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-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
-  USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+  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-YAFF)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -183,14 +191,16 @@ 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()
 
+include_directories(${LAMMPS_SOURCE_DIR})
+
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -211,7 +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)
@@ -299,7 +309,7 @@ pkg_depends(USER-SCAFACOS MPI)
 
 find_package(OpenMP QUIET)
 option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
@@ -417,16 +427,30 @@ if(WITH_FFMPEG)
   add_definitions(-DLAMMPS_FFMPEG)
 endif()
 
+if(BUILD_SHARED_LIBS)
+  set(CONFIGURE_REQUEST_PIC "--with-pic")
+  set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}")
+  set(CUDA_REQUEST_PIC "-Xcompiler ${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
+else()
+  set(CONFIGURE_REQUEST_PIC)
+  set(CMAKE_REQUEST_PIC)
+  set(CUDA_REQUEST_PIC)
+endif()
+
+
 if(PKG_VORONOI)
-  option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
+  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
   if(DOWNLOAD_VORO)
+    message(STATUS "Voro++ download requested - we will build our own")
     include(ExternalProject)
 
     if(BUILD_SHARED_LIBS)
-        set(VORO_BUILD_OPTIONS "CFLAGS=-fPIC")
+      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     else()
-        set(VORO_BUILD_OPTIONS)
+      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     endif()
+    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
+    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
 
     ExternalProject_Add(voro_build
       URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
@@ -440,7 +464,7 @@ if(PKG_VORONOI)
   else()
     find_package(VORO)
     if(NOT VORO_FOUND)
-      message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
     endif()
   endif()
   include_directories(${VORO_INCLUDE_DIRS})
@@ -448,26 +472,26 @@ if(PKG_VORONOI)
 endif()
 
 if(PKG_LATTE)
-  option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
+  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
   if(DOWNLOAD_LATTE)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
     endif()
-    message(STATUS "LATTE not found - we will build our own")
+    message(STATUS "LATTE download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
       URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
       URL_MD5 85ac414fdada2d04619c8f936344df14
       SOURCE_SUBDIR cmake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
-      )
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+    )
     ExternalProject_get_property(latte_build INSTALL_DIR)
     set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
     list(APPEND LAMMPS_DEPS latte_build)
   else()
     find_package(LATTE)
     if(NOT LATTE_FOUND)
-      message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
     endif()
   endif()
   list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
@@ -475,24 +499,22 @@ endif()
 
 if(PKG_USER-SCAFACOS)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
   if(DOWNLOAD_SCAFACOS)
+    message(STATUS "ScaFaCoS download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(scafacos_build
       URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
       URL_MD5 bd46d74e3296bd8a444d731bb10c1738
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> 
-                                               --disable-doc 
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                                --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
-                                               --with-internal-fftw
-                                               --with-internal-pfft
-                                               --with-internal-pnfft
-                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                               
-                                               FC=${CMAKE_MPI_Fortran_COMPILER} 
-                                               CXX=${CMAKE_MPI_CXX_COMPILER} 
+                                               --with-internal-fftw --with-internal-pfft
+                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                               FC=${CMAKE_MPI_Fortran_COMPILER}
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
                                                CC=${CMAKE_MPI_C_COMPILER}
                                                F77=
-      )
+    )
     ExternalProject_get_property(scafacos_build INSTALL_DIR)
     set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
     set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
@@ -524,6 +546,59 @@ if(PKG_USER-SCAFACOS)
   include_directories(${SCAFACOS_INCLUDE_DIRS})
 endif()
 
+if(PKG_USER-PLUMED)
+  find_package(GSL REQUIRED)
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
+  if(DOWNLOAD_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/v2.4.4/plumed-src-2.4.4.tgz
+      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                                --enable-modules=all
+                                               CXX=${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})
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
+    endif()
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED plumed REQUIRED)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()
+
 if(PKG_USER-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@@ -539,12 +614,13 @@ if(PKG_USER-NETCDF)
 endif()
 
 if(PKG_USER-SMD)
-  option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
   if(DOWNLOAD_EIGEN3)
+    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)
@@ -580,8 +656,9 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
+  option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
   if(DOWNLOAD_KIM)
+    message(STATUS "KIM-API v1 download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(kim_build
       URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
@@ -596,7 +673,7 @@ if(PKG_KIM)
   else()
     find_package(KIM)
     if(NOT KIM_FOUND)
-      message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+      message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
     endif()
   endif()
   list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
@@ -609,12 +686,7 @@ if(PKG_MESSAGE)
       ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
       ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
-  if(BUILD_SHARED_LIBS)
-      add_library(cslib SHARED ${cslib_SOURCES})
-  else()
-      add_library(cslib STATIC ${cslib_SOURCES})
-  endif()
-
+  add_library(cslib STATIC ${cslib_SOURCES})
   if(BUILD_MPI)
     target_compile_definitions(cslib PRIVATE -DMPI_YES)
     set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
@@ -639,10 +711,10 @@ endif()
 
 if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
   if(DOWNLOAD_MSCG)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
-      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
     endif()
     include(ExternalProject)
     if(NOT LAPACK_FOUND)
@@ -652,7 +724,7 @@ if(PKG_MSCG)
       URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
       URL_MD5 8c45e269ee13f60b303edd7823866a91
       SOURCE_SUBDIR src/CMake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
       BUILD_COMMAND make mscg INSTALL_COMMAND ""
       )
     ExternalProject_get_property(mscg_build BINARY_DIR)
@@ -689,7 +761,7 @@ endif()
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
 include(CheckIncludeFileCXX)
-foreach(HEADER math.h)
+foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")
@@ -700,7 +772,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
 if (CMAKE_VERSION VERSION_LESS "3.4")
-  enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
+  enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
 endif()
 # RB: disabled this check because it breaks with KOKKOS CUDA enabled
 #foreach(FUNC sin cos)
@@ -738,6 +810,13 @@ foreach(PKG ${DEFAULT_PACKAGES})
   endif()
 endforeach()
 
+# packages that need defines set
+foreach(PKG MPIIO)
+  if(PKG_${PKG})
+    add_definitions(-DLMP_${PKG})
+  endif()
+endforeach()
+
 # dedicated check for entire contents of accelerator packages
 foreach(PKG ${ACCEL_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
@@ -752,7 +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}")
@@ -766,7 +845,7 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
     if(PKG_LIB STREQUAL awpmd)
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
-      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
     elseif(PKG_LIB STREQUAL colvars)
       target_compile_options(colvars PRIVATE -DLEPTON)
       target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
@@ -782,6 +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()
 
@@ -789,6 +871,7 @@ if(PKG_USER-H5MD)
   find_package(HDF5 REQUIRED)
   target_link_libraries(h5md ${HDF5_LIBRARIES})
   target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIRS})
 endif()
 
 
@@ -874,6 +957,20 @@ if(PKG_USER-OMP)
     include_directories(${USER-OMP_SOURCES_DIR})
 endif()
 
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()
+
 if(PKG_KOKKOS)
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -951,7 +1048,7 @@ if(PKG_USER-INTEL)
     endif()
 
     if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
-        message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+        message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
     endif()
 
     if(NOT BUILD_OMP)
@@ -1016,7 +1113,7 @@ if(PKG_USER-INTEL)
 endif()
 
 if(PKG_GPU)
-    if (CMAKE_VERSION VERSION_LESS "3.1") 
+    if (CMAKE_VERSION VERSION_LESS "3.1")
       message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
     endif()
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
@@ -1051,11 +1148,11 @@ if(PKG_GPU)
       find_package(CUDA REQUIRED)
       find_program(BIN2C bin2c)
       if(NOT BIN2C)
-        message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
+        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
       endif()
       option(CUDPP_OPT "Enable CUDPP_OPT" ON)
 
-      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
       file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
       list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@@ -1068,11 +1165,39 @@ if(PKG_GPU)
         file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
       endif()
 
-      cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-                   -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
+      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+      endif()
+      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+      if(CUDA_VERSION VERSION_GREATER "4.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER "5.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER "7.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER "8.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER "9.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+      endif()
 
-      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
-                   -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
+      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
 
       foreach(CU_OBJ ${GPU_GEN_OBJS})
         get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -1164,7 +1289,6 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
-include_directories(${LAMMPS_SOURCE_DIR})
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
 ######################################
@@ -1206,7 +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()
@@ -1221,7 +1345,7 @@ if(BUILD_EXE)
       add_dependencies(lmp ${LAMMPS_DEPS})
     endif()
   endif()
-  
+
   set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
   install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
@@ -1342,7 +1466,6 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
   endif()
 endforeach()
 
-string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
@@ -1358,14 +1481,14 @@ message(STATUS "<<< Build configuration >>>
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_index} GREATER -1)
-  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
+  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
            Type     ${CMAKE_Fortran_COMPILER_ID}
            Version  ${CMAKE_Fortran_COMPILER_VERSION}
    Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
 list (FIND LANGUAGES "C" _index)
 if (${_index} GREATER -1)
-  message(STATUS "C Compiler ${CMAKE_C_COMPILER} 
+  message(STATUS "C Compiler ${CMAKE_C_COMPILER}
      Type     ${CMAKE_C_COMPILER_ID}
      Version  ${CMAKE_C_COMPILER_VERSION}
      C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
@@ -1373,7 +1496,7 @@ endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Linker flags:
    Executable      ${CMAKE_EXE_LINKER_FLAGS}")
-  endif()
+endif()
 if(BUILD_SHARED_LIBS)
   message(STATUS "Shared libraries  ${CMAKE_SHARED_LINKER_FLAGS}")
 else()

cmake/Modules/PreventInSourceBuilds.cmake

@@ -0,0 +1,23 @@
+# - Prevent in-source builds.
+# https://stackoverflow.com/questions/1208681/with-cmake-how-would-you-disable-in-source-builds/
+
+function(prevent_in_source_builds)
+  # make sure the user doesn't play dirty with symlinks
+  get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
+  get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH)
+  get_filename_component(srcdir3 "${CMAKE_SOURCE_DIR}/../src" REALPATH)
+  get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
+
+  # disallow in-source builds
+  if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
+    message(FATAL_ERROR "\
+
+CMake must not to be run in the source directory. \
+Rather create a dedicated build directory and run CMake there. \
+To clean up after this aborted in-place compilation:
+  rm -r CMakeCache.txt CMakeFiles
+")
+  endif()
+endfunction()
+
+prevent_in_source_builds()

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>
@@ -195,6 +195,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   <td><code>CMAKE_INSTALL_PREFIX</code></td>
   <td>Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do.</td>
   <td>
+   Default setting is <code>$HOME/.local</code>.
   </td>
 </tr>
 <tr>
@@ -207,6 +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>
 
@@ -1492,6 +1503,11 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BIN2C</code> (CUDA only)</td>
+  <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
+</tr>
 </tbody>
 </table>
 
@@ -1647,9 +1663,8 @@ requires `gzip` to be in your `PATH`
 </tr>
 <tr>
   <td><code>GZIP_EXECUTABLE</code></td>
-  <td></td>
-  <td>
-  </td>
+  <td>Path to gzip executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
 </tr>
 </tbody>
 </table>
@@ -1679,9 +1694,8 @@ requires `ffmpeg` to be in your `PATH`
 </tr>
 <tr>
   <td><code>FFMPEG_EXECUTABLE</code></td>
-  <td></td>
-  <td>
-  </td>
+  <td>Path to ffmpeg executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
 </tr>
 </tbody>
 </table>
@@ -1725,6 +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>
 

cmake/pkgconfig/liblammps.pc.in

@@ -1,9 +1,29 @@
 # pkg-config file for lammps
 # https://people.freedesktop.org/~dbn/pkg-config-guide.html
-# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
-# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+
+# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
 # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
 
+# Use this on commandline with:
+# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp
+
+# Use this in a Makefile:
+# myapp: myapp.cpp
+# 	$(CC) `pkg-config --cflags --libs lammps` -o $@ $<
+
+# Use this in autotools:
+# configure.ac:
+# PKG_CHECK_MODULES([LAMMPS], [lammps])
+# Makefile.am:
+# myapp_CFLAGS = $(LAMMPS_CFLAGS)
+# myapp_LDADD = $(LAMMPS_LIBS)
+
+# Use this in CMake:
+# CMakeLists.txt:
+# find_package(PkgConfig)
+# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
+# target_link_libraries(<lib> PkgConfig::LAMMPS)
+
 prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@

cmake/presets/all_off.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/all_on.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/manual_selection.cmake

@@ -56,11 +56,13 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
 set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
 set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/std.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/std_nolib.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/user.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

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"
 
 # ------------------------------------------
 
@@ -95,9 +96,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	@echo "Spell check finished."
 
 epub: $(OBJECTS)
-	@mkdir -p epub
+	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
+	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
@@ -123,9 +125,9 @@ pdf: utils/txt2html/txt2html.exe
 		cd ..; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
 		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q $$s lammps.book || \
-			echo doc file $$s missing in src/lammps.book; done; \
+		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q ^$$s lammps.book || \
+			echo WARNING: doc file $$s missing in src/lammps.book; done; \
 		rm *.html; \
 	)
 
@@ -175,7 +177,6 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
-		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 

doc/github-development-workflow.md

@@ -0,0 +1,196 @@
+# Outline of the GitHub Development Workflow
+
+This purpose of this document is to provide a point of reference for the
+core LAMMPS developers and other LAMMPS contributors to understand the
+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 2018-12-19.
+
+## Table of Contents
+
+  * [GitHub Merge Management](#github-merge-management)
+  * [Pull Requests](#pull-requests)
+    * [Pull Request Assignments](#pull-request-assignments)
+    * [Pull Request Reviews](#pull-request-reviews)
+    * [Pull Request Discussions](#pull-request-discussions)
+    * [Checklist for Pull Requests](#checklist-for-pull-requests)
+  * [GitHub Issues](#github-issues)
+  * [Milestones and Release Planning](#milestones-and-release-planning)
+
+## GitHub Merge Management
+
+In the interest of consistency, ONLY ONE of the core LAMMPS developers
+should doing the merging itself.  This is currently
+[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
+If this assignment needs to be changed, it shall be done right after a
+stable release.  If the currently assigned developer cannot merge outstanding pull 
+requests in a timely manner, or in other extenuating circumstances, 
+other core LAMMPS developers with merge rights can merge pull requests,
+when necessary. 
+
+## Pull Requests
+
+ALL changes to the LAMMPS code and documentation, however trivial, MUST
+be submitted as a pull request to GitHub. All changes to the "master"
+branch must be made exclusively through merging pull requests. The
+"unstable" and "stable" branches, respectively are only to be updated
+upon patch or stable releases with fast-forward merges based on the
+associated tags. Pull requests may also be submitted to (long-running)
+feature branches created by LAMMPS developers inside the LAMMPS project,
+if needed. Those are not subject to the merge and review restrictions
+discussed in this document, though, but get managed as needed on a
+case-by-case basis.
+
+### Pull Request Assignments
+
+Pull requests can be "chaperoned" by one of the LAMMPS core developers.
+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 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
+period the `work_in_progress` label shall be applied to the pull
+request.  The assignee gets to decide what happens to the pull request
+next, e.g. whether it should be assigned to a different developer for
+additional checks and changes, or is recommended to be merged.  Removing
+the `work_in_progress` label and assigning the pull request to the
+developer tasked with merging signals that a pull request is ready to be
+merged.
+
+### Pull Request Reviews
+
+People can be assigned to review a pull request in two ways:
+
+  * They can be assigned manually to review a pull request
+    by the submitter or a LAMMPS developer
+  * They can be automatically assigned, because a developers matches
+    a file pattern in the `.github/CODEOWNERS` file, which associates
+    developers with the code they contributed and maintain.
+
+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 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.
+
+### Pull Request Discussions
+
+All discussions about a pull request should be kept as much as possible
+on the pull request discussion page on GitHub, so that other developers
+can later review the entire discussion after the fact and understand the
+rationale behind choices made.  Exceptions to this policy are technical
+discussions, that are centered on tools or policies themselves
+(git, github, c++) rather than on the content of the pull request.
+
+### Checklist for Pull Requests
+
+Here are some items to check:
+  * source and text files should not have CR/LF line endings (use dos2unix to remove)
+  * every new command or style should have documentation. The names of
+  source files (c++ and manual) should follow the name of the style.
+  (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  * all new style names should be lower case, the must be no dashes,
+  blanks, or underscores separating words, only forward slashes.
+  * new style docs should be added to the "overview" files in
+  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
+  and `doc/src/lammps.book`
+  * check whether manual cleanly translates with `make html` and `make pdf`
+  * check spelling of manual with `make spelling` in doc folder
+  * new source files in packages should be added to `src/.gitignore`
+  * removed or renamed files in packages should be added to `src/Purge.list`
+  * C++ source files should use C++ style include files for accessing
+  C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
+  And they should use angular brackets instead of double quotes. Full list:
+    * assert.h -> cassert
+    * ctype.h -> cctype
+    * errno.h -> cerrno
+    * float.h -> cfloat
+    * limits.h -> climits
+    * math.h -> cmath
+    * omplex.h -> complex
+    * setjmp.h -> csetjmp
+    * signal.h -> csignal
+    * stddef.h -> cstddef
+    * stdint.h -> cstdint
+    * stdio.h -> cstdio
+    * stdlib.h -> cstdlib
+    * string.h -> cstring
+    * time.h -> ctime
+    * 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 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
+  compiling LAMMPS with `-DLAMMPS_BIGBIG`.
+  * when including both `lmptype.h` (and using defines or macros from it)
+  and `mpi.h`, `lmptype.h` must be included first.
+  * when pair styles are added, check if settings for flags like
+  `single_enable`, `writedata`, `reinitflag`, `manybody_flag`
+  and others are correctly set and supported.
+
+## GitHub Issues
+
+The GitHub issue tracker is the location where the LAMMPS developers
+and other contributors or LAMMPS users can report issues or bugs with
+the LAMMPS code or request new features to be added. Feature requests
+are usually indicated by a `[Feature Request]` marker in the subject.
+Issues are assigned to a person, if this person is working on this
+feature or working to resolve an issue. Issues that have nobody working
+on them at the moment, have the label `volunteer needed` attached.
+
+When an issue, say `#125` is resolved by a specific pull request,
+the comment for the pull request shall contain the text `closes #125`
+or `fixes #125`, so that the issue is automatically deleted when
+the pull request is merged.
+
+## Milestones and Release Planning
+
+LAMMPS uses a continuous release development model with incremental
+changes, i.e. significant effort is made - including automated pre-merge
+testing - that the code in the branch "master" does not get broken.
+More extensive testing (including regression testing) is performed after
+code is merged to the "master" branch. There are patch releases of
+LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
+a sufficient amount of changes have happened, and the post-merge testing
+has been successful. These patch releases are marked with a
+`patch_<version date>` tag and the "unstable" branch follows only these
+versions (and thus is always supposed to be of production quality,
+unlike "master", which may be temporary broken, in the case of larger
+change sets or unexpected incompatibilities or side effects.
+
+About 3-4 times each year, there are going to be "stable" releases
+of LAMMPS.  These have seen additional, manual testing and review of
+results from testing with instrumented code and static code analysis.
+Also, in the last 2-3 patch releases before a stable release are
+"release candidate" versions which only contain bugfixes and
+documentation updates.  For release planning and the information of
+code contributors, issues and pull requests being actively worked on
+are assigned a "milestone", which corresponds to the next stable
+release or the stable release after that, with a tentative release
+date.
+

doc/src/Build_basics.txt

@@ -49,7 +49,7 @@ make mybox :pre         # uses Makefile.mybox to produce lmp_mybox :pre
 
 Serial build (see src/MAKE/Makefile.serial):
 
-MPI_INC =       -I../STUBS 
+MPI_INC =       -I../STUBS
 MPI_PATH =      -L../STUBS
 MPI_LIB =	-lmpi_stubs :pre
 
@@ -137,9 +137,9 @@ simply loading the appropriate module before building LAMMPS.
 -D CMAKE_C_COMPILER=name              # name of C compiler
 -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
 
--D CMAKE_CXX_FlAGS=string             # flags to use with C++ compiler
--D CMAKE_C_FlAGS=string               # flags to use with C compiler
--D CMAKE_Fortran_FlAGS=string         # flags to use with Fortran compiler :pre
+-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+-D CMAKE_C_FLAGS=string               # flags to use with C compiler
+-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
 
 By default CMake will use a compiler it finds and it will add
 optimization flags appropriate to that compiler and any "accelerator
@@ -172,7 +172,7 @@ want.
 Parallel build (see src/MAKE/Makefile.mpi):
 
 CC =		mpicxx
-CCFLAGS =	-g -O3 
+CCFLAGS =	-g -O3
 LINK =		mpicxx
 LINKFLAGS =	-g -O :pre
 
@@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
 you can browse them locally on your system.  Type "make" from the
 lammps/doc dir to see other options.
 
-NOTE: You can also download a tarball of the documention for the
+NOTE: You can also download a tarball of the documentation for the
 current LAMMPS version (HTML and PDF files), from the website
 "download page"_http://lammps.sandia.gov/download.html.
 

doc/src/Build_cmake.txt

@@ -27,7 +27,7 @@ make command to build LAMMPS, which uses the created
 Makefile(s). Example:
 
 cd lammps                        # change to the LAMMPS distribution directory
-mkdir build; cd build            # create a new directory (folder) for build       
+mkdir build; cd build            # create a new directory (folder) for build
 cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
 make                             # compilation :pre
 
@@ -44,7 +44,7 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up compilation even more.
 
 After compilation, you can optionally copy the LAMMPS executable and
-library into your system folders (by default under /usr/local) with:
+library into your system folders (by default under $HOME/.local) with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 

doc/src/Build_extras.txt

@@ -36,7 +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,
@@ -45,6 +44,7 @@ This is the list of packages that may require additional steps.
 "USER-INTEL"_#user-intel,
 "USER-MOLFILE"_#user-molfile,
 "USER-NETCDF"_#user-netcdf,
+"USER-PLUMED"_#user-plumed,
 "USER-OMP"_#user-omp,
 "USER-QMMM"_#user-qmmm,
 "USER-QUIP"_#user-quip,
@@ -63,7 +63,7 @@ available on your system.
 
 If CMake cannot find the library, you can set these variables:
 
--D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
 -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file :pre
 
 [Traditional make]:
@@ -86,22 +86,31 @@ which GPU hardware to build for.
                       # value = double or mixed (default) or single
 -D OCL_TUNE=value     # hardware choice for GPU_API=opencl
                       # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
--D GPU_ARCH=value     # hardware choice for GPU_API=cuda
+-D GPU_ARCH=value     # primary GPU hardware choice for GPU_API=cuda
                       # value = sm_XX, see below
                       # default is Cuda-compiler dependent, but typically sm_20
--D CUDPP_OPT=value    # optimization setting for GPU_API=cudea
+-D CUDPP_OPT=value    # optimization setting for GPU_API=cuda
                       # enables CUDA Performance Primitives Optimizations
                       # yes (default) or no :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
-sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
-sm_30 for Kepler (K10)
-sm_35 for Kepler (K40) or GeForce GTX Titan or similar
-sm_37 for Kepler (dual K80)
-sm_50 for Maxwell
-sm_60 for Pascal (P100)
-sm_70 for Volta :ul
+sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
+sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
+sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
+sm_50 or sm_52 for Maxwell (supported since CUDA 6)
+sm_60 or sm_61 for Pascal (supported since CUDA 8)
+sm_70 for Volta (supported since CUDA 9)
+sm_75 for Turing (supported since CUDA 10) :ul
+
+A more detailed list can be found, for example,
+at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported
+
+CMake can detect which version of the CUDA toolkit is used and thus can
+include support for [all] major GPU architectures supported by this toolkit.
+Thus the GPU_ARCH setting is merely an optimization, to have code for
+the preferred GPU architecture directly included rather than having to wait
+for the JIT compiler of the CUDA driver to translate it.
 
 [Traditional make]:
 
@@ -127,7 +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:
 
@@ -136,6 +145,11 @@ CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
 CUDA_PRECISION = precision (double, mixed, single)
 EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
 
+The file Makefile.linux_multi is set up to include support for multiple
+GPU architectures as supported by the CUDA toolkit in use. This is done
+through using the "--gencode " flag, which can be used multiple times and
+thus support all GPU architectures supported by your CUDA compiler.
+
 If the library build is successful, 3 files should be created:
 lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and
 lib/gpu/Makefile.lammps.  The latter has settings that enable LAMMPS
@@ -149,8 +163,9 @@ re-build LAMMPS.  This is because the compilation of files in the GPU
 package uses the library settings from the lib/gpu/Makefile.machine
 used to build the GPU library.
 
+
 :line
- 
+
 KIM package :h4,link(kim)
 
 To build with this package, the KIM library must be downloaded and
@@ -177,7 +192,7 @@ package?" page.
 [CMake build]:
 
 -D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # KIM library file (only needed if a custom location) 
+-D KIM_LIBRARY=path      # KIM library file (only needed if a custom location)
 -D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
@@ -254,7 +269,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables:
 -D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU
                                    # archGPU = GPU from list above
 -D KOKKOS_ENABLE_CUDA=yes
--D KOKKOS_ENABLE_OPENMP=yes 
+-D KOKKOS_ENABLE_OPENMP=yes
 -D CMAKE_CXX_COMPILER=wrapper      # wrapper = full path to Cuda nvcc wrapper :pre
 
 The wrapper value is the Cuda nvcc compiler wrapper provided in the
@@ -296,7 +311,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
 CC =		mpicxx :pre
 
 :line
- 
+
 LATTE package :h4,link(latte)
 
 To build with this package, you must download and build the LATTE
@@ -324,7 +339,7 @@ args:
 make lib-latte                          # print help message
 make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
 make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
+make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
                                         #   copy Makefile.lammps.gfortran to Makefile.lammps
 :pre
 
@@ -335,7 +350,7 @@ also check that the Makefile.lammps file you create is appropriate for
 the compiler you use on your system to build LATTE.
 
 :line
- 
+
 MEAM package :h4,link(meam)
 
 NOTE: the use of the MEAM package is discouraged, as it has been
@@ -378,7 +393,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
 file.
 
 :line
- 
+
 MESSAGE package :h4,link(message)
 
 This package can optionally include support for messaging via sockets,
@@ -407,7 +422,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ
 library if requested in the build.
 
 :line
- 
+
 MSCG package :h4,link(mscg)
 
 To build with this package, you must download and build the MS-CG
@@ -419,7 +434,7 @@ lib/mscg/README and MSCG/Install files for more details.
 [CMake build]:
 
 -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
--D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location) 
+-D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location)
 -D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location) :pre
 
 If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
@@ -464,7 +479,7 @@ line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
 an example.
 
 :line
- 
+
 POEMS package :h4,link(poems)
 
 [CMake build]:
@@ -493,7 +508,7 @@ for your system, which should define an EXTRAMAKE variable to specify
 a corresponding Makefile.lammps.machine file.
 
 :line
- 
+
 PYTHON package :h4,link(python)
 
 Building with the PYTHON package requires you have a Python shared
@@ -519,58 +534,19 @@ process to find Python.  You should only need to create a new
 Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
 build fails.
 
-:line
- 
-REAX package :h4,link(reax)
-
-NOTE: the use of the REAX package and its "pair_style
-reax"_pair_reax.html command is discouraged, as it is no longer
-maintained.  Please use the USER-REAXC package and its "pair_style
-reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
-enabled variant (pair_style reax/c/kk), which has a more robust memory
-management.  See the "pair_style reax/c"_pair_reaxc.html doc page for
-details.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_REAX=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the REAX library in lib/reax.
-You can do this manually if you prefer; follow the instructions in
-lib/reax/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/reax/Install.py script with the specified args:
-
-make lib-reax                    # print help message
-make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library).  Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
 :line
 
 VORONOI package :h4,link(voronoi)
 
 To build with this package, you must download and build the "Voro++
-library"_voro_home.
+library"_voro-home.
 
-:link(voro_home,http://math.lbl.gov/voro++)
+:link(voro-home,http://math.lbl.gov/voro++)
 
 [CMake build]:
 
 -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
--D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location) 
+-D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
 -D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location) :pre
 
 If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
@@ -606,8 +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]:
 
@@ -712,6 +688,114 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
+USER-PLUMED package :h4,link(user-plumed)
+
+Before building LAMMPS with this package, you must first build PLUMED.
+PLUMED can be built as part of the LAMMPS build or installed separately
+from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
+:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
+
+PLUMED can be linked into MD codes in three different modes: static,
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
+
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
+
+[CMake build]:
+
+When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
+
+-D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
+-D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
+
+If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG_CONFIG_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
+
+The PLUMED_MODE setting determines the linkage mode for the PLUMED
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
+mode is recommended.
+
+[Traditional make]:
+
+PLUMED needs to be installed before the USER-PLUMED package is installed
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
+
+Download/compilation/configuration of the plumed library can be done
+from the src folder through the following make args:
+
+make lib-plumed                         # print help message
+make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+                                                # /usr/local and use shared linkage mode
+:pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink" are
+created in lib/plumed that point to the location of the PLUMED build to
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
+
+make yes-user-plumed
+make machine :pre
+
+Once this compilation completes you should be able to run LAMMPS in the
+usual way.  For shared linkage mode, libplumed.so must be found by the
+LAMMPS executable, which on many operating systems means, you have to
+set the LD_LIBRARY_PATH environment variable accordingly.
+
+Support for the different linkage modes in LAMMPS varies for different
+operating systems, using the static linkage is expected to be the most
+portable, and thus set to be the default.
+
+If you want to change the linkage mode, you have to re-run "make
+lib-plumed" with the desired settings [and] do a re-install if the
+USER-PLUMED package with "make yes-user-plumed" to update the required
+makefile settings with the changes in the lib/plumed folder.
+
+:line
+
 USER-H5MD package :h4,link(user-h5md)
 
 To build with this package you must have the HDF5 software package
@@ -869,7 +953,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version
 [CMake build]:
 
 The CMake build system currently does not support building the full
-QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.  
+QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
 You must use the traditional make build for this package.
 
 [Traditional make]:
@@ -932,14 +1016,14 @@ successfully build on your system.
 USER-SCAFACOS package :h4,link(user-scafacos)
 
 To build with this package, you must download and build the "ScaFaCoS
-Coulomb solver library"_scafacos_home
+Coulomb solver library"_scafacos-home
 
-:link(scafacos_home,http://www.scafacos.de)
+:link(scafacos-home,http://www.scafacos.de)
 
 [CMake build]:
 
 -D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes
--D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location) 
+-D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location)
 -D SCAFACOS_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location) :pre
 
 If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded

doc/src/Build_link.txt

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

doc/src/Build_package.txt

@@ -47,7 +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,
@@ -56,6 +55,7 @@ packages:
 "USER-INTEL"_Build_extras.html#user-intel,
 "USER-MOLFILE"_Build_extras.html#user-molfile,
 "USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-PLUMED"_Build_extras.html#user-plumed,
 "USER-OMP"_Build_extras.html#user-omp,
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,

doc/src/Build_settings.txt

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

doc/src/Build_windows.txt

@@ -53,20 +53,20 @@ are included, but may not always up-to-date for recently added functionality
 and the corresponding new code. A machine makefile for using cygwin for
 the old build system is provided. The CMake build system is untested
 for this; you will have to request that makefiles are generated and
-manually set the compiler.  
+manually set the compiler.
 
 When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
 in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
-flags in LIB makefile variable. Try adding -static-libgcc or -static or 
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
 both to the linker flags when your resulting LAMMPS Windows executable
 complains about missing .dll files. The CMake configuration should set
-this up automatically, but is untested. 
+this up automatically, but is untested.
 
 In case of problems, you are recommended to contact somebody with
 experience in using cygwin.  If you do come across portability problems
 requiring changes to the LAMMPS source code, or figure out corrections
 yourself, please report them on the lammps-users mailing list, or file
-them as an issue or pull request on the LAMMPS github project.
+them as an issue or pull request on the LAMMPS GitHub project.
 
 
 Using a cross-compiler :h4,link(cross)

doc/src/Commands.txt

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

doc/src/Commands_all.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 "Improper styles"_Commands_bond.html#improper,
 "KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
 
-All commands :h3
+General commands :h3
 
-An alphabetic list of all LAMMPS commands.
+An alphabetic list of all general LAMMPS commands.
 
 "angle_coeff"_angle_coeff.html,
 "angle_style"_angle_style.html,
@@ -59,6 +59,7 @@ An alphabetic list of all LAMMPS commands.
 "fix_modify"_fix_modify.html,
 "group"_group.html,
 "group2ndx"_group2ndx.html,
+"hyper"_hyper.html,
 "if"_if.html,
 "info"_info.html,
 "improper_coeff"_improper_coeff.html,

doc/src/Commands_bond.txt

@@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(ld,Manual.html)
 :link(lc,Commands_all.html)
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -34,9 +34,10 @@ OPT.
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
+"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,
@@ -57,18 +58,22 @@ OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html :tb(c=3,ea=c)
 
-"charmm (ko)"_angle_charmm.html,
+"charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
+"class2/p6"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
+"cosine/buck6d"_angle_cosine_buck6d.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
 "cosine/shift (o)"_angle_cosine_shift.html,
 "cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
 "cosine/squared (o)"_angle_cosine_squared.html,
+"cross"_angle_cross.html,
 "dipole (o)"_angle_dipole.html,
 "fourier (o)"_angle_fourier.html,
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
+"mm3"_angle_mm3.html,
 "quartic (o)"_angle_quartic.html,
 "sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
@@ -97,7 +102,7 @@ OPT.
 "nharmonic (o)"_dihedral_nharmonic.html,
 "opls (iko)"_dihedral_opls.html,
 "quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
+"spherical"_dihedral_spherical.html,
 "table (o)"_dihedral_table.html,
 "table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
 
@@ -112,13 +117,16 @@ OPT.
 
 "none"_improper_none.html,
 "zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html  :tb(c=3,ea=c)
+"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
 
 "class2 (ko)"_improper_class2.html,
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,
 "distance"_improper_distance.html,
+"distharm"_improper_distharm.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
+"inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.html,
+"sqdistharm"_improper_sqdistharm.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_category.txt

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

doc/src/Commands_compute.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -25,6 +25,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
 "ackland/atom"_compute_ackland_atom.html,
+"adf"_compute_adf.html,
 "aggregate/atom"_compute_cluster_atom.html,
 "angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
@@ -92,6 +93,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "pe/tally"_compute_tally.html,
 "plasticity/atom"_compute_plasticity_atom.html,
 "pressure"_compute_pressure.html,
+"pressure/cylinder"_compute_pressure_cylinder.html,
 "pressure/uef"_compute_pressure_uef.html,
 "property/atom"_compute_property_atom.html,
 "property/chunk"_compute_property_chunk.html,
@@ -118,7 +120,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "smd/tlsph/strain"_compute_smd_tlsph_strain.html,
 "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
 "smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html,
+"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
 "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
 "smd/ulsph/strain"_compute_smd_ulsph_strain.html,
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
@@ -129,6 +131,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "snav/atom"_compute_sna_atom.html,
 "spin"_compute_spin.html,
 "stress/atom"_compute_stress_atom.html,
+"stress/mop"_compute_stress_mop.html,
+"stress/mop/profile"_compute_stress_mop.html,
 "stress/tally"_compute_tally.html,
 "tdpd/cc/atom"_compute_tdpd_cc_atom.html,
 "temp (k)"_compute_temp.html,
@@ -136,6 +140,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "temp/body"_compute_temp_body.html,
 "temp/chunk"_compute_temp_chunk.html,
 "temp/com"_compute_temp_com.html,
+"temp/cs"_compute_temp_cs.html,
 "temp/deform"_compute_temp_deform.html,
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/drude"_compute_temp_drude.html,

doc/src/Commands_fix.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -40,11 +40,13 @@ OPT.
 "ave/time"_fix_ave_time.html,
 "aveforce"_fix_aveforce.html,
 "balance"_fix_balance.html,
+"bocs"_fix_bocs.html,
 "bond/break"_fix_bond_break.html,
 "bond/create"_fix_bond_create.html,
 "bond/react"_fix_bond_react.html,
 "bond/swap"_fix_bond_swap.html,
 "box/relax"_fix_box_relax.html,
+"client/md"_fix_client_md.html,
 "cmap"_fix_cmap.html,
 "colvars"_fix_colvars.html,
 "controller"_fix_controller.html,
@@ -54,7 +56,7 @@ OPT.
 "drag"_fix_drag.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
+"drude/transform/inverse"_fix_drude_transform.html,
 "dt/reset"_fix_dt_reset.html,
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
@@ -68,14 +70,16 @@ OPT.
 "ffl"_fix_ffl.html,
 "filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
-"freeze"_fix_freeze.html,
+"freeze (k)"_fix_freeze.html,
 "gcmc"_fix_gcmc.html,
 "gld"_fix_gld.html,
 "gle"_fix_gle.html,
-"gravity (o)"_fix_gravity.html,
+"gravity (ko)"_fix_gravity.html,
 "grem"_fix_grem.html,
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
+"hyper/global"_fix_hyper_global.html,
+"hyper/local"_fix_hyper_local.html,
 "imd"_fix_imd.html,
 "indent"_fix_indent.html,
 "ipi"_fix_ipi.html,
@@ -92,6 +96,7 @@ OPT.
 "lineforce"_fix_lineforce.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso"_fix_meso.html,
+"meso/move"_fix_meso_move.html,
 "meso/stationary"_fix_meso_stationary.html,
 "momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
@@ -107,15 +112,16 @@ OPT.
 "nph/eff"_fix_nh_eff.html,
 "nph/sphere (o)"_fix_nph_sphere.html,
 "nphug (o)"_fix_nphug.html,
-"npt (kio)"_fix_nh.html,
+"npt (iko)"_fix_nh.html,
 "npt/asphere (o)"_fix_npt_asphere.html,
 "npt/body"_fix_npt_body.html,
 "npt/eff"_fix_nh_eff.html,
 "npt/sphere (o)"_fix_npt_sphere.html,
 "npt/uef"_fix_nh_uef.html,
-"nve (kio)"_fix_nve.html,
+"nve (iko)"_fix_nve.html,
 "nve/asphere (i)"_fix_nve_asphere.html,
 "nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/awpmd"_fix_nve_awpmd.html,
 "nve/body"_fix_nve_body.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
@@ -124,7 +130,7 @@ OPT.
 "nve/line"_fix_nve_line.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/sphere (ko)"_fix_nve_sphere.html,
 "nve/spin"_fix_nve_spin.html,
 "nve/tri"_fix_nve_tri.html,
 "nvk"_fix_nvk.html,
@@ -143,6 +149,7 @@ OPT.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "planeforce"_fix_planeforce.html,
+"plumed"_fix_plumed.html,
 "poems"_fix_poems.html,
 "pour"_fix_pour.html,
 "precession/spin"_fix_precession_spin.html,
@@ -162,34 +169,34 @@ OPT.
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reaxc_bonds.html,
 "reax/c/species (k)"_fix_reaxc_species.html,
 "recenter"_fix_recenter.html,
 "restrain"_fix_restrain.html,
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.html,
+"rigid/meso"_fix_rigid_meso.html,
 "rigid/nph (o)"_fix_rigid.html,
+"rigid/nph/small"_fix_rigid.html,
 "rigid/npt (o)"_fix_rigid.html,
+"rigid/npt/small"_fix_rigid.html,
 "rigid/nve (o)"_fix_rigid.html,
+"rigid/nve/small"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
+"rigid/nvt/small"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
 "rx (k)"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "shardlow (k)"_fix_shardlow.html,
 "smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/adjust_dt"_fix_smd_adjust_dt.html,
+"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
+"smd/wall_surface"_fix_smd_wall_surface.html,
 "spring"_fix_spring.html,
 "spring/chunk"_fix_spring_chunk.html,
 "spring/rg"_fix_spring_rg.html,
@@ -227,4 +234,4 @@ OPT.
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,
 "wall/region/ees"_fix_wall_ees.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
+"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

doc/src/Commands_kspace.txt

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

doc/src/Commands_pair.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-"All commands"_Commands_all.html,
+"General commands"_Commands_all.html,
 "Fix styles"_Commands_fix.html,
 "Compute styles"_Commands_compute.html,
 "Pair styles"_Commands_pair.html,
@@ -31,8 +31,8 @@ OPT.
 
 "adp (o)"_pair_adp.html,
 "agni (o)"_pair_agni.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
+"airebo (io)"_pair_airebo.html,
+"airebo/morse (io)"_pair_airebo.html,
 "atm"_pair_atm.html,
 "awpmd/cut"_pair_awpmd.html,
 "beck (go)"_pair_beck.html,
@@ -42,37 +42,39 @@ OPT.
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
 "born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
+"born/coul/dsf/cs"_pair_cs.html,
 "born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
+"born/coul/long/cs (g)"_pair_cs.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
+"born/coul/wolf/cs (g)"_pair_cs.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
 "buck (giko)"_pair_buck.html,
 "buck/coul/cut (giko)"_pair_buck.html,
 "buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/long/cs"_pair_cs.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
 "buck/mdf"_pair_mdf.html,
+"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
+"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
 "colloid (go)"_pair_colloid.html,
 "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"_pair_coul.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"coul/msm"_pair_coul.html,
+"coul/long/cs (g)"_pair_cs.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,
 "coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
+"coul/wolf/cs"_pair_cs.html,
 "dpd (gio)"_pair_dpd.html,
 "dpd/fdt"_pair_dpd_fdt.html,
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
@@ -91,11 +93,11 @@ OPT.
 "exp6/rx (k)"_pair_exp6_rx.html,
 "extep"_pair_extep.html,
 "gauss (go)"_pair_gauss.html,
-"gauss/cut"_pair_gauss.html,
+"gauss/cut (o)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
+"gran/hooke/history (ko)"_pair_gran.html,
 "gw"_pair_gw.html,
 "gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
@@ -105,50 +107,57 @@ 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 (giko)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmm/coul/long (gikot)"_pair_charmm.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_lj.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/long/cs"_pair_cs.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"_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,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/coul/long (iot)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/long/tip4p/long (o)"_pair_lj_long.html,
 "lj/mdf"_pair_mdf.html,
 "lj/sdk (gko)"_pair_sdk.html,
 "lj/sdk/coul/long (go)"_pair_sdk.html,
 "lj/sdk/coul/msm (o)"_pair_sdk.html,
+"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,
@@ -156,16 +165,15 @@ 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,
-"mie/cut (o)"_pair_mie.html,
+"mie/cut (g)"_pair_mie.html,
 "momb"_pair_momb.html,
 "morse (gkot)"_pair_morse.html,
-"morse/smooth/linear"_pair_morse.html,
-"morse/soft"_pair_morse.html,
+"morse/smooth/linear (o)"_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,
@@ -180,7 +188,9 @@ OPT.
 "oxdna2/coaxstk"_pair_oxdna2.html,
 "oxdna2/dh"_pair_oxdna2.html,
 "oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/hbond"_pair_oxdna2.html,
 "oxdna2/stk"_pair_oxdna2.html,
+"oxdna2/xstk"_pair_oxdna2.html,
 "peri/eps"_pair_peri.html,
 "peri/lps (o)"_pair_peri.html,
 "peri/pmb (o)"_pair_peri.html,
@@ -188,13 +198,13 @@ OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "quip"_pair_quip.html,
-"reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
-"rebo (oi)"_pair_airebo.html,
+"rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html,
 "smd/ulsph"_pair_smd_ulsph.html,
 "smtbq"_pair_smtbq.html,
 "snap (k)"_pair_snap.html,
@@ -223,11 +233,11 @@ 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 (ko)"_pair_vashishta.html,
+"vashishta (gko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
+"yukawa (gko)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
+"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Commands_parse.txt

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

doc/src/Developer/.gitignore

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

doc/src/Developer/developer.tex

@@ -22,10 +22,10 @@ users.
 LAMMPS source files are in two directories of the distribution
 tarball.  The src directory has the majority of them, all of which are
 C++ files (*.cpp and *.h).  Many of these files are in the src
-directory itself.  There are also dozens of "packages", which can be
+directory itself.  There are also dozens of ``packages'', which can be
 included or excluded when LAMMPS is built.  See the
 doc/Section\_build.html section of the manual for more information
-about packages, or type "make" from within the src directory, which
+about packages, or type ``make'' from within the src directory, which
 lists package-related commands, such as ``make package-status''.  The
 source files for each package are in an all-uppercase sub-directory of
 src, like src/MOLECULE or src/USER-CUDA.  If the package is currently
@@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries,
 used by a few of the packages.  Each sub-directory, like meam or gpu,
 contains the source files, some of which are in different languages
 such as Fortran.  The files are compiled into libraries from within
-each sub-directory, e.g. performing a "make" in the lib/meam directory
+each sub-directory, e.g. performing a ``make'' in the lib/meam directory
 creates a libmeam.a file.  These libraries are linked to during a
 LAMMPS build, if the corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as run.cpp
 and run.h.  The pair of files defines a C++ class, the Run class in
-this case, which contains the code invoked by the "run" command in a
+this case, which contains the code invoked by the ``run'' command in a
 LAMMPS input script.  As this example illustrates, source file and
 class names often have a one-to-one correspondence with a command used
 in a LAMMPS input script.  Some source files and classes do not have a
-corresponding input script command, e.g. force.cpp and the Force
+corresponding input script command, e.g. ``force.cpp'' and the Force
 class.  They are discussed in the next section.
 
 \pagebreak
@@ -57,12 +57,12 @@ class.  They are discussed in the next section.
 Though LAMMPS has a lot of source files and classes, its class
 hierarchy is quite simple, as outlined in Fig \ref{fig:classes}.  Each
 boxed name refers to a class and has a pair of associated source files
-in lammps/src, e.g. memory.cpp and memory.h.  More details on the
+in lammps/src, e.g. ``memory.cpp'' and ``memory.h''.  More details on the
 class and its methods and data structures can be found by examining
 its *.h file.
 
 LAMMPS (lammps.cpp/h) is the top-level class for the entire code.  It
-holds an "instance" of LAMMPS and can be instantiated one or more
+holds an ``instance'' of LAMMPS and can be instantiated one or more
 times by a calling code.  For example, the file src/main.cpp simply
 instantiates one instance of LAMMPS and passes it the input script.
 
@@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see
 src/pointers.h) which every class inherits from.
 
 There are a handful of virtual parent classes in LAMMPS that define
-what LAMMPS calls "styles".  They are shaded red in Fig
+what LAMMPS calls ``styles''.  They are shaded red in Fig
 \ref{fig:classes}.  Each of these are parents of a number of child
 classes that implement the interface defined by the parent class.  For
 example, the fix style has around 100 child classes.  They are the
@@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input
 script, e.g. fix nve, fix shake, fix ave/time, etc.  The corresponding
 classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
 etc.  The source files for these classes are easy to identify in the
-src directory, since they begin with the word "fix", e,g,
+src directory, since they begin with the word ``fix'', e,g,
 fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
 
-The one exception is child class files for the "command" style.  These
+The one exception is child class files for the ``command'' style.  These
 implement specific commands in the input script that can be invoked
 before/after/between runs or which launch a simulation.  Examples are
 the create\_box, minimize, run, and velocity commands which encode the
 CreateBox, Minimize, Run, and Velocity classes.  The corresponding
 files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
-The list of command style files can be found by typing "grep
-COMMAND\_CLASS *.h" from within the src directory, since that word in
+The list of command style files can be found by typing ``grep
+COMMAND\_CLASS *.h'' from within the src directory, since that word in
 the header file identifies the class as an input script command.
 Similar words can be grepped to list files for the other LAMMPS
 styles.  E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
@@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine)
   \end{verbatim}
  \end{center}
 
-Where "your/fix/name" is a name of your fix in the script and FixMine
+Where ``your/fix/name'' is a name of your fix in the script and FixMine
 is the name of the class. This code allows LAMMPS to find your fix
 when it parses input script. In addition, your fix header must be
-included in the file "style\_fix.h". In case if you use LAMMPS make,
+included in the file ``style\_fix.h''. In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
 fix\_ are included, so call your header the same way. Otherwise, don't
-forget to add your include into "style\_fix.h".
+forget to add your include into ``style\_fix.h''.
 
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
@@ -567,11 +567,11 @@ void FixPrintVel::end_of_step()
 \end{center}
 
 In the code above, we use MathExtra routines defined in
-"math\_extra.h".  There are bunch of math functions to work with
+``math\_extra.h''.  There are bunch of math functions to work with
 arrays of doubles as with math vectors.
 
 In this code we use an instance of Atom class. This object is stored
-in the Pointers class (see "pointers.h"). This object contains all
+in the Pointers class (see ``pointers.h''). This object contains all
 global information about the simulation system. Data from Pointers
 class available to all classes inherited from it using protected
 inheritance. Hence when you write you own class, which is going to use
@@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf)
 
 Now, a little bit about memory allocation. We used Memory class which
 is just a bunch of template functions for allocating 1D and 2D
-arrays. So you need to add include "memory.h" to have access to them.
+arrays. So you need to add include ``memory.h'' to have access to them.
 
 Finally, if you need to write/read some global information used in
 your fix to the restart file, you might do it by setting flag

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.txt

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

doc/src/Errors_common.txt

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

doc/src/Errors_messages.txt

@@ -279,12 +279,6 @@ multibody joint).  The bodies you have defined exceed this limit. :dd
 This is an internal LAMMPS error.  Please report it to the
 developers. :dd
 
-{Atom sorting has bin size = 0.0} :dt
-
-The neighbor cutoff is being used as the bin size, but it is zero.
-Thus you must explicitly list a bin size in the atom_modify sort
-command or turn off sorting. :dd
-
 {Atom style hybrid cannot have hybrid as an argument} :dt
 
 Self-explanatory. :dd
@@ -421,9 +415,9 @@ This is an internal error.  It should normally not occur. :dd
 
 This is an internal error.  It should normally not occur. :dd
 
-{Bad real space Coulomb cutoff in fix tune/kspace} :dt
+{Bad real space Coulombic cutoff in fix tune/kspace} :dt
 
-Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
+Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
 the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd
 
 {Balance command before simulation box is defined} :dt
@@ -460,7 +454,7 @@ compute. :dd
 
 {Big particle in fix srd cannot be point particle} :dt
 
-Big particles must be extended spheriods or ellipsoids. :dd
+Big particles must be extended spheroids or ellipsoids. :dd
 
 {Bigint setting in lmptype.h is invalid} :dt
 
@@ -780,7 +774,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd
 
 Self-explanatory. :dd
 
-{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt
+{Cannot change box z boundary to non-periodic for a 2d simulation} :dt
 
 Self-explanatory. :dd
 
@@ -1288,7 +1282,7 @@ are defined. :dd
 You cannot reset the timestep when a fix that keeps track of elapsed
 time is in place. :dd
 
-{Cannot run 2d simulation with nonperiodic Z dimension} :dt
+{Cannot run 2d simulation with non-periodic Z dimension} :dt
 
 Use the boundary command to make the z dimension periodic in order to
 run a 2d simulation. :dd
@@ -2116,29 +2110,29 @@ Self-explanatory. :dd
 Fix setforce cannot be used in this manner.  Use fix addforce
 instead. :dd
 
-{Cannot use nonperiodic boundares with fix ttm} :dt
+{Cannot use non-periodic boundares with fix ttm} :dt
 
 This fix requires a fully periodic simulation box. :dd
 
-{Cannot use nonperiodic boundaries with Ewald} :dt
+{Cannot use non-periodic boundaries with Ewald} :dt
 
 For kspace style ewald, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with EwaldDisp} :dt
+{Cannot use non-periodic boundaries with EwaldDisp} :dt
 
 For kspace style ewald/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
 slab with a non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPM} :dt
+{Cannot use non-periodic boundaries with PPPM} :dt
 
 For kspace style pppm, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPMDisp} :dt
+{Cannot use non-periodic boundaries with PPPMDisp} :dt
 
 For kspace style pppm/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
@@ -3351,21 +3345,21 @@ probably due to errors in the Python code. :dd
 The default minimum order is 2.  This can be reset by the
 kspace_modify minorder command. :dd
 
-{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt
+{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/coul/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
+{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt
 
-If using a Kspace solver, all Coulomb cutoffs of long pair styles must
+If using a Kspace solver, all Coulombic cutoffs of long pair styles must
 be the same. :dd
 
 {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt
@@ -5938,9 +5932,9 @@ map command will force an atom map to be created. :dd
 
 Self-explanatory. :dd
 
-{Input line quote not followed by whitespace} :dt
+{Input line quote not followed by white-space} :dt
 
-An end quote must be followed by whitespace. :dd
+An end quote must be followed by white-space. :dd
 
 {Insertion region extends outside simulation box} :dt
 
@@ -6923,7 +6917,7 @@ types. :dd
 
 {Invalid use of library file() function} :dt
 
-This function is called thru the library interface.  This
+This function is called through the library interface.  This
 error should not occur.  Contact the developers if it does. :dd
 
 {Invalid value in set command} :dt
@@ -7014,7 +7008,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd
 
 {KSpace accuracy too large to estimate G vector} :dt
 
-Reduce the accuracy request or specify gwald explicitly
+Reduce the accuracy request or specify gewald explicitly
 via the kspace_modify command. :dd
 
 {KSpace accuracy too low} :dt
@@ -8014,7 +8008,7 @@ Self-explanatory. :dd
 
 {Package command after simulation box is defined} :dt
 
-The package command cannot be used afer a read_data, read_restart, or
+The package command cannot be used after a read_data, read_restart, or
 create_box command. :dd
 
 {Package gpu command without GPU package installed} :dt
@@ -9198,7 +9192,7 @@ creates one large file for all processors. :dd
 {Restart file byte ordering is not recognized} :dt
 
 The file does not appear to be a LAMMPS restart file since it doesn't
-contain a recognized byte-orderomg flag at the beginning. :dd
+contain a recognized byte-ordering flag at the beginning. :dd
 
 {Restart file byte ordering is swapped} :dt
 
@@ -9410,7 +9404,7 @@ You may also want to boost the page size. :dd
 
 {Small to big integers are not sized correctly} :dt
 
-This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
+This error occurs when the sizes of smallint, imageint, tagint, bigint,
 as defined in src/lmptype.h are not what is expected.  Contact
 the developers if this occurs. :dd
 

doc/src/Errors_warnings.txt

@@ -757,7 +757,7 @@ Self-explanatory. :dd
 
 This may indicate the shell command did not operate as expected. :dd
 
-{Should not allow rigid bodies to bounce off relecting walls} :dt
+{Should not allow rigid bodies to bounce off reflecting walls} :dt
 
 LAMMPS allows this, but their dynamics are not computed correctly. :dd
 
@@ -850,10 +850,10 @@ Most FENE models need this setting for the special_bonds command. :dd
 
 Most FENE models need this setting for the special_bonds command. :dd
 
-{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt
+{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt
 
 This is likely not what you want to do.  The exclusion settings will
-eliminate neighbors in the neighbor list, which the manybody potential
+eliminate neighbors in the neighbor list, which the many-body potential
 needs to calculated its terms correctly. :dd
 
 {Using compute temp/deform with inconsistent fix deform remap option} :dt

doc/src/Examples.txt

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

doc/src/Howto.txt

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

doc/src/Howto_barostat.txt

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

doc/src/Howto_bash.txt

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

doc/src/Howto_body.txt

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

doc/src/Howto_chunk.txt

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

doc/src/Howto_client_server.txt

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

doc/src/Howto_coreshell.txt

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

doc/src/Howto_couple.txt

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

doc/src/Howto_dispersion.txt

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

doc/src/Howto_drude.txt

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

doc/src/Howto_drude2.txt

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

doc/src/Howto_elastic.txt

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

doc/src/Howto_github.txt

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

doc/src/Howto_library.txt

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

doc/src/Howto_manifold.txt

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

doc/src/Howto_nemd.txt

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

doc/src/Howto_polarizable.txt

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

doc/src/Howto_pylammps.txt

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

doc/src/Howto_replica.txt

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

doc/src/Howto_spc.txt

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

doc/src/Howto_spherical.txt

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

doc/src/Howto_spins.txt

@@ -12,48 +12,48 @@ Magnetic spins :h3
 The magnetic spin simulations are enabled by the SPIN package, whose
 implementation is detailed in "Tranchida"_#Tranchida7.
 
-The model represents the simulation of atomic magnetic spins coupled 
-to lattice vibrations. The dynamics of those magnetic spins can be used 
-to simulate a broad range a phenomena related to magneto-elasticity, or 
-or to study the influence of defects on the magnetic properties of 
-materials. 
+The model represents the simulation of atomic magnetic spins coupled
+to lattice vibrations. The dynamics of those magnetic spins can be used
+to simulate a broad range a phenomena related to magneto-elasticity, or
+or to study the influence of defects on the magnetic properties of
+materials.
 
-The magnetic spins are interacting with each others and with the 
-lattice via pair interactions. Typically, the magnetic exchange 
-interaction can be defined using the 
+The magnetic spins are interacting with each others and with the
+lattice via pair interactions. Typically, the magnetic exchange
+interaction can be defined using the
 "pair/spin/exchange"_pair_spin_exchange.html command. This exchange
 applies a magnetic torque to a given spin, considering the orientation
-of its neighboring spins and their relative distances. 
-It also applies a force on the atoms as a function of the spin 
-orientations and their associated inter-atomic distances. 
- 
+of its neighboring spins and their relative distances.
+It also applies a force on the atoms as a function of the spin
+orientations and their associated inter-atomic distances.
+
 The command "fix precession/spin"_fix_precession_spin.html allows to
 apply a constant magnetic torque on all the spins in the system. This
 torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy. 
+uniaxial magnetic anisotropy.
 
-A Langevin thermostat can be applied to those magnetic spins using 
-"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat 
-can be coupled to another Langevin thermostat applied to the atoms 
-using "fix langevin"_fix_langevin.html in order to simulate 
-thermostated spin-lattice system. 
+A Langevin thermostat can be applied to those magnetic spins using
+"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
+can be coupled to another Langevin thermostat applied to the atoms
+using "fix langevin"_fix_langevin.html in order to simulate
+thermostatted spin-lattice system.
 
-The magnetic Gilbert damping can also be applied using "fix 
-langevin/spin"_fix_langevin_spin.html. It allows to either dissipate 
-the thermal energy of the Langevin thermostat, or to perform a 
+The magnetic Gilbert damping can also be applied using "fix
+langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
+the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
-All the computed magnetic properties can be output by two main 
-commands. The first one is "compute spin"_compute_spin.html, that 
-enables to evaluate magnetic averaged quantities, such as the total 
+All the computed magnetic properties can be output by two main
+commands. The first one is "compute spin"_compute_spin.html, that
+enables to evaluate magnetic averaged quantities, such as the total
 magnetization of the system along x, y, or z, the spin temperature, or
-the magnetic energy. The second command is "compute 
+the magnetic energy. The second command is "compute
 property/atom"_compute_property_atom.html. It enables to output all the
-per atom magnetic quantities. Typically, the orientation of a given 
+per atom magnetic quantities. Typically, the orientation of a given
 magnetic spin, or the magnetic force acting on this spin.
 
 :line
 
 :link(Tranchida7)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, 
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
 arXiv preprint arXiv:1801.10233, (2018).

doc/src/Howto_thermostat.txt

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

doc/src/Howto_triclinic.txt

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

doc/src/Howto_viscosity.txt

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

doc/src/Install_git.txt

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

doc/src/Install_linux.txt

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

doc/src/Install_mac.txt

@@ -49,7 +49,8 @@ Lennard-Jones benchmark file:
 % brew test lammps -v :pre
 
 If you have problems with the installation you can post issues to
-"this link"_https://github.com/Homebrew/homebrew-science/issues.
+"this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
+:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)

doc/src/Install_patch.txt

@@ -17,7 +17,7 @@ how to stay current are on the "Install git"_Install_git.html and
 If you prefer to download a tarball, as described on the "Install
 git"_Install_tarball.html doc page, you can stay current by
 downloading "patch files" when new patch releases are made.  A link to
-a patch file is posted on the "bug and feature 
+a patch file is posted on the "bug and feature
 page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
 with a list of changed files and details about what is in the new patch
 release.  This page explains how to apply the patch file to your local

doc/src/Install_svn.txt

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

doc/src/Install_windows.txt

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

doc/src/Intro_authors.txt

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

doc/src/Intro_features.txt

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

doc/src/Intro_nonfeatures.txt

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="10 Oct 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
-10 Oct 2018 version :c,h2
+1 Feb 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Manual_build.txt

@@ -61,10 +61,12 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 make old          # generate old-style HTML pages in old dir via txt2html
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data :pre
+make anchor_check # check for duplicate anchor labels
+make spelling     # spell-check the manual
 
 :line
 
@@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
+Building the PDF manual requires a working C++ compiler (to
+compile the txt2html tool and a working installation of
+"HTMLDOC"_https://www.msweet.org/htmldoc/
+HTMLDOC has its own list of prerequisites, but in most cases
+you can install a binary package of it either through your
+Linux package manager or MacOS (dmg) and Windows installer
+(msi) packages from its
+"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
 
 :line
 

doc/src/Modify_contribute.txt

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

doc/src/Modify_pair.txt

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

doc/src/Modify_region.txt

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