Merge pull request #1223 from akohlmey/next-patch-release

Patch release 27 November 2018

.github/CODEOWNERS

@@ -17,6 +17,7 @@ src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
+src/MESSAGE/*         @sjplimp
 src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
@@ -28,20 +29,88 @@ 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
 src/USER-QMMM/*       @akohlmey
 src/USER-REAXC/*      @hasanmetin
+src/USER-SCAFACOS/*   @rhalver
 src/USER-TALLY/*      @akohlmey
 src/USER-UEF/*        @danicholson
 src/USER-VTK/*        @rbberger
 
+
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
+src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/USER-MISC/fix_bond_react.*      @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
+src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+
+# core LAMMPS classes
+src/lammps.*              @sjplimp
+src/pointers.h            @sjplimp
+src/atom.*                @sjplimp
+src/atom_vec.*            @sjplimp
+src/angle.*               @sjplimp
+src/bond.*                @sjplimp
+src/comm*.*               @sjplimp
+src/compute.*             @sjplimp
+src/dihedral.*            @sjplimp
+src/domain.*              @sjplimp
+src/dump*.*               @sjplimp
+src/error.*               @sjplimp
+src/finish.*              @sjplimp
+src/fix.*                 @sjplimp
+src/force.*               @sjplimp
+src/group.*               @sjplimp
+src/improper.*            @sjplimp
+src/kspace.*              @sjplimp
+src/lmptyp.h              @sjplimp
+src/library.*             @sjplimp
+src/main.cpp              @sjplimp
+src/memory.*              @sjplimp
+src/modify.*              @sjplimp
+src/molecule.*            @sjplimp
+src/my_page.h             @sjplimp
+src/my_pool_chunk.h       @sjplimp
+src/npair*.*              @sjplimp
+src/ntopo*.*              @sjplimp
+src/nstencil*.*           @sjplimp
+src/neighbor.*            @sjplimp
+src/nbin*.*               @sjplimp
+src/neigh_*.*             @sjplimp
+src/output.*              @sjplimp
+src/pair.*                @sjplimp
+src/rcb.*                 @sjplimp
+src/random_*.*            @sjplimp
+src/region*.*             @sjplimp
+src/rcb.*                 @sjplimp
+src/read*.*               @sjplimp
+src/rerun.*               @sjplimp
+src/run.*                 @sjplimp
+src/respa.*               @sjplimp
+src/set.*                 @sjplimp
+src/special.*             @sjplimp
+src/suffix.h              @sjplimp
+src/thermo.*              @sjplimp
+src/universe.*            @sjplimp
+src/update.*              @sjplimp
+src/variable.*            @sjplimp
+src/verlet.*              @sjplimp
+src/velocity.*            @sjplimp
+src/write_data.*          @sjplimp
+src/write_restart.*       @sjplimp
+
+# overrides for specific files
+src/dump_movie.*          @akohlmey
+src/exceptions.h          @rbberger
+src/fix_nh.*              @athomps
+src/info.*                @akohlmey @rbberger
+src/timer.*               @akohlmey
 
 # tools
 tools/msi2lmp/*       @akohlmey

.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.
 

cmake/CMakeLists.txt

@@ -11,9 +11,13 @@ 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)
+file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
 
@@ -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
@@ -136,6 +143,7 @@ if(BUILD_EXE)
   if(LAMMPS_MACHINE)
     set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
   endif()
+  set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 endif()
 
 option(BUILD_LIB "Build LAMMPS library" OFF)
@@ -162,6 +170,38 @@ set(LAMMPS_LINK_LIBS)
 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
+  SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
+  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
+  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
+  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
+  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
+  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
+  USER-QUIP USER-QMMM)
+set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(OTHER_PACKAGES CORESHELL QEQ)
+foreach(PKG ${DEFAULT_PACKAGES})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+  enable_language(Fortran)
+endif()
+
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+  enable_language(C)
+endif()
+
+include_directories(${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})
 if(BUILD_MPI)
@@ -206,25 +246,52 @@ endif()
 option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
 
 option(ENABLE_TESTING "Enable testing" OFF)
-if(ENABLE_TESTING)
+if(ENABLE_TESTING AND BUILD_EXE)
   enable_testing()
-endif(ENABLE_TESTING)
+  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
 
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX 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-QTB USER-REAXC USER-SMD
-  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
-set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ)
-foreach(PKG ${DEFAULT_PACKAGES})
-  option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
-  option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
+  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
+    include(FetchContent)
+
+    FetchContent_Declare(lammps-testing
+      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
+    )
+
+    FetchContent_GetProperties(lammps-testing)
+    if(NOT lammps-testing_POPULATED)
+      message(STATUS "Downloading tests...")
+      FetchContent_Populate(lammps-testing)
+    endif()
+
+    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+  endif()
+
+  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
+    message(STATUS "Running test discovery...")
+
+    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
+    foreach(script_path ${TEST_SCRIPTS})
+      get_filename_component(TEST_NAME ${script_path} EXT)
+      get_filename_component(SCRIPT_NAME ${script_path} NAME)
+      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+      set(TEST_NAME "test_core_${TEST_NAME}_serial")
+      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+    endforeach()
+    list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+    message(STATUS "Found ${NUM_TESTS} tests.")
+  endif()
+endif()
 
 macro(pkg_depends PKG1 PKG2)
   if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
@@ -238,21 +305,11 @@ pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)
 pkg_depends(USER-PHONON KSPACE)
-
-######################################################
-# 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)
-  enable_language(Fortran)
-endif()
-
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
-  enable_language(C)
-endif()
+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}")
@@ -297,12 +354,12 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
     enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
     set(LAPACK_LIBRARIES linalg)
   else()
@@ -370,16 +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
@@ -393,7 +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})
@@ -401,31 +472,128 @@ 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})
 endif()
 
+if(PKG_USER-SCAFACOS)
+  find_package(GSL REQUIRED)
+  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
+                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                               --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)
+    list(APPEND LAMMPS_DEPS scafacos_build)
+    # list and order from pkg_config file of ScaFaCoS build
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
+    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+  else()
+    FIND_PACKAGE(PkgConfig REQUIRED)
+    PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+  endif()
+  include_directories(${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/v2.4.3/plumed-src-2.4.3.tgz
+      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
+        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})
+    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)
@@ -435,17 +603,18 @@ endif()
 
 if(PKG_USER-NETCDF)
   find_package(NetCDF REQUIRED)
-  include_directories(NETCDF_INCLUDE_DIR)
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
+  include_directories(${NETCDF_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 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 http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
       URL_MD5 1a47e78efe365a97de0c022d127607c3
       CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     )
@@ -453,8 +622,9 @@ if(PKG_USER-SMD)
     set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
     list(APPEND LAMMPS_DEPS Eigen3_build)
   else()
-    find_package(Eigen3)
-    if(NOT Eigen3_FOUND)
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
       message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
     endif()
   endif()
@@ -481,8 +651,9 @@ 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
@@ -497,19 +668,48 @@ 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 ${KIM_LIBRARIES})
   include_directories(${KIM_INCLUDE_DIRS})
 endif()
 
+if(PKG_MESSAGE)
+  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+  add_library(cslib STATIC ${cslib_SOURCES})
+  if(BUILD_MPI)
+    target_compile_definitions(cslib PRIVATE -DMPI_YES)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+  else()
+    target_compile_definitions(cslib PRIVATE -DMPI_NO)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+  endif()
+
+  if(MESSAGE_ZMQ)
+    target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+    find_package(ZMQ REQUIRED)
+    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+  else()
+    target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+  endif()
+
+  list(APPEND LAMMPS_LINK_LIBS cslib)
+  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+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)
@@ -519,7 +719,7 @@ 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} ${EXTRA_MSCG_OPTS}
       BUILD_COMMAND make mscg INSTALL_COMMAND ""
       )
     ExternalProject_get_property(mscg_build BINARY_DIR)
@@ -567,7 +767,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
 if (CMAKE_VERSION VERSION_LESS "3.4")
-  enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
+  enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
 endif()
 # RB: disabled this check because it breaks with KOKKOS CUDA enabled
 #foreach(FUNC sin cos)
@@ -590,8 +790,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 foreach(PKG ${DEFAULT_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -605,12 +805,19 @@ 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})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -624,14 +831,16 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
     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)
@@ -654,6 +863,7 @@ 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()
 
 
@@ -700,6 +910,7 @@ if(PKG_USER-OMP)
     set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
     set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
                          ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
                          ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
                          ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
                          ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
@@ -708,7 +919,7 @@ if(PKG_USER-OMP)
 
     # detects styles which have USER-OMP version
     RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-
+    RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
 
     get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
 
@@ -738,6 +949,20 @@ 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)
@@ -815,7 +1040,7 @@ 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)
@@ -880,7 +1105,7 @@ 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)
@@ -908,35 +1133,63 @@ if(PKG_GPU)
       set(GPU_PREC_SETTING "SINGLE_SINGLE")
     endif()
 
-    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
     file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
     if(GPU_API STREQUAL "CUDA")
       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)
+      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)
 
       cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
       if(CUDPP_OPT)
         cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
-        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+        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)
@@ -978,7 +1231,7 @@ if(PKG_GPU)
       include(OpenCLUtils)
       set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
       list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
 
       foreach(GPU_KERNEL ${GPU_LIB_CU})
@@ -1028,7 +1281,6 @@ 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})
 
 ######################################
@@ -1085,12 +1337,12 @@ if(BUILD_EXE)
       add_dependencies(lmp ${LAMMPS_DEPS})
     endif()
   endif()
-  
-  set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+
+  set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
   install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1)
+  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
   if(ENABLE_TESTING)
-    add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+    add_test(ShowHelp ${LAMMPS_BINARY} -help)
   endif()
 endif()
 
@@ -1105,7 +1357,7 @@ if(BUILD_DOC)
 
   set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
   file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
   list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
 
@@ -1200,13 +1452,12 @@ endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
   if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()
 endforeach()
 
-string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
@@ -1222,14 +1473,14 @@ message(STATUS "<<< Build configuration >>>
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_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}}")
@@ -1237,7 +1488,7 @@ 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/FindZMQ.cmake

@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)

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/Modules/StyleHeaderUtils.cmake

@@ -85,19 +85,23 @@ function(RegisterNPairStyle path)
     AddStyleHeader(${path} NPAIR)
 endfunction(RegisterNPairStyle)
 
+function(RegisterFixStyle path)
+    AddStyleHeader(${path} FIX)
+endfunction(RegisterFixStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
     FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
     FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   ""         COMMAND   ) # command   ) # input
+    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
     FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
     FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
     FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
     FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
     FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS ""         INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    ""         KSPACE    ) # kspace    ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
     FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
     FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
     FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor

cmake/README.md

@@ -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>
@@ -1492,6 +1493,11 @@ 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 +1653,8 @@ 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 +1684,8 @@ 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>

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 = $(LAMMPS_LIBS)
+
+# Use this in CMake:
+# CMakeLists.txt:
+# find_package(PkgConfig)
+# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
+# target_link_libraries(<lib> PkgConfig::LAMMPS)
+
 prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
@@ -11,7 +31,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
 Requires:
 Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
 Libs.private: -lm

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

@@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
-	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
 	@echo "  old        create old-style HTML doc pages in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
@@ -95,9 +95,10 @@ 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)/ ;\
@@ -116,17 +117,17 @@ mobi: epub
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		set -e; \
-		cd src; \
-		../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; \
-		rm *.html; \
-		cd Developer; \
+		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
+		cd ..; \
+		../utils/txt2html/txt2html.exe -b *.txt; \
+		htmldoc --batch lammps.book;          \
+		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; \
 	)
 
 old: utils/txt2html/txt2html.exe
@@ -175,7 +176,6 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
-		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 

doc/github-development-workflow.md

@@ -0,0 +1,192 @@
+# 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 2018-11-15.
+
+## 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 what 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 one review from a LAMMPS developer with write access is required
+before merging in addition to the automated compilation tests.  The
+feature, that reviews from code owners are "hard" reviews (i.e. they
+must all be approved before merging is allowed), is currently disabled
+and it is in the discretion of the merge maintainer to assess when
+a sufficient degree of approval has been reached.  Reviews may be
+(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 two 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.
+  * 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
 
@@ -292,6 +292,10 @@ 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 documentation for the
+current LAMMPS version (HTML and PDF files), from the website
+"download page"_http://lammps.sandia.gov/download.html.
+
 :line
 
 Install LAMMPS after a build :h4,link(install)

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

@@ -31,6 +31,7 @@ This is the list of packages that may require additional steps.
 "KOKKOS"_#kokkos,
 "LATTE"_#latte,
 "MEAM"_#meam,
+"MESSAGE"_#message,
 "MSCG"_#mscg,
 "OPT"_#opt,
 "POEMS"_#poems,
@@ -44,9 +45,11 @@ 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,
+"USER-SCAFACOS"_#user-scafacos,
 "USER-SMD"_#user-smd,
 "USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
 
@@ -61,7 +64,7 @@ available on your system.
 
 If CMake cannot find the library, you can set these variables:
 
--D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
 -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file :pre
 
 [Traditional make]:
@@ -84,22 +87,30 @@ 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_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]:
 
@@ -134,6 +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
@@ -147,8 +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
@@ -175,7 +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
@@ -252,7 +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
@@ -294,7 +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
@@ -322,7 +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
 
@@ -333,7 +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
@@ -361,6 +378,10 @@ make lib-meam args="-m mpi"    # build with default Fortran compiler compatible
 make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
 make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
 
+NOTE: You should test building the MEAM library with both the Intel
+and GNU compilers to see if a simulation runs faster with one versus
+the other on your system.
+
 The build should produce two files: lib/meam/libmeam.a and
 lib/meam/Makefile.lammps.  The latter is copied from an existing
 Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
@@ -372,7 +393,36 @@ 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,
+using the open-source "ZeroMQ library"_http://zeromq.org, which must
+be installed on your system.
+
+[CMake build]:
+
+-D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the CSlib library in
+lib/message.  You can build the CSlib library manually if you prefer;
+follow the instructions in lib/message/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/message/Install.py script with the specified args:
+
+make lib-message               # print help message
+make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
+make lib-message args="-s"     # build as serial lib with no ZMQ support
+
+The build should produce two files: lib/message/cslib/src/libmessage.a
+and lib/message/Makefile.lammps.  The latter is copied from an
+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
@@ -384,7 +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
@@ -429,7 +479,7 @@ line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
 an example.
 
 :line
- 
+
 POEMS package :h4,link(poems)
 
 [CMake build]:
@@ -458,7 +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
@@ -485,7 +535,7 @@ 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
@@ -528,14 +578,14 @@ file.
 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
@@ -677,6 +727,103 @@ 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 required PLUMED code
+is linked statically into the MD code. The MD code is then fully
+independent from the PLUMED installation, but also you have to
+rebuild/relink the MD code to update the PLUMED code inside it.  With
+"shared" linkage mode, the MD code is linked to a shared library
+containing the PLUMED code, preferably after it was installed in a
+globally accessible location. This way the same installed PLUMED code
+can be shared across multiple MD packages and can be updated, for as
+long as the shared PLUMED library is ABI-compatible. The third linkage
+mode is "runtime" which allows to switch the PLUMED kernel at runtime
+between different variants through setting the PLUMED_KERNEL environment
+variable, which has to point to the location of the libplumedKernel.so
+dynamical shared object, which is then loaded at runtime. This is
+particularly convenient for doing PLUMED development and comparing
+multiple PLUMED versions without having to recompile the hosting MD
+code. All three linkage modes are supported by LAMMPS on selected
+operating systems (e.g. Linux) and using either CMake or traditional
+make build. The "static" mode should be most portable, the "runtime"
+mode support in LAMMPS makes the most assumptions about operating
+system and compiler environment. If one mode does not work, try a
+different one, or switch to a different build system, or consider
+a global PLUMED installation or downloading it during building LAMMPS.
+
+[CMake build]:
+
+-D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
+-D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
+
+If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
+downloaded (the version of that is hard-coded to a vetted version of
+PLUMED, usually a recent stable release version) and built inside the
+CMake build directory.  If DOWNLOAD_PLUMED is set to "no" (the default),
+CMake will try to detect an installed version of PLUMED and link to
+that. For this to work, the PLUMED library has to be installed into a
+location where the pkg-config tool can find it or the PKG_CONFIG_PATH
+environment variable has to be set up accordingly.
+
+The PLUMED_MODE setting determines the linkage mode of the PLUMED
+library.  Allowed values are "static" (default), "shared", or "runtime".
+For a discussion of PLUMED linkage modes, please see above.  When
+enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.
+
+[Traditional make]:
+
+Before installing the USER-PLUMED package, first the PLUMED library
+needs to be configured so that LAMMPS can find the right settings when
+compiling and linking the LAMMPS executable itself. You can either
+download and build PLUMED inside the LAMMPS plumed library folder or use
+a previously installed PLUMED library and point LAMMPS to its
+location. You also have to choose the linkage mode: "static" (default),
+"shared" or "runtime".  For a discussion of PLUMED linkage modes, please
+see above.
+
+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 to point into the location of the PLUMED build to
+use and also a new file lib/plumed/Makefile.lammps is created with
+settings suitable for LAMMPS to compile and link PLUMED in the desired
+linkage mode. After this step is completed, you can install the
+USER-PLUMED package and compile LAMMPS in the usual manner:
+
+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
@@ -834,7 +981,7 @@ 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]:
@@ -894,6 +1041,45 @@ successfully build on your system.
 
 :line
 
+USER-SCAFACOS package :h4,link(user-scafacos)
+
+To build with this package, you must download and build the "ScaFaCoS
+Coulomb solver library"_scafacos-home
+
+: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_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
+and built inside the CMake build directory.  If the ScaFaCoS library
+is already on your system (in a location CMake cannot find it),
+SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
+file, not the directory the library file is in.  SCAFACOS_INCLUDE_DIR
+is the directory the ScaFaCoS include file is in.
+
+[Traditional make]:
+
+You can download and build the ScaFaCoS library manually if you
+prefer; follow the instructions in lib/scafacos/README.  You can also
+do it in one step from the lammps/src dir, using a command like these,
+which simply invoke the lib/scafacos/Install.py script with the
+specified args:
+
+make lib-scafacos                         # print help message
+make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>
+make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/scafacos to point to the ScaFaCoS src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/scafacos/Makefile.lammps file.
+
+:line
+
 USER-SMD package :h4,link(user-smd)
 
 To build with this package, you must download the Eigen3 library.

doc/src/Build_package.txt

@@ -42,6 +42,7 @@ packages:
 "KOKKOS"_Build_extras.html#kokkos,
 "LATTE"_Build_extras.html#latte,
 "MEAM"_Build_extras.html#meam,
+"MESSAGE"_Build_extras.html#message,
 "MSCG"_Build_extras.html#mscg,
 "OPT"_Build_extras.html#opt,
 "POEMS"_Build_extras.html#poems,
@@ -55,9 +56,11 @@ 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,
+"USER-SCAFACOS"_Build_extras.html#user-scafacos,
 "USER-SMD"_Build_extras.html#user-smd,
 "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
 

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,
@@ -71,6 +72,7 @@ An alphabetic list of all LAMMPS commands.
 "lattice"_lattice.html,
 "log"_log.html,
 "mass"_mass.html,
+"message"_message.html,
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
@@ -103,6 +105,7 @@ An alphabetic list of all LAMMPS commands.
 "restart"_restart.html,
 "run"_run.html,
 "run_style"_run_style.html,
+"server"_server.html,
 "set"_set.html,
 "shell"_shell.html,
 "special_bonds"_special_bonds.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,
@@ -34,7 +34,7 @@ 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,
 "morse (o)"_bond_morse.html,
@@ -57,9 +57,11 @@ 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,
@@ -70,7 +72,7 @@ OPT.
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
 "quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html,
+"sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
 
 :line
@@ -97,7 +99,7 @@ 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)
 
@@ -112,7 +114,7 @@ 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,
@@ -120,5 +122,6 @@ OPT.
 "distance"_improper_distance.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
+"inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.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,
@@ -35,6 +36,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "bond/local"_compute_bond_local.html,
 "centro/atom"_compute_centro_atom.html,
 "chunk/atom"_compute_chunk_atom.html,
+"chunk/spread/atom"_compute_chunk_spread_atom.html,
 "cluster/atom"_compute_cluster_atom.html,
 "cna/atom"_compute_cna_atom.html,
 "cnp/atom"_compute_cnp_atom.html,
@@ -91,12 +93,15 @@ 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,
 "property/local"_compute_property_local.html,
+"ptm/atom"_compute_ptm_atom.html,
 "rdf"_compute_rdf.html,
 "reduce"_compute_reduce.html,
+"reduce/chunk"_compute_reduce_chunk.html,
 "reduce/region"_compute_reduce.html,
 "rigid/local"_compute_rigid_local.html,
 "saed"_compute_saed.html,
@@ -115,7 +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_mesh_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,
@@ -126,6 +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,
@@ -133,6 +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,
@@ -65,16 +67,19 @@ OPT.
 "eos/table/rx (k)"_fix_eos_table_rx.html,
 "evaporate"_fix_evaporate.html,
 "external"_fix_external.html,
+"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,
@@ -91,6 +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,
@@ -106,15 +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,
@@ -123,7 +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,
@@ -142,6 +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,
@@ -168,27 +176,28 @@ OPT.
 "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,
@@ -216,7 +225,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
+"wall/gran (o)"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
@@ -226,4 +235,4 @@ 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,
@@ -33,4 +33,5 @@ OPT.
 "pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,
 "pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
+"pppm/tip4p (o)"_kspace_style.html,
+"scafacos"_kspace_style.html :tb(c=4,ea=c)

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,
@@ -26,13 +26,13 @@ OPT.
 
 "none"_pair_none.html,
 "zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
+"hybrid (k)"_pair_hybrid.html,
 "hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
 
 "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,
@@ -42,21 +42,23 @@ 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,
@@ -66,13 +68,13 @@ OPT.
 "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/cs (g)"_pair_cs.html,
 "coul/long/soft (o)"_pair_lj_soft.html,
-"coul/msm"_pair_coul.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,
@@ -81,6 +83,7 @@ OPT.
 "eam (gikot)"_pair_eam.html,
 "eam/alloy (gikot)"_pair_eam.html,
 "eam/cd (o)"_pair_eam.html,
+"eam/cd/old (o)"_pair_eam.html,
 "eam/fs (gikot)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
@@ -90,11 +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,
@@ -109,9 +112,9 @@ OPT.
 "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_lj_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,
@@ -124,12 +127,12 @@ OPT.
 "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/cs"_pair_cs.html,
 "lj/cut/coul/long/soft (o)"_pair_lj_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/thole/long (o)"_pair_thole.html,
@@ -137,15 +140,17 @@ OPT.
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
 "lj/cut/tip4p/long/soft (o)"_pair_lj_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,
 "lj96/cut (go)"_pair_lj96.html,
@@ -160,14 +165,14 @@ OPT.
 "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/smooth/linear (o)"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nb3b/harmonic"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.html,
 "nm/cut/coul/long (o)"_pair_nm.html,
@@ -179,7 +184,9 @@ 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,
@@ -189,11 +196,12 @@ OPT.
 "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,
@@ -225,8 +233,8 @@ OPT.
 "tip4p/long/soft (o)"_pair_lj_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/ptm_rmsd.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
+
+\begin{document}
+
+\begin{equation*}
+\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+\norm{
+s[\vec{u_i} - \mean{\set{u}}]
+-
+\set{Q} \vec{v_i}
+}^2}
+\end{equation*}
+
+\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_messages.txt

@@ -421,9 +421,9 @@ 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 +460,7 @@ 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 +780,7 @@ 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
 
@@ -1092,11 +1092,6 @@ correct. :dd
 The specified file cannot be opened.  Check that the path and name are
 correct. :dd
 
-{Cannot open fix ave/spatial file %s} :dt
-
-The specified file cannot be opened.  Check that the path and name are
-correct. :dd
-
 {Cannot open fix ave/time file %s} :dt
 
 The specified file cannot be opened.  Check that the path and name are
@@ -1293,7 +1288,7 @@ 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
@@ -1677,10 +1672,6 @@ provided by an atom map.  An atom map does not exist (by default) for
 non-molecular problems.  Using the atom_modify map command will force
 an atom map to be created. :dd
 
-{Cannot use fix ave/spatial z for 2 dimensional model} :dt
-
-Self-explanatory. :dd
-
 {Cannot use fix bond/break with non-molecular systems} :dt
 
 Only systems with bonds that can be changed can be used.  Atom_style
@@ -2125,29 +2116,29 @@ 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
@@ -2425,10 +2416,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Compute ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Compute ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -3364,21 +3351,21 @@ 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
@@ -4074,10 +4061,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Fix ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Fix ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -4379,51 +4362,6 @@ same style. :dd
 
 Self-explanatory. :dd
 
-{Fix ave/spatial compute does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial compute does not calculate a per-atom vector} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute does not calculate per-atom values} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom vector} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix does not calculate per-atom values} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial for triclinic boxes requires units reduced} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial settings invalid with changing box size} :dt
-
-If the box size changes, only the units reduced option can be
-used. :dd
-
-{Fix ave/spatial variable is not atom-style variable} :dt
-
-A variable used by fix ave/spatial must generate per-atom values. :dd
-
 {Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
 
 One of more of the vector inputs has individual elements which are
@@ -6000,9 +5938,9 @@ 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
 
@@ -7076,7 +7014,7 @@ 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
@@ -8076,7 +8014,7 @@ 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
@@ -9260,7 +9198,7 @@ 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
 
@@ -9472,7 +9410,7 @@ 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

@@ -291,24 +291,6 @@ This may cause accuracy problems. :dd
 
 This may cause accuracy problems. :dd
 
-{Fix thermal/conductivity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that fix
-thermal/conductivity comes first.  If you are using fix ave/spatial to
-measure the temperature profile induced by fix viscosity, then this
-may cause a glitch in the profile since you are averaging immediately
-after swaps have occurred.  Flipping the order of the 2 fixes
-typically helps. :dd
-
-{Fix viscosity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that
-fix viscosity comes first.  If you are using fix ave/spatial
-to measure the velocity profile induced by fix viscosity, then
-this may cause a glitch in the profile since you are averaging
-immediately after swaps have occurred.  Flipping the order
-of the 2 fixes typically helps. :dd
-
 {Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
 
 This is current restriction with Kokkos. :dd
@@ -775,7 +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
 
@@ -868,10 +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
@@ -54,6 +54,7 @@ General howto :h3
    Howto_replica
    Howto_library
    Howto_couple
+   Howto_client_server
 
 END_RST -->
 
@@ -64,7 +65,8 @@ END_RST -->
 "Run multiple simulations from one input script"_Howto_multiple.html
 "Multi-replica simulations"_Howto_replica.html
 "Library interface to LAMMPS"_Howto_library.html
-"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+"Couple LAMMPS to other codes"_Howto_couple.html
+"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
 
 <!-- END_HTML_ONLY -->
 

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 3 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
@@ -83,8 +83,9 @@ chunk.
 
 Compute */chunk commands: :h4
 
-Currently the following computes operate on chunks of atoms to produce
-per-chunk values.
+The following computes operate on chunks of atoms to produce per-chunk
+values.  Any compute whose style name ends in "/chunk" is in this
+category:
 
 "compute com/chunk"_compute_com_chunk.html
 "compute gyration/chunk"_compute_gyration_chunk.html
@@ -111,8 +112,8 @@ of a center of mass, which requires summing mass*position over the
 atoms and then dividing by summed mass.
 
 All of these computes produce a global vector or global array as
-output, wih one or more values per chunk.  They can be used
-in various ways:
+output, wih one or more values per chunk.  The output can be used in
+various ways:
 
 As input to the "fix ave/time"_fix_ave_time.html command, which can
 write the values to a file and optionally time average them. :ulb,l
@@ -122,9 +123,27 @@ histogram values across chunks.  E.g. a histogram of cluster sizes or
 molecule diffusion rates. :l
 
 As input to special functions of "equal-style
-variables"_variable.html, like sum() and max().  E.g. to find the
-largest cluster or fastest diffusing molecule. :l
-:ule
+variables"_variable.html, like sum() and max() and ave().  E.g. to
+find the largest cluster or fastest diffusing molecule or average
+radius-of-gyration of a set of molecules (chunks). :l,ule
+
+Other chunk commands: :h4
+
+"compute chunk/spread/atom"_compute_chunk_spread_atom.html
+"compute reduce/chunk"_compute_reduce_chunk.html :ul
+
+The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
+spreads per-chunk values to each atom in the chunk, producing per-atom
+values as its output.  This can be useful for outputting per-chunk
+values to a per-atom "dump file"_dump.html.  Or for using an atom's
+associated chunk value in an "atom-style variable"_variable.html.
+
+The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
+peratom value across the atoms in each chunk to produce a value per
+chunk.  When used with the "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html command it can
+create peratom values that induce a new set of chunks with a second
+"compute chunk/atom"_compute_chunk_atom.html command.
 
 Example calculations with chunks :h4
 
@@ -164,3 +183,13 @@ compute cluster all cluster/atom 1.0
 compute cc1 all chunk/atom c_cluster compress yes
 compute size all property/chunk cc1 count
 fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
+
+(6) An example of using a per-chunk value to apply per-atom forces to
+compress individual polymer chains (molecules) in a mixture, is
+explained on the "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
+
+(7) An example of using one set of per-chunk values for molecule
+chunks, to create a 2nd set of micelle-scale chunks (clustered
+molecules, due to hydrophobicity), is explained on the "compute
+chunk/reduce"_compute_reduce_chunk.html command doc page.

doc/src/Howto_client_server.txt

@@ -0,0 +1,131 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Using LAMMPS in client/server mode :h3
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages to a "server" code.  The server responds to
+each request with a reply message.  This enables the two codes to work
+in tandem to perform a simulation.  LAMMPS can act as either a client
+or server code.
+
+Some advantages of client/server coupling are that the two codes run
+as stand-alone executables; they are not linked together.  Thus
+neither code needs to have a library interface.  This often makes it
+easier to run the two codes on different numbers of processors.  If a
+message protocol (format and content) is defined for a particular kind
+of simulation, then in principle any code that implements the
+client-side protocol can be used in tandem with any code that
+implements the server-side protocol, without the two codes needing to
+know anything more specific about each other.
+
+A simple example of client/server coupling is where LAMMPS is the
+client code performing MD timestepping.  Each timestep it sends a
+message to a server quantum code containing current coords of all the
+atoms.  The quantum code computes energy and forces based on the
+coords.  It returns them as a message to LAMMPS, which completes the
+timestep.
+
+Alternate methods for code coupling with LAMMPS are described on
+the "Howto couple"_Howto_couple.html doc page.
+
+LAMMPS support for client/server coupling is in its "MESSAGE
+package"_Packages_details.html#PKG-MESSAGE which implements several
+commands that enable LAMMPS to act as a client or server, as discussed
+below.  The MESSAGE package also wraps a client/server library called
+CSlib which enables two codes to exchange messages in different ways,
+either via files, sockets, or MPI.  The CSlib is provided with LAMMPS
+in the lib/message dir.  The CSlib has its own
+"website"_http://cslib.sandia.gov with documentation and test
+programs.
+
+NOTE: For client/server coupling to work between LAMMPS and another
+code, the other code also has to use the CSlib.  This can sometimes be
+done without any modifications to the other code by simply wrapping it
+with a Python script that exchanges CSlib messages with LAMMPS and
+prepares input for or processes output from the other code.  The other
+code also has to implement a matching protocol for the format and
+content of messages that LAMMPS exchanges with it.
+
+These are the commands currently in the MESSAGE package for two
+protocols, MD and MC (Monte Carlo).  New protocols can easily be
+defined and added to this directory, where LAMMPS acts as either the
+client or server.
+
+"message"_message.html
+"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
+"server md"_server_md.html = LAMMPS is a server for computing MD forces
+"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 between the client and server.
+
+These example directories illustrate how to use LAMMPS as either a
+client or server code:
+
+examples/message
+examples/COUPLE/README
+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.
+
+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.
+
+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 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
+background.  For all modes except {mpi/one}, you could also launch the
+codes in separate windows on your desktop machine.  It does not
+matter whether you launch the client or server first.
+
+In these examples either code can be run on one or more processors.
+If running in a non-MPI mode (file or zmq) you can launch a code on a
+single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch both codes via
+mpirun, even if one or both of them runs on a single processor.  This
+is so that MPI can figure out how to connect both MPI processes
+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 2 lmp_mpi -log log.server < in.server :pre
+
+% 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 4 lmp_mpi -log log.server < in.server :pre
+
+For message exchange in {mpi/one} mode:
+
+Launch both codes in a single mpirun command:
+
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as their its option, where color is an integer
+label that will be used to distinguish one executable from another in
+the multiple executables that the mpirun command launches.  In this
+example the client was colored with a 0, and the server with a 1.

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

@@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS.  Or a continuum finite element
 nodal points, compute a FE solution, and return interpolated forces on
 MD atoms.
 
-LAMMPS can be coupled to other codes in at least 3 ways.  Each has
+LAMMPS can be coupled to other codes in at least 4 ways.  Each has
 advantages and disadvantages, which you'll have to think about in the
 context of your application.
 
+:line
+
 (1) Define a new "fix"_fix.html command that calls the other code.  In
 this scenario, LAMMPS is the driver code.  During its timestepping,
 the fix is invoked, and can make library calls to the other code,
@@ -32,6 +34,8 @@ LAMMPS.
 
 :link(poems,http://www.rpi.edu/~anderk5/lab)
 
+:line
+
 (2) Define a new LAMMPS command that calls the other code.  This is
 conceptually similar to method (1), but in this case LAMMPS and the
 other code are on a more equal footing.  Note that now the other code
@@ -52,6 +56,8 @@ command writes and reads.
 See the "Modify command"_Modify_command.html doc page for info on how
 to add a new command to LAMMPS.
 
+:line
+
 (3) Use LAMMPS as a library called by another code.  In this case the
 other code is the driver and calls LAMMPS as needed.  Or a wrapper
 code could link and call both LAMMPS and another code as libraries.
@@ -102,3 +108,9 @@ on all the processors.  Or it might allocate half the processors to
 LAMMPS and half to the other code and run both codes simultaneously
 before syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
+
+:line
+
+(4) Couple LAMMPS with another code in a client/server mode.  This is
+described on the "Howto client/server"_Howto_client_server.html doc
+page.

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

@@ -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

@@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms.  The
 velocity profile or other properties of the fluid can be monitored via
 the "fix ave/chunk"_fix_ave_chunk.html command.
 
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermostatting generally, for both simple and complex fluids,
+e.g. molecular systems.  The latter can be tricky to do correctly.
+
 As discussed in the previous section on non-orthogonal simulation
 boxes, the amount of tilt or skew that can be applied is limited by
 LAMMPS for computational efficiency to be 1/2 of the parallel box
@@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
 NEMD simulations can also be used to measure transport properties of a fluid
 through a pore or channel. Simulations of steady-state flow can be performed
 using the "fix flow/gauss"_fix_flow_gauss.html command.
+
+:line
+
+:link(Daivis-nemd)
+[(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

@@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
 velocities but also rotational velocities for spherical and aspherical
 particles.
 
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermostatting generally, for both simple and complex fluids,
+e.g. molecular systems.  The latter can be tricky to do correctly.
+
 DPD thermostatting alters pairwise interactions in a manner analogous
 to the per-particle thermostatting of "fix
 langevin"_fix_langevin.html.
@@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
 custom"_thermo_style.html command.  Or you can use the
 "thermo_modify"_thermo_modify.html command to re-define what
 temperature compute is used for default thermodynamic output.
+
+:line
+
+:link(Daivis-thermostat)
+[(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

@@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of
 thermostat that modifies only the thermal (non-shearing) components of
 velocity to prevent the fluid from heating up.
 
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermostatting generally, for both simple and complex fluids,
+e.g. molecular systems.  The latter can be tricky to do correctly.
+
 In both cases, the velocity profile setup in the fluid by this
 procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
 command, which determines grad(Vstream) in the equation above.
@@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
 time-integrated momentum fluxes play the role of Cartesian
 coordinates, whose mean-square displacement increases linearly
 with time at sufficiently long times.
+
+:line
+
+:link(Daivis-viscosity)
+[(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

@@ -45,7 +45,7 @@ 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:

doc/src/Install_linux.txt

@@ -9,39 +9,16 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Download an executable for Linux :h3
 
-Binaries are available for many different versions of Linux:
+Binaries are available for different versions of Linux:
 
-"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
 "Pre-built Ubuntu Linux executables"_#ubuntu
+"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)
 
 :line
 
-Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
-
-Pre-built LAMMPS executables for various Linux distributions
-can be downloaded as binary RPM files from this site:
-
-"http://rpm.lammps.org"_http://rpm.lammps.org
-
-There are multiple package variants supporting serial, parallel and
-Python wrapper versions.  The LAMMPS binaries contain all optional
-packages included in the source distribution except: GPU, KIM, REAX,
-and USER-INTEL.
-
-Installation instructions for the various versions are here:
-
-"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
-
-The instructions show how to enable the repository in the respective
-system's package management system.  Installing and updating are then
-straightforward and automatic.  
-
-Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
-up this RPM capability.
-
-:line
-
 Pre-built Ubuntu Linux executables :h4,link(ubuntu)
 
 A pre-built LAMMPS executable suitable for running on the latest
@@ -60,10 +37,10 @@ To install LAMMPS do the following once:
 
 sudo apt-get install lammps-daily :pre
 
-This downloads an executable named "lammps-daily" to your box, which
+This downloads an executable named "lmp_daily" to your box, which
 can then be used in the usual way to run input scripts:
 
-lammps-daily < in.lj :pre
+lmp_daily -in in.lj :pre
 
 To update LAMMPS to the most current version, do the following:
 
@@ -99,6 +76,80 @@ Ubuntu package capability.
 
 :line
 
+Pre-built Fedora Linux executables :h4,link(fedora)
+
+Pre-built LAMMPS packages for stable releases are available
+in the Fedora Linux distribution as of version 28. The packages
+can be installed via the dnf package manager. There are 3 basic
+varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+lammps-openmpi = OpenMPI MPI library) and for each support for
+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
+("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
+Then the corresponding parallel LAMMPS executable is 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:
+
+dnf install lammps-openmpi
+module load mpi/openmpi-x86_64
+mpirun -np 2 lmp -in in.lj :pre
+
+The "dnf install" command is needed only once. In case of a new LAMMPS
+stable release, "dnf update" will automatically update to the newer
+version as soon at the RPM files are built and uploaded to the download
+mirrors. The "module load" command is needed once per (shell) session
+or shell terminal instance, unless it is automatically loaded from the
+shell profile.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
+
+:line
+
+Pre-built EPEL Linux executable :h4,link(epel)
+
+Pre-built LAMMPS packages for stable releases are available
+in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL
+for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
+and compatible Linux distributions. Names of packages, executable,
+and content are the same as described above for Fedora Linux.
+But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
+in Fedora 28.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
+
+:line
+
+Pre-built OpenSuse Linux executable :h4,link(opensuse)
+
+A pre-built LAMMPS package for stable releases is available
+in OpenSuse as of Leap 15.0. You can install the package with:
+
+zypper install lammps :pre
+
+This includes support for OpenMPI. The name of the LAMMPS executable
+is {lmp}. Thus to run an input in parallel on 2 CPUs you would do:
+
+mpirun -np 2 lmp -in in.lj :pre
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
+
+:line
+
 Pre-built Gentoo Linux executable :h4,link(gentoo)
 
 LAMMPS is part of Gentoo's main package tree and can be installed by

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_tarball.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Download source as a tarball :h3
+Download source and documentation as a tarball :h3
 
 You can download a current LAMMPS tarball from the "download page"_download
 of the "LAMMPS website"_lws.
@@ -22,6 +22,10 @@ few times per year, and undergo more testing before release.  Patch
 releases occur a couple times per month.  The new contents in all
 releases are listed on the "bug and feature page"_bug of the website.
 
+Both tarballs include LAMMPS documentation (HTML and PDF files)
+corresponding to that version.  The download page also has an option
+to download the current-version LAMMPS documentation by itself.
+
 Older versions of LAMMPS can also be downloaded from "this
 page"_older.
 

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

@@ -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

@@ -13,15 +13,19 @@ 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 thru a GUI
+build 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 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
@@ -29,7 +33,7 @@ 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
 of them convert input files in formats produced by other MD codes such
@@ -40,28 +44,36 @@ 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 to reconstruct topology, as well as
+the option to insert molecule templates instead of atoms.:l
 
 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. :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
+on-the-fly via its "dump image"_dump_image.html command and pass
+them to an external program FFmpeg to generate movies from them.  For
 high-quality, interactive visualization there are many excellent and
 free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="31 Aug 2018 version">
+<META NAME="docnumber" CONTENT="27 Nov 2018 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-31 Aug 2018 version :c,h2
+27 Nov 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Manual_build.txt

@@ -61,7 +61,7 @@ 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

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.

doc/src/Modify_pair.txt

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

doc/src/Modify_region.txt

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

doc/src/Packages_details.txt

@@ -46,6 +46,7 @@ as contained in the file name.
 "MANYBODY"_#PKG-MANYBODY,
 "MC"_#PKG-MC,
 "MEAM"_#PKG-MEAM,
+"MESSAGE"_#PKG-MESSAGE,
 "MISC"_#PKG-MISC,
 "MOLECULE"_#PKG-MOLECULE,
 "MPIIO"_#PKG-MPIIO,
@@ -88,10 +89,14 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"USER-PLUMED"_#PKG-USER-PLUMED,
+"USER-PTM"_#PKG-USER-PTM,
 "USER-QMMM"_#PKG-USER-QMMM,
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
 "USER-REAXC"_#PKG-USER-REAXC,
+"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
+"USER-SDPD"_#PKG-USER-SDPD,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -200,7 +205,7 @@ available on your system.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -281,7 +286,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
 [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
 (Northwestern U) while at ORNL.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -349,7 +354,7 @@ API which the "pair_style kim"_pair_kim.html command uses.  He
 developed the pair style in collaboration with Valeriu Smirichinski (U
 Minnesota).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -395,7 +400,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
 Sandia, and which is included in the LAMMPS distribution in
 lib/kokkos.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -459,10 +464,10 @@ dynamics can be run with LAMMPS using density-functional tight-binding
 quantum forces calculated by LATTE.
 
 More information on LATTE can be found at this web site:
-"https://github.com/lanl/LATTE"_latte_home.  A brief technical
+"https://github.com/lanl/LATTE"_latte-home.  A brief technical
 description is given with the "fix latte"_fix_latte.html command.
 
-:link(latte_home,https://github.com/lanl/LATTE)
+:link(latte-home,https://github.com/lanl/LATTE)
 
 [Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
 itself is developed at Los Alamos National Laboratory by Marc
@@ -489,7 +494,7 @@ MANYBODY package :link(PKG-MANYBODY),h4
 
 [Contents:]
 
-A variety of manybody and bond-order potentials.  These include
+A variety of many-body and bond-order potentials.  These include
 (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
 
 [Supporting info:]
@@ -513,7 +518,7 @@ MC package :link(PKG-MC),h4
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjuction with dynamics.
+(GCMC) in conjunction with dynamics.
 
 [Supporting info:]
 
@@ -543,16 +548,12 @@ and user interface.
 
 [Author:] Greg Wagner (Northwestern U) while at Sandia.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
 extras"_Build_extras.html doc page.
 
-NOTE: You should test building the MEAM library with both the Intel
-and GNU compilers to see if a simulation runs faster with one versus
-the other on your system.
-
 [Supporting info:]
 
 src/MEAM: filenames -> commands
@@ -563,6 +564,31 @@ examples/meam :ul
 
 :line
 
+MESSAGE package :link(PKG-MESSAGE),h4
+
+[Contents:]
+
+Commands to use LAMMPS as either a client or server and couple it to
+another application.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#message on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/MESSAGE: filenames -> commands
+lib/message/README
+"message"_message.html
+"fix client/md"_fix_client_md.html
+"server md"_server_md.html
+"server mc"_server_mc.html
+examples/message :ul
+
+:line
+
 MISC package :link(PKG-MISC),h4
 
 [Contents:]
@@ -644,9 +670,9 @@ MSCG package :link(PKG-mscg),h4
 
 A "fix mscg"_fix_mscg.html command which can parameterize a
 Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
-library"_mscg_home.
+library"_mscg-home.
 
-:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
+:link(mscg-home,https://github.com/uchicago-voth/MSCG-release)
 
 To use this package you must have the MS-CG library available on your
 system.
@@ -655,7 +681,7 @@ system.
 library was developed by Jacob Wagner in Greg Voth's group at the
 University of Chicago.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -687,7 +713,7 @@ have styles optimized for CPU performance.
 [Authors:] James Fischer (High Performance Technologies), David Richie,
 and Vincent Natoli (Stone Ridge Technolgy).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -744,7 +770,7 @@ connections at hinge points.
 
 [Author:] Rudra Mukherjee (JPL) while at RPI.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -776,7 +802,7 @@ shared library available on your system, which needs to be a Python 2
 version, 2.6 or later.  Python 3 is not yet supported.  See the
 lib/python/README for more details.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -824,7 +850,7 @@ as bonds are created and destroyed.
 
 [Author:] Aidan Thompson (Sandia).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -984,11 +1010,11 @@ VORONOI package :link(PKG-VORONOI),h4
 [Contents:]
 
 A compute command which calculates the Voronoi tesselation of a
-collection of atoms by wrapping the "Voro++ library"_voro_home.  This
+collection of atoms by wrapping the "Voro++ library"_voro-home.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-:link(voro_home,http://math.lbl.gov/voro++)
+:link(voro-home,http://math.lbl.gov/voro++)
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -997,7 +1023,7 @@ system.
 library was written by Chris Rycroft (Harvard U) while at UC Berkeley
 and LBNL.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1024,7 +1050,7 @@ atomic information to continuum fields.
 
 [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1051,7 +1077,7 @@ model.
 
 [Author:] Ilya Valuev (JIHT, Russia).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1074,7 +1100,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
 of "fix npt"_fix_nh.html which includes the pressure correction to
 the barostat as outlined in:
 
-N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
 molecular liquids," J. Chem. Phys. 143, 243148 (2015).
 
@@ -1159,10 +1185,10 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
 the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
 (Temple U) provided the interface to LAMMPS.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-colvars on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1176,6 +1202,36 @@ examples/USER/colvars :ul
 
 :line
 
+USER-PLUMED package :link(PKG-USER-PLUMED),h4
+
+[Contents:]
+
+The fix plumed command allows you to use the PLUMED free energy plugin
+for molecular dynamics to analyze and bias your LAMMPS trajectory on
+the fly.  The PLUMED library is called from within the LAMMPS input
+script by using the "fix plumed _fix_plumed.html command.
+
+[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
+Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
+Tribello.
+
+:link(PLUMED,http://www.plumed.org)
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-PLUMED/README
+lib/plumed/README
+"fix plumed"_fix_plumed.html
+examples/USER/plumed :ul
+
+:line
+
 USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
 
 [Contents:]
@@ -1339,7 +1395,7 @@ system.
 [Author:] Pierre de Buyl (KU Leuven) created both the package and the
 H5MD format.
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1377,7 +1433,7 @@ NOTE: the USER-INTEL package contains styles that require using the
 
 [Author:] Mike Brown (Intel).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1496,7 +1552,7 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
 [Contents:]
 
 A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_MEAM package
+translated from the Fortran version in the "MEAM"_#PKG-MEAM package
 to plain C++. In contrast to the MEAM package, no library
 needs to be compiled and the pair style can be instantiated
 multiple times.
@@ -1547,17 +1603,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
 [Contents:]
 
 Pair, angle and improper styles needed to employ the MOF-FF
-force field by Schmid and coworkers with LAMMPS. 
+force field by Schmid and coworkers with LAMMPS.
 MOF-FF is a first principles derived force field with the primary aim
-to simulate MOFs and related porous framework materials, using spherical 
+to simulate MOFs and related porous framework materials, using spherical
 Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
 2013, 250, 1128-1141.
-For the usage of MOF-FF see the example in the example directory as 
+For the usage of MOF-FF see the example in the example directory as
 well as the "MOF+"_MOFplus website.
 
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
 
-[Author:] Hendrik Heenen (Technical U of Munich), 
+[Author:] Hendrik Heenen (Technical U of Munich),
 Rochus Schmid (Ruhr-University Bochum).
 
 [Supporting info:]
@@ -1577,7 +1633,7 @@ USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
 [Contents:]
 
 A "dump molfile"_dump_molfile.html command which uses molfile plugins
-that are bundled with the "VMD"_vmd_home
+that are bundled with the "VMD"_vmd-home
 molecular visualization and analysis program, to enable LAMMPS to dump
 snapshots in formats compatible with various molecular simulation
 tools.
@@ -1598,7 +1654,7 @@ at
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1629,16 +1685,16 @@ Note that NetCDF files can be directly visualized with the following
 tools:
 
 "Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
-"VMD"_vmd_home
+"VMD"_vmd-home
 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
 
 :link(ovito,http://www.ovito.org)
-:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
+:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/)
 :link(atomeye,http://www.libatoms.org)
 
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1682,7 +1738,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1721,6 +1777,25 @@ examples/USER/phonon :ul
 
 :line
 
+USER-PTM package :link(PKG-USER-PTM),h4
+
+[Contents:]
+
+A "compute ptm/atom"_compute_ptm_atom.html command that calculates
+local structure characterization using the Polyhedral Template
+Matching methodology.
+
+[Author:] Peter Mahler Larsen (MIT).
+
+[Supporting info:]
+
+src/USER-PTM: filenames not starting with ptm_ -> commands
+src/USER-PTM: filenames starting with ptm_ -> supporting code
+src/USER-PTM/LICENSE
+"compute ptm/atom"_compute_ptm_atom.html :ul
+
+:line
+
 USER-QMMM package :link(PKG-USER-QMMM),h4
 
 [Contents:]
@@ -1742,7 +1817,7 @@ without changes to LAMMPS itself.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1800,7 +1875,7 @@ on your system.
 
 [Author:] Albert Bartok (Cambridge University)
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1838,6 +1913,66 @@ examples/reax :ul
 
 :line
 
+USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
+
+[Contents:]
+
+A KSpace style which wraps the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de to compute long-range Coulombic
+interactions.
+
+To use this package you must have the ScaFaCoS library available on
+your system.
+
+[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS itself was developed by a consortium of German research
+facilities with a BMBF (German Ministry of Science and Education)
+funded project in 2009-2012. Participants of the consortium were the
+Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
+the Forschungszentrum Juelich.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-scafacos on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-SCAFACOS: filenames -> commands
+src/USER-SCAFACOS/README
+"kspace_style scafacos"_kspace_style.html
+"kspace_modify"_kspace_modify.html
+examples/USER/scafacos :ul
+
+:line
+
+USER-SDPD package :link(PKG-USER-SDPD),h4
+
+[Contents:]
+
+A pair style for smoothed dissipative particle dynamics (SDPD), which
+is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
+where thermal fluctuations are important (see the
+"USER-SPH package"_#PKG-USER-SPH).
+Also two fixes for moving and rigid body integration of SPH/SDPD particles
+(particles of atom_style meso).
+
+[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
+Sciences, Iran).
+
+[Supporting info:]
+
+src/USER-SDPD: filenames -> commands
+src/USER-SDPD/README
+"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
+"fix meso/move"_fix_meso_move.html
+"fix rigid/meso"_fix_rigid_meso.html
+examples/USER/sdpd :ul
+
+:line
+
 USER-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]
@@ -1859,7 +1994,7 @@ specified as surface geometries from *.STL files.
 [Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
 Dynamics, Ernst Mach Institute, Germany).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1985,7 +2120,7 @@ system.
 
 [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build

doc/src/Packages_standard.txt

@@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library
 "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
 "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
 "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
 "MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
 "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
 "MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no

doc/src/Packages_user.txt

@@ -38,8 +38,8 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
-"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
-"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
+"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
 "USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
 "USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
@@ -62,13 +62,20 @@ Package, Description, Doc page, Example, Library
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext
+"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
 "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
+"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
+"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, USER/sdpd, no
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
 "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
 "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
 "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
 "USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+
+:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
+:link(PLUMED,http://www.plumed.org)

doc/src/Python_call.txt

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

doc/src/Python_examples.txt

@@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
 :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
 :link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
 
-The latter link is to AtomEye 3 which has the scriping
+The latter link is to AtomEye 3 which has the scripting
 capability needed by these Python scripts.
 
 Note that for PyMol, you need to have built and installed the

doc/src/Run_options.txt

@@ -18,13 +18,15 @@ letter abbreviation can be used:
 "-i or -in"_#file
 "-k or -kokkos"_#run-kokkos
 "-l or -log"_#log
+"-m or -mpicolor"_#mpicolor
 "-nc or -nocite"_#nocite
 "-pk or -package"_#package
 "-p or -partition"_#partition
 "-pl or -plog"_#plog
 "-ps or -pscreen"_#pscreen
-"-r or -restart"_#restart
 "-ro or -reorder"_#reorder
+"-r2data or -restart2data"_#restart2data
+"-r2dump or -restart2dump"_#restart2dump
 "-sc or -screen"_#screen
 "-sf or -suffix"_#suffix
 "-v or -var"_#var :ul
@@ -175,6 +177,30 @@ Option -plog will override the name of the partition log files file.N.
 
 :line
 
+[-mpicolor] color :link(mpicolor)
+
+If used, this must be the first command-line argument after the LAMMPS
+executable name.  It is only used when LAMMPS is launched by an mpirun
+command which also launches another executable(s) at the same time.
+(The other executable could be LAMMPS as well.)  The color is an
+integer value which should be different for each executable (another
+application may set this value in a different way).  LAMMPS and the
+other executable(s) perform an MPI_Comm_split() with their own colors
+to shrink the MPI_COMM_WORLD communication to be the subset of
+processors they are actually running on.
+
+Currently, this is only used in LAMMPS to perform client/server
+messaging with another application.  LAMMPS can act as either a client
+or server (or both).  More details are given on the "Howto
+client/server"_Howto_client_server.html doc page.
+
+Specifically, this refers to the "mpi/one" mode of messaging provided
+by the "message"_message.html command and the CSlib library LAMMPS
+links with from the lib/message directory.  See the
+"message"_message.html command for more details.
+
+:line
+
 [-nocite] :link(nocite)
 
 Disable writing the log.cite file which is normally written to list
@@ -255,34 +281,6 @@ specified by the -screen command-line option.
 
 :line
 
-[-restart restartfile {remap} datafile keyword value ...] :link(restart)
-
-Convert the restart file into a data file and immediately exit.  This
-is the same operation as if the following 2-line input script were
-run:
-
-read_restart restartfile {remap}
-write_data datafile keyword value ... :pre
-
-Note that the specified restartfile and datafile can have wild-card
-characters ("*",%") as described by the
-"read_restart"_read_restart.html and "write_data"_write_data.html
-commands.  But a filename such as file.* will need to be enclosed in
-quotes to avoid shell expansion of the "*" character.
-
-Note that following restartfile, the optional flag {remap} can be
-used.  This has the same effect as adding it to the
-"read_restart"_read_restart.html command, as explained on its doc
-page.  This is only useful if the reading of the restart file triggers
-an error that atoms have been lost.  In that case, use of the remap
-flag should allow the data file to still be produced.
-
-Also note that following datafile, the same optional keyword/value
-pairs can be listed as used by the "write_data"_write_data.html
-command.
-
-:line
-
 [-reorder] :link(reorder)
 
 This option has 2 forms:
@@ -356,6 +354,80 @@ the LAMMPS simulation domain.
 
 :line
 
+[-restart2data restartfile \[remap\] datafile keyword value ...]
+:link(restart2data)
+
+Convert the restart file into a data file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+read_restart restartfile \[remap\]
+write_data datafile keyword value ... :pre
+
+The specified restartfile and/or datafile name may contain the wild-card
+character "*".  The restartfile name may also contain the wild-card
+character "%".  The meaning of these characters is explained on the
+"read_restart"_read_restart.html and "write_data"_write_data.html doc
+pages.  The use of "%" means that a parallel restart file can be read.
+Note that a filename such as file.* may need to be enclosed in quotes or
+the "*" character prefixed with a backslash ("\") to avoid shell
+expansion of the "*" character.
+
+Following restartfile argument, the optional word "remap" may be used.
+This has the same effect like adding it to a
+"read_restart"_read_restart.html command, and operates as explained on
+its doc page.  This is useful if reading the restart file triggers an
+error that atoms have been lost.  In that case, use of the remap flag
+should allow the data file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+datafile keyword value ... :pre
+
+is identical to the arguments of the "write_data"_write_data.html
+command.  See its doc page for details.  This includes its
+optional keyword/value settings.
+
+:line
+
+[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
+
+Convert the restart file into a dump file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+read_restart restartfile \[remap\]
+write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
+
+Note that the specified restartfile and dumpfile names may contain
+wild-card characters ("*","%") as explained on the
+"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
+pages.  The use of "%" means that a parallel restart file and/or
+parallel dump file can be read and/or written.  Note that a filename
+such as file.* may need to be enclosed in quotes or the "*" character
+prefixed with a backslash ("\") to avoid shell expansion of the "*"
+character.
+
+Note that following the restartfile argument, the optional word "remap"
+can be used.  This has the effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc page.
+This is useful if reading the restart file triggers an error that atoms
+have been lost.  In that case, use of the remap flag should allow the
+dump file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+group-ID dumpstyle dumpfile arg1 arg2 ... :pre
+
+is identical to the arguments of the "write_dump"_write_dump.html
+command.  See its doc page for details.  This includes what per-atom
+fields are written to the dump file and optional dump_modify settings,
+including ones that affect how parallel dump files are written, e.g.
+the {nfile} and {fileper} keywords.  See the
+"dump_modify"_dump_modify.html doc page for details.
+
+:line
+
 [-screen file] :link(screen)
 
 Specify a file for LAMMPS to write its screen information to.  In
@@ -455,7 +527,7 @@ option is equivalent to putting the line "variable name index value1
 value2 ..."  at the beginning of the input script.  Defining an index
 variable as a command-line argument overrides any setting for the same
 index variable in the input script, since index variables cannot be
-re-defined.  
+re-defined.
 
 See the "variable"_variable.html command for more info on defining
 index and other kinds of variables and the "Commands

doc/src/Run_windows.txt

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

doc/src/Speed.txt

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

doc/src/Speed_intel.txt

@@ -14,11 +14,11 @@ Corporation.  It provides two methods for accelerating simulations,
 depending on the hardware you have.  The first is acceleration on
 Intel CPUs by running in single, mixed, or double precision with
 vectorization.  The second is acceleration on Intel Xeon Phi
-coprocessors via offloading neighbor list and non-bonded force
+co-processors via offloading neighbor list and non-bonded force
 calculations to the Phi.  The same C++ code is used in both cases.
-When offloading to a coprocessor from a CPU, the same routine is run
+When offloading to a co-processor from a CPU, the same routine is run
 twice, once on the CPU and once with an offload flag. This allows
-LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
+LAMMPS to run on the CPU cores and co-processor cores simultaneously.
 
 [Currently Available USER-INTEL Styles:]
 
@@ -27,9 +27,9 @@ Bond Styles: fene, fourier, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
-buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
-lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, 
+Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
+buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
 rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
@@ -47,7 +47,7 @@ These are scalable in size; the results given are with 512K
 particles (524K for Liquid Crystal). Most of the simulations are
 standard LAMMPS benchmarks (indicated by the filename extension in
 parenthesis) with modifications to the run length and to add a
-warmup run (for use with offload benchmarks).
+warm-up run (for use with offload benchmarks).
 
 :c,image(JPG/user_intel.png)
 
@@ -134,19 +134,19 @@ Do not use thread affinity (set KMP_AFFINITY=none) :l
 The "newton off" setting may provide better scalability :l
 :ule
 
-For Intel Xeon Phi coprocessors (Offload):
+For Intel Xeon Phi co-processors (Offload):
 
-Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
+Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l
 "-pk intel N omp 1" added to command-line where N is the number of
-coprocessors per node. :l
+co-processors per node. :l
 :ule
 
 :line
 
 [Required hardware/software:]
 
-In order to use offload to coprocessors, an Intel Xeon Phi
-coprocessor and an Intel compiler are required. For this, the
+In order to use offload to co-processors, an Intel Xeon Phi
+co-processor and an Intel compiler are required. For this, the
 recommended version of the Intel compiler is 14.0.1.106 or
 versions 15.0.2.044 and higher.
 
@@ -214,7 +214,7 @@ Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
 Makefile.knl                # Intel Compiler, Intel MPI, No Offload
 Makefile.intel_cpu_mpich    # Intel Compiler, MPICH, No Offload
 Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
-Makefile.intel_coprocessor  # Intel Compiler, Intel MPI, Offload :pre
+Makefile.intel_co-processor  # Intel Compiler, Intel MPI, Offload :pre
 
 Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
 it explicitly specifies that vectorization should be for Intel Xeon
@@ -227,18 +227,18 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre
 
-Note that if you build with support for a Phi coprocessor, the same
-binary can be used on nodes with or without coprocessors installed.
-However, if you do not have coprocessors on your system, building
+Note that if you build with support for a Phi co-processor, the same
+binary can be used on nodes with or without co-processors installed.
+However, if you do not have co-processors on your system, building
 without offload support will produce a smaller binary.
 
 The general requirements for Makefiles with the USER-INTEL package
-are as follows. When using Intel compilers, "-restrict" is required 
-and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. 
+are as follows. When using Intel compilers, "-restrict" is required
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
 CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
 are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
 (unless Intel Math Kernel Library (MKL) is not available in the build
-environment). For Intel compilers, LIB should include "-ltbbmalloc" 
+environment). For Intel compilers, LIB should include "-ltbbmalloc"
 or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
 to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
 required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
@@ -272,7 +272,7 @@ Advanced performance tuning options are also described below to get
 the best performance.
 
 When running on a single node (including runs using offload to a
-coprocessor), best performance is normally obtained by using 1 MPI
+co-processor), best performance is normally obtained by using 1 MPI
 task per physical core and additional OpenMP threads with SMT. For
 Intel Xeon processors, 2 OpenMP threads should be used for SMT.
 For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
@@ -290,7 +290,7 @@ NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
 threads to a core or group of cores so that memory access can be
 uniform. Unless disabled at build time, affinity for MPI tasks and
 OpenMP threads on the host (CPU) will be set by default on the host
-{when using offload to a coprocessor}. In this case, it is unnecessary
+{when using offload to a co-processor}. In this case, it is unnecessary
 to use other methods to control affinity (e.g. taskset, numactl,
 I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
 option to the "package intel"_package.html command or by disabling the
@@ -310,15 +310,15 @@ editing the input script. This switch will automatically append
 options for the USER-INTEL package.  The default package command will
 specify that USER-INTEL calculations are performed in mixed precision,
 that the number of OpenMP threads is specified by the OMP_NUM_THREADS
-environment variable, and that if coprocessors are present and the
-binary was built with offload support, that 1 coprocessor per node
+environment variable, and that if co-processors are present and the
+binary was built with offload support, that 1 co-processor per node
 will be used with automatic balancing of work between the CPU and the
-coprocessor.
+co-processor.
 
 You can specify different options for the USER-INTEL package by using
 the "-pk intel Nphi" "command-line switch"_Run_options.html with
 keyword/value pairs as specified in the documentation. Here, Nphi = #
-of Xeon Phi coprocessors/node (ignored without offload
+of Xeon Phi co-processors/node (ignored without offload
 support). Common options to the USER-INTEL package include {omp} to
 override any OMP_NUM_THREADS setting and specify the number of OpenMP
 threads, {mode} to set the floating-point precision mode, and {lrt} to
@@ -332,7 +332,7 @@ Examples (see documentation for your MPI/Machine for differences in
 launching MPI applications):
 
 mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
-mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision :pre
+mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre
 
 [Or run with the USER-INTEL package by editing an input script:]
 
@@ -364,7 +364,7 @@ intel"_package.html command that can improve performance when using
 "PPPM"_kspace_style.html for long-range electrostatics on processors
 with SMT. It generates an extra pthread for each MPI task. The thread
 is dedicated to performing some of the PPPM calculations and MPI
-communications. This feature requires setting the preprocessor flag
+communications. This feature requires setting the pre-processor flag
 -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
 in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but
 it is set in all makefiles tuned for the USER-INTEL package.  On Intel
@@ -399,7 +399,7 @@ the "suffix hybrid intel omp"_suffix.html command can also be used
 within the input script to automatically append the "omp" suffix to
 styles when USER-INTEL styles are not available.
 
-NOTE: For simulations on higher node counts, add "processors * * * 
+NOTE: For simulations on higher node counts, add "processors * * *
 grid numa"_processors.html to the beginning of the input script for
 better scalability.
 
@@ -422,29 +422,29 @@ that MPI runs are performed in MCDRAM.
 
 The default settings for offload should give good performance.
 
-When using LAMMPS with offload to Intel coprocessors, best performance
+When using LAMMPS with offload to Intel co-processors, best performance
 will typically be achieved with concurrent calculations performed on
-both the CPU and the coprocessor. This is achieved by offloading only
-a fraction of the neighbor and pair computations to the coprocessor or
+both the CPU and the co-processor. This is achieved by offloading only
+a fraction of the neighbor and pair computations to the co-processor or
 using "hybrid"_pair_hybrid.html pair styles where only one style uses
 the "intel" suffix. For simulations with long-range electrostatics or
 bond, angle, dihedral, improper calculations, computation and data
-transfer to the coprocessor will run concurrently with computations
+transfer to the co-processor will run concurrently with computations
 and MPI communications for these calculations on the host CPU. This
 is illustrated in the figure below for the rhodopsin protein benchmark
 running on E5-2697v2 processors with a Intel Xeon Phi 7120p
-coprocessor. In this plot, the vertical access is time and routines
+co-processor. In this plot, the vertical access is time and routines
 running at the same time are running concurrently on both the host and
-the coprocessor.
+the co-processor.
 
 :c,image(JPG/offload_knc.png)
 
 The fraction of the offloaded work is controlled by the {balance}
 keyword in the "package intel"_package.html command. A balance of 0
 runs all calculations on the CPU.  A balance of 1 runs all
-supported calculations on the coprocessor.  A balance of 0.5 runs half
-of the calculations on the coprocessor.  Setting the balance to -1
-(the default) will enable dynamic load balancing that continously
+supported calculations on the co-processor.  A balance of 0.5 runs half
+of the calculations on the co-processor.  Setting the balance to -1
+(the default) will enable dynamic load balancing that continuously
 adjusts the fraction of offloaded work throughout the simulation.
 Because data transfer cannot be timed, this option typically produces
 results within 5 to 10 percent of the optimal fixed balance.
@@ -455,23 +455,23 @@ near-optimal setting that will carry over to additional runs.
 
 The default for the "package intel"_package.html command is to have
 all the MPI tasks on a given compute node use a single Xeon Phi
-coprocessor.  In general, running with a large number of MPI tasks on
+co-processor.  In general, running with a large number of MPI tasks on
 each node will perform best with offload.  Each MPI task will
 automatically get affinity to a subset of the hardware threads
-available on the coprocessor.  For example, if your card has 61 cores,
+available on the co-processor.  For example, if your card has 61 cores,
 with 60 cores available for offload and 4 hardware threads per core
 (240 total threads), running with 24 MPI tasks per node will cause
-each MPI task to use a subset of 10 threads on the coprocessor.  Fine
+each MPI task to use a subset of 10 threads on the co-processor.  Fine
 tuning of the number of threads to use per MPI task or the number of
 threads to use per core can be accomplished with keyword settings of
 the "package intel"_package.html command.
 
 The USER-INTEL package has two modes for deciding which atoms will be
-handled by the coprocessor.  This choice is controlled with the {ghost}
+handled by the co-processor.  This choice is controlled with the {ghost}
 keyword of the "package intel"_package.html command.  When set to 0,
 ghost atoms (atoms at the borders between MPI tasks) are not offloaded
 to the card.  This allows for overlap of MPI communication of forces
-with computation on the coprocessor when the "newton"_newton.html
+with computation on the co-processor when the "newton"_newton.html
 setting is "on".  The default is dependent on the style being used,
 however, better performance may be achieved by setting this option
 explicitly.
@@ -482,24 +482,24 @@ cores.  This is due to the fact that additional threads are generated
 internally to handle the asynchronous offload tasks.
 
 If pair computations are being offloaded to an Intel Xeon Phi
-coprocessor, a diagnostic line is printed to the screen (not to the
+co-processor, a diagnostic line is printed to the screen (not to the
 log file), during the setup phase of a run, indicating that offload
-mode is being used and indicating the number of coprocessor threads
+mode is being used and indicating the number of co-processor threads
 per MPI task.  Additionally, an offload timing summary is printed at
 the end of each run.  When offloading, the frequency for "atom
 sorting"_atom_modify.html is changed to 1 so that the per-atom data is
 effectively sorted at every rebuild of the neighbor lists. All the
-available coprocessor threads on each Phi will be divided among MPI
+available co-processor threads on each Phi will be divided among MPI
 tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Run_options.html is used to limit the coprocessor threads per
+switch"_Run_options.html is used to limit the co-processor threads per
 MPI task.
 
 [Restrictions:]
 
-When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
+When offloading to a co-processor, "hybrid"_pair_hybrid.html styles
 that require skip lists for neighbor builds cannot be offloaded.
 Using "hybrid/overlay"_pair_hybrid.html is allowed.  Only one intel
-accelerated style may be used with hybrid styles.
+accelerated style may be used with hybrid styles when offloading.
 "Special_bonds"_special_bonds.html exclusion lists are not currently
 supported with offload, however, the same effect can often be
 accomplished by setting cutoffs for excluded atom types to 0.  None of
@@ -510,7 +510,7 @@ supported.
 
 [References:]
 
-Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
+Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
 
 Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l
 

doc/src/Speed_kokkos.txt

@@ -13,11 +13,11 @@ Kokkos is a templated C++ library that provides abstractions to allow
 a single implementation of an application kernel (e.g. a pair style)
 to run efficiently on different kinds of hardware, such as GPUs, Intel
 Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
-different backend languages such as CUDA, OpenMP, or Pthreads.  The
+different back end languages such as CUDA, OpenMP, or Pthreads.  The
 Kokkos library also provides data abstractions to adjust (at compile
 time) the memory layout of data structures like 2d and 3d arrays to
 optimize performance on different hardware. For more information on
-Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
+Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part
 of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
 library was written primarily by Carter Edwards, Christian Trott, and
 Dan Sunderland (all Sandia).
@@ -106,6 +106,11 @@ modification to the input script is needed. Alternatively, one can run
 with the KOKKOS package by editing the input script as described
 below.
 
+NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e.
+Makefile.kokkos_mpi_only) will give better performance than the OpenMP
+back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
+the code thread-safe is removed.
+
 NOTE: The default for the "package kokkos"_package.html command is to
 use "full" neighbor lists and set the Newton flag to "off" for both
 pairwise and bonded interactions. However, when running on CPUs, it
@@ -122,6 +127,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
 If the "newton"_newton.html command is used in the input
 script, it can also override the Newton flag defaults.
 
+For half neighbor lists and OpenMP, the KOKKOS package uses data
+duplication (i.e. thread-private arrays) by default to avoid
+thread-level write conflicts in the force arrays (and other data
+structures as necessary). Data duplication is typically fastest for
+small numbers of threads (i.e. 8 or less) but does increase memory
+footprint and is not scalable to large numbers of threads. An
+alternative to data duplication is to use thread-level atomic operations
+which do not require data duplication. The use of atomic operations can
+be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS"
+pre-processor flag. Most but not all Kokkos-enabled pair_styles support
+data duplication. Alternatively, full neighbor lists avoid the need for
+duplication or atomic operations but require more compute operations per
+atom.  When using the Kokkos Serial back end or the OpenMP back end with
+a single thread, no duplication or atomic operations are used. For CUDA
+and half neighbor lists, the KOKKOS package always uses atomic operations.
+
 [Core and Thread Affinity:]
 
 When using multi-threading, it is important for performance to bind
@@ -172,7 +193,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
 NOTE: The default for the "package kokkos"_package.html command is to
 use "full" neighbor lists and set the Newton flag to "off" for both
 pairwise and bonded interactions. When running on KNL, this will
-typically be best for pair-wise potentials. For manybody potentials,
+typically be best for pair-wise potentials. For many-body potentials,
 using "half" neighbor lists and setting the Newton flag to "on" may be
 faster. It can also be faster to use non-threaded communication.  Use
 the "-pk kokkos" "command-line switch"_Run_options.html to change the
@@ -186,7 +207,7 @@ mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half co
 NOTE: MPI tasks and threads should be bound to cores as described
 above for CPUs.
 
-NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
+NOTE: To build with Kokkos support for Intel Xeon Phi co-processors
 such as Knight's Corner (KNC), your system must be configured to use
 them in "native" mode, not "offload" mode like the USER-INTEL package
 supports.

doc/src/Speed_omp.txt

@@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l
 The system has a spatially inhomogeneous particle density which does
 not map well to the "domain decomposition scheme"_processors.html or
 "load-balancing"_balance.html options that LAMMPS provides.  This is
-because multi-threading achives parallelism over the number of
+because multi-threading achieves parallelism over the number of
 particles, not via their distribution in space. :l
 
 A machine is being used in "capability mode", i.e. near the point
@@ -143,7 +143,7 @@ the performance-limiting factor.  Using multi-threading allows less
 MPI tasks to be invoked and can speed-up the long-range solver, while
 increasing overall performance by parallelizing the pairwise and
 bonded calculations via OpenMP.  Likewise additional speedup can be
-sometimes be achived by increasing the length of the Coulombic cutoff
+sometimes be achieved by increasing the length of the Coulombic cutoff
 and thus reducing the work done by the long-range solver.  Using the
 "run_style verlet/split"_run_style.html command, which is compatible
 with the USER-OMP package, is an alternative way to reduce the number

doc/src/Speed_packages.txt

@@ -14,7 +14,7 @@ Accelerated versions of various "pair_style"_pair_style.html,
 been added to LAMMPS, which will typically run faster than the
 standard non-accelerated versions.  Some require appropriate hardware
 to be present on your system, e.g. GPUs or Intel Xeon Phi
-coprocessors.
+co-processors.
 
 All of these commands are in packages provided with LAMMPS.  An
 overview of packages is give on the "Packages"_Packages.html doc
@@ -161,7 +161,7 @@ package. These styles support vectorized single and mixed precision
 calculations, in addition to full double precision.  In extreme cases,
 this can provide speedups over 3.5x on CPUs.  The package also
 supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
-coprocessors.  This can result in additional speedup over 2x depending
+co-processors.  This can result in additional speedup over 2x depending
 on the hardware configuration. :l
 
 Styles with a "kk" suffix are part of the KOKKOS package, and can be

doc/src/Tools.txt

@@ -163,7 +163,7 @@ for the "chain benchmark"_Speed_bench.html.
 
 colvars tools :h4,link(colvars)
 
-The colvars directory contains a collection of tools for postprocessing
+The colvars directory contains a collection of tools for post-processing
 data produced by the colvars collective variable library.
 To compile the tools, edit the makefile for your system and run "make".
 
@@ -263,7 +263,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
 
 emacs tool :h4,link(emacs)
 
-The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs 
+The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
 that enables a lammps-mode for editing input scripts when using GNU Emacs,
 with various highlighting options set up.
 
@@ -406,15 +406,15 @@ supports it.  It has its own WWW page at
 msi2lmp tool :h4,link(msi)
 
 The msi2lmp sub-directory contains a tool for creating LAMMPS template
-input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
-Insight MD code, formerly MSI/Biosym and its Discover MD code).
+input and data files from BIOVIA's Materias Studio files (formerly
+Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code).
 
 This tool was written by John Carpenter (Cray), Michael Peachey
 (Cray), and Steve Lustig (Dupont). Several people contributed changes
 to remove bugs and adapt its output to changes in LAMMPS.
 
 This tool has several known limitations and is no longer under active
-development, so there are no changes except for the occasional bugfix.
+development, so there are no changes except for the occasional bug fix.
 
 See the README file in the tools/msi2lmp folder for more information.
 

doc/src/angle_class2.txt

@@ -7,8 +7,8 @@
 :line
 
 angle_style class2 command :h3
-angle_style class2/omp command :h3
 angle_style class2/kk command :h3
+angle_style class2/omp command :h3
 angle_style class2/p6 command :h3
 
 [Syntax:]

doc/src/angle_coeff.txt

@@ -60,26 +60,14 @@ doc page for details.
 
 :line
 
-Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
-the style to display the formula it computes and coefficients
-specified by the associated "angle_coeff"_angle_coeff.html command.
-
-Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution.  The full list of all
-angle styles is on the "Commands bond"_Commands_bond.html#angle doc
+The list of all angle styles defined in LAMMPS is given on the
+"angle_style"_angle_style.html doc page.  They are also listed in more
+compact form on the "Commands angle"_Commands_bond.html#angle doc
 page.
 
-"angle_style none"_angle_none.html - turn off angle interactions
-"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
-
-"angle_style charmm"_angle_charmm.html - CHARMM angle
-"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
-"angle_style cosine"_angle_cosine.html - cosine angle potential
-"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
-"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
-"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
-"angle_style harmonic"_angle_harmonic.html - harmonic angle
-"angle_style table"_angle_table.html - tabulated by angle :ul
+On either of those pages, click on the style to display the formula it
+computes and its coefficients as specified by the associated
+angle_coeff command.
 
 :line
 

doc/src/angle_cosine_buck6d.txt

@@ -23,25 +23,25 @@ The {cosine/buck6d} angle style uses the potential
 
 :c,image(Eqs/angle_cosine_buck6d.jpg)
 
-where K is the energy constant, n is the periodic multiplicity and 
+where K is the energy constant, n is the periodic multiplicity and
 Theta0 is the equilibrium angle.
 
-The coefficients must be defined for each angle type via the 
+The coefficients must be defined for each angle type via the
 "angle_coeff"_angle_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands in the following order:
 
 K (energy)
-n 
+n
 Theta0 (degrees) :ul
 
-Theta0 is specified in degrees, but LAMMPS converts it to radians 
+Theta0 is specified in degrees, but LAMMPS converts it to radians
 internally.
 
-Additional to the cosine term the {cosine/buck6d} angle style computes 
-the short range (vdW) interaction belonging to the 
-"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of 
-the angle.  For this reason this angle style only works in combination
+Additional to the cosine term the {cosine/buck6d} angle style computes
+the short range (vdW) interaction belonging to the
+"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the
+angle.  For this reason this angle style only works in combination
 with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs
 the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
 0.0 to prevent double counting.
@@ -51,8 +51,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
 [Restrictions:]
 
 {cosine/buck6d} can only be used in combination with the
-"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a 
-"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.  
+"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
+"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
 
 This angle style can only be used if LAMMPS was built with the
 USER-MOFFF package.  See the "Build package"_Build_package.html doc

doc/src/angle_cosine_shift.txt

@@ -63,7 +63,7 @@ instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-USER-MISC package.  
+USER-MISC package.
 
 [Related commands:]
 

doc/src/angle_sdk.txt

@@ -7,6 +7,7 @@
 :line
 
 angle_style sdk command :h3
+angle_style sdk/omp command :h3
 
 [Syntax:]
 
@@ -27,7 +28,7 @@ The {sdk} angle style is a combination of the harmonic angle potential,
 where theta0 is the equilibrium value of the angle and K a prefactor,
 with the {repulsive} part of the non-bonded {lj/sdk} pair style
 between the atoms 1 and 3.  This angle potential is intended for
-coarse grained MD simulations with the CMM parametrization using the
+coarse grained MD simulations with the CMM parameterization using the
 "pair_style lj/sdk"_pair_sdk.html.  Relative to the pair_style
 {lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
 jumps.  Note that the usual 1/2 factor is included in K.
@@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
 The also required {lj/sdk} parameters will be extracted automatically
 from the pair_style.
 
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the

doc/src/angle_style.txt

@@ -57,23 +57,37 @@ Here is an alphabetic list of angle styles defined in LAMMPS.  Click on
 the style to display the formula it computes and coefficients
 specified by the associated "angle_coeff"_angle_coeff.html command.
 
-Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution.  The full list of all
-angle styles are is on the "Commands bond"_Commands_bond.html#angle
-doc page.
+Click on the style to display the formula it computes, any additional
+arguments specified in the angle_style command, and coefficients
+specified by the associated "angle_coeff"_angle_coeff.html command.
 
-"angle_style none"_angle_none.html - turn off angle interactions
-"angle_style zero"_angle_zero.html - topology but no interactions
-"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
+There are also additional accelerated pair styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands
+angle"_Commands_bond.html#angle doc page are followed by one or more
+of (g,i,k,o,t) to indicate which accelerated styles exist.
 
-"angle_style charmm"_angle_charmm.html - CHARMM angle
-"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
-"angle_style cosine"_angle_cosine.html - cosine angle potential
-"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
-"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
-"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
-"angle_style harmonic"_angle_harmonic.html - harmonic angle
-"angle_style table"_angle_table.html - tabulated by angle :ul
+"none"_angle_none.html - turn off angle interactions
+"zero"_angle_zero.html - topology but no interactions
+"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
+
+"charmm"_angle_charmm.html - CHARMM angle
+"class2"_angle_class2.html - COMPASS (class 2) angle
+"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
+"cosine"_angle_cosine.html - angle with cosine term
+"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
+"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
+"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
+"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
+"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
+"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
+"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
+"fourier"_angle_fourier.html - angle with multiple cosine terms
+"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
+"harmonic"_angle_harmonic.html - harmonic angle
+"quartic"_angle_quartic.html - angle with cubic and quartic terms
+"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
+"table"_angle_table.html - tabulated by angle :ul
 
 :line
 

doc/src/atom_style.txt

@@ -39,7 +39,7 @@ atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
 atom_style spin
-atom_style template myMols 
+atom_style template myMols
 atom_style tdpd 2 :pre
 
 [Description:]
@@ -87,7 +87,7 @@ quantities.
 {line} | end points, angular velocity | rigid bodies |
 {meso} | rho, e, cv | SPH particles |
 {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
-{peri} | mass, volume | mesocopic Peridynamic models |
+{peri} | mass, volume | mesoscopic Peridynamic models |
 {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
 {sphere} | diameter, mass, angular velocity | granular models |
 {spin} | magnetic moment | system with magnetic particles |
@@ -309,9 +309,9 @@ force fields"_pair_eff.html.
 The {dpd} style is part of the USER-DPD package for dissipative
 particle dynamics (DPD).
 
-The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package 
-for energy-conserving dissipative particle dynamics (eDPD), many-body 
-dissipative particle dynamics (mDPD), and transport dissipative particle 
+The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
+for energy-conserving dissipative particle dynamics (eDPD), many-body
+dissipative particle dynamics (mDPD), and transport dissipative particle
 dynamics (tDPD), respectively.
 
 The {meso} style is part of the USER-SPH package for smoothed particle

doc/src/balance.txt

@@ -247,7 +247,7 @@ to {Niter} times.  After each dimension finishes, the imbalance factor
 is re-computed, and the balancing operation halts if the {stopthresh}
 criterion is met.
 
-A rebalance operation in a single dimension is performed using a
+A re-balance operation in a single dimension is performed using a
 recursive multisectioning algorithm, where the position of each
 cutting plane (line in 2d) in the dimension is adjusted independently.
 This is similar to a recursive bisectioning for a single value, except
@@ -261,11 +261,11 @@ information, so that they become closer together over time.  Thus as
 the recursion progresses, the count of particles on either side of the
 plane gets closer to the target value.
 
-Once the rebalancing is complete and final processor sub-domains
+Once the re-balancing is complete and final processor sub-domains
 assigned, particles are migrated to their new owning processor, and
 the balance procedure ends.
 
-NOTE: At each rebalance operation, the bisectioning for each cutting
+NOTE: At each re-balance operation, the bisectioning for each cutting
 plane (line in 2d) typically starts with low and high bounds separated
 by the extent of a processor's sub-domain in one dimension.  The size
 of this bracketing region shrinks by 1/2 every iteration.  Thus if
@@ -348,7 +348,7 @@ specified groups, its weight is not changed.  If it belongs to
 multiple groups, its weight is the product of the weight factors.
 
 This weight style is useful in combination with pair style
-"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody
+"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body
 potential with a fast pair-wise potential.  It is also useful when
 using "run_style respa"_run_style.html where some portions of the
 system have many bonded interactions and others none.  It assumes that
@@ -510,9 +510,13 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES".
 For 2d simulations, the {z} style cannot be used.  Nor can a "z"
 appear in {dimstr} for the {shift} style.
 
+Balancing through recursive bisectioning ({rcb} style) requires
+"comm_style tiled"_comm_style.html
+
 [Related commands:]
 
 "group"_group.html, "processors"_processors.html,
-"fix balance"_fix_balance.html
+"fix balance"_fix_balance.html, "comm_style"_comm_style.html
 
 [Default:] none
+:link(pizza,http://pizza.sandia.gov)