Merge pull request #1253 from akohlmey/final-cosmetic-changes

Final cosmetic changes for stable release, update version.

.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
@@ -57,3 +126,6 @@ python/*              @rbberger
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.github/CONTRIBUTING.md

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

.gitignore

@@ -1,6 +1,7 @@
 *~
 *.o
 *.so
+*.lo
 *.cu_o
 *.ptx
 *_ptx.h
@@ -21,6 +22,7 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*
@@ -32,6 +34,7 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 
 #cmake
 /build*

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})
 
@@ -43,13 +47,39 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+function(get_lammps_version version_header variable)
+    file(READ ${version_header} line)
+    set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+    string(STRIP ${day} day)
+    string(STRIP ${month} month)
+    string(STRIP ${year} year)
+    list(FIND MONTHS "${month}" month)
+    string(LENGTH ${day} day_length)
+    string(LENGTH ${month} month_length)
+    if(day_length EQUAL 1)
+        set(day "0${day}")
+    endif()
+    if(month_length EQUAL 1)
+        set(month "0${month}")
+    endif()
+    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+get_lammps_version(${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
@@ -113,6 +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)
@@ -121,10 +152,10 @@ if(BUILD_LIB)
   if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
   endif()
-  set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
-  mark_as_advanced(LIB_SUFFIX)
-  if(LIB_SUFFIX)
-    set(LIB_SUFFIX "_${LIB_SUFFIX}")
+  set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
+  mark_as_advanced(LAMMPS_LIB_SUFFIX)
+  if(LAMMPS_LIB_SUFFIX)
+    set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
   endif()
 endif()
 
@@ -139,6 +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)
@@ -158,7 +221,7 @@ else()
 endif()
 
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
@@ -183,25 +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}))
@@ -215,21 +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}")
@@ -276,11 +356,14 @@ endif()
 
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
-  if(NOT LAPACK_FOUND)
+  find_package(BLAS)
+  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
     enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
     set(LAPACK_LIBRARIES linalg)
+  else()
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
 endif()
 
@@ -344,16 +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
@@ -367,7 +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})
@@ -375,31 +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})
+    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)
@@ -409,17 +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 ""
     )
@@ -427,8 +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()
@@ -455,8 +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
@@ -471,19 +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)
@@ -493,7 +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} ${EXTRA_MSCG_OPTS}
       BUILD_COMMAND make mscg INSTALL_COMMAND ""
       )
     ExternalProject_get_property(mscg_build BINARY_DIR)
@@ -541,7 +767,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
 if (CMAKE_VERSION VERSION_LESS "3.4")
-  enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
+  enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
 endif()
 # RB: disabled this check because it breaks with KOKKOS CUDA enabled
 #foreach(FUNC sin cos)
@@ -564,8 +790,8 @@ RegisterStyles(${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})
@@ -579,12 +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})
@@ -598,14 +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)
@@ -621,6 +856,9 @@ if(PKG_USER-AWPMD)
 endif()
 
 if(PKG_USER-ATC)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
@@ -628,6 +866,7 @@ 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()
 
 
@@ -674,13 +913,16 @@ 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}/fix_nh_sphere_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+    add_definitions(-DLMP_USER_OMP)
     set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
 
     # 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)
 
@@ -710,6 +952,20 @@ 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)
@@ -787,7 +1043,7 @@ 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)
@@ -852,7 +1108,7 @@ 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)
@@ -880,35 +1136,63 @@ 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)
@@ -950,7 +1234,7 @@ 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})
@@ -1000,7 +1284,6 @@ 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})
 
 ######################################
@@ -1008,7 +1291,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ######################################
 set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
 set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+list(SORT temp_PKG_LIST)
+foreach(PKG ${temp_PKG_LIST})
     if(PKG_${PKG})
         set(temp "${temp}  \"${PKG}\",\n")
     endif()
@@ -1033,14 +1318,14 @@ if(BUILD_LIB)
   if(LAMMPS_DEPS)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
-  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
-  if(BUILD_SHARED_LIBS)
-    set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-    install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-    configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-  endif()
+  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
+  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+  configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
 else()
   list(APPEND LMP_SOURCES ${LIB_SOURCES})
 endif()
@@ -1055,11 +1340,12 @@ 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 ${LAMMPS_BINARY}.1)
   if(ENABLE_TESTING)
-    add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+    add_test(ShowHelp ${LAMMPS_BINARY} -help)
   endif()
 endif()
 
@@ -1074,7 +1360,7 @@ 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})
 
@@ -1127,7 +1413,7 @@ endif()
 # Install potential files in data directory
 ###############################################################################
 set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
 
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
@@ -1169,13 +1455,12 @@ 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 ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
@@ -1191,14 +1476,14 @@ message(STATUS "<<< Build configuration >>>
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_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}}")
@@ -1206,7 +1491,7 @@ 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/FindLAMMPS.cmake.in

@@ -0,0 +1,48 @@
+# - Find liblammps
+# Find the native liblammps headers and libraries.
+#
+# The following variables will set:
+#  LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
+#  LAMMPS_LIBRARIES    - List of libraries when using lammps.
+#  LAMMPS_API_DEFINES  - lammps library api defines
+#  LAMMPS_VERSION      - lammps library version 
+#  LAMMPS_FOUND        - True if liblammps found.
+#
+# In addition a LAMMPS::LAMMPS imported target is getting created.
+#
+#  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+#  http://lammps.sandia.gov, Sandia National Laboratories
+#  Steve Plimpton, sjplimp@sandia.gov
+#
+#  Copyright (2003) Sandia Corporation.  Under the terms of Contract
+#  DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+#  certain rights in this software.  This software is distributed under
+#  the GNU General Public License.
+#
+#  See the README file in the top-level LAMMPS directory.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
+find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
+
+set(LAMMPS_VERSION @LAMMPS_VERSION@)
+set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
+
+find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+
+set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
+set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
+
+mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
+
+if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
+  add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
+endif()

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

@@ -48,8 +48,13 @@ function(CreateStyleHeader path filename)
     set(temp "")
     if(ARGC GREATER 2)
         list(REMOVE_AT ARGV 0 1)
+        set(header_list)
         foreach(FNAME ${ARGV})
             get_filename_component(FNAME ${FNAME} NAME)
+            list(APPEND header_list ${FNAME})
+        endforeach()
+        list(SORT header_list)
+        foreach(FNAME ${header_list})
             set(temp "${temp}#include \"${FNAME}\"\n")
         endforeach()
     endif()
@@ -80,19 +85,23 @@ function(RegisterNPairStyle path)
     AddStyleHeader(${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

@@ -1,18 +1,38 @@
 # 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
 
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+# 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@
 
 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${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

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

cmake/presets/all_on.cmake

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

cmake/presets/manual_selection.cmake

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

cmake/presets/nolib.cmake

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

cmake/presets/std.cmake

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

cmake/presets/std_nolib.cmake

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

cmake/presets/user.cmake

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

doc/Makefile

@@ -1,7 +1,7 @@
 # Makefile for LAMMPS documentation
 
-SHELL 	      = /bin/bash
-SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+SHELL         = /bin/bash
+SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
@@ -31,17 +31,19 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
 
 # ------------------------------------------
 
 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"
+	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
+	@echo "                      (requires ebook-convert tool from calibre)"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
@@ -93,9 +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)/ ;\
@@ -106,20 +109,25 @@ epub: $(OBJECTS)
 	@rm -rf epub
 	@echo "Build finished. The ePUB manual file is created."
 
+mobi: epub
+	@rm -f LAMMPS.mobi
+	@ebook-convert LAMMPS.epub LAMMPS.mobi
+	@echo "Conversion finished. The MOBI manual file is created."
+
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		set -e; \
-		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
@@ -168,7 +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/lammps.1

@@ -0,0 +1,45 @@
+.TH LAMMPS "2018-08-22"
+.SH NAME
+.B LAMMPS
+\- Molecular Dynamics Simulator.
+
+.SH SYNOPSIS
+.B lmp 
+-in in.file
+
+or
+
+mpirun \-np 2 
+.B lmp 
+-in in.file
+
+.SH DESCRIPTION
+.B LAMMPS 
+LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale 
+Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft 
+materials (biomolecules, polymers) and solid-state materials (metals, 
+semiconductors) and coarse-grained or mesoscopic systems. It can be used to 
+model atoms or, more generically, as a parallel particle simulator at the 
+atomic, meso, or continuum scale.
+
+See http://lammps.sandia.gov/ for documentation.
+
+.SH OPTIONS
+See https://lammps.sandia.gov/doc/Run_options.html for details on
+command-line options.
+
+.SH COPYRIGHT 
+© 2003--2018 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL-2'.

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
 
@@ -61,7 +61,7 @@ library files.  Failing this, these 3 variables can be used to specify
 where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
 are found, and the name of the library files (MPI_LIB).
 
-For a serial build, you need to specify the 3 varaibles, as shown
+For a serial build, you need to specify the 3 variables, as shown
 above.
 
 For a serial LAMMPS build, use the dummy MPI library provided in
@@ -137,15 +137,15 @@ 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
 packages"_Speed_packages.html you have included in the build.
 
-You can tell CMake to look for a specific compiler with these varaible
+You can tell CMake to look for a specific compiler with these variable
 settings.  Likewise you can specify the FLAGS variables if you want to
 experiment with alternate optimization flags.  You should specify all
 3 compilers, so that the small number of LAMMPS source files written
@@ -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
 
@@ -216,8 +216,8 @@ LAMMPS can be built as either an executable or as a static or shared
 library.  The LAMMPS library can be called from another application or
 a scripting language.  See the "Howto couple"_Howto_couple.html doc
 page for more info on coupling LAMMPS to other codes.  See the
-"Python"_Python doc page for more info on wrapping and running LAMMPS
-from Python via its library interface.
+"Python"_Python_head.html doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
 
 [CMake variables]:
 
@@ -247,7 +247,7 @@ Note that for a shared library to be usable by a calling program, all
 the auxiliary libraries it depends on must also exist as shared
 libraries.  This will be the case for libraries included with LAMMPS,
 such as the dummy MPI library in src/STUBS or any package libraries in
-the lib/packages directroy, since they are always built as shared
+the lib/packages directory, since they are always built as shared
 libraries using the -fPIC switch.  However, if a library like MPI or
 FFTW does not exist as a shared library, the shared library build will
 generate an error.  This means you will need to install a shared
@@ -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)
@@ -299,7 +303,7 @@ Install LAMMPS after a build :h4,link(install)
 After building LAMMPS, you may wish to copy the LAMMPS executable of
 library, along with other LAMMPS files (library header, doc files) to
 a globally visible place on your system, for others to access.  Note
-that you may need super-user priveleges (e.g. sudo) if the directory
+that you may need super-user privileges (e.g. sudo) if the directory
 you want to copy files to is protected.
 
 [CMake variable]:

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
 
@@ -40,17 +40,17 @@ executable called "lmp" and a library called "liblammps.a" in the
 If your machine has multiple CPU cores (most do these days), using a
 command like "make -jN" (with N being the number of available local
 CPU cores) can be much faster.  If you plan to do development on
-LAMMPS or need to recompile LAMMPS repeatedly, installation of the
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up compilation even more.
 
 After compilation, you can optionally copy the LAMMPS executable and
-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
 
 :line
 
-There are 3 variants of CMake: a command-line verison (cmake), a text mode
+There are 3 variants of CMake: a command-line version (cmake), a text mode
 UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
 any of them interchangeably to configure and create the LAMMPS build
 environment.  On Linux all the versions produce a Makefile as their
@@ -188,7 +188,7 @@ module list            # is a cmake module already loaded?
 module avail           # is a cmake module available?
 module load cmake3     # load cmake module with appropriate name :pre
 
-Most Linux distributions offer precompiled cmake packages through
+Most Linux distributions offer pre-compiled cmake packages through
 their package management system. If you do not have CMake or a new
 enough version, you can download the latest version at
 "https://cmake.org/download/"_https://cmake.org/download/.

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
 
@@ -333,14 +350,14 @@ 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
 superseded by the USER-MEAMC package, which is a direct translation of
 the Fortran code in the MEAM library to C++. The code in USER-MEAMC
 should be functionally equivalent to the MEAM package, fully supports
-use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
+use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
 not), and has optimizations that make it significantly faster than the
 MEAM package.
 
@@ -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
@@ -470,7 +520,7 @@ lib/python/README for more details.
 
 -D PYTHON_EXECUTABLE=path   # path to Python executable to use :pre
 
-Without this setting, CMake will ues the default Python on your
+Without this setting, CMake will guess the default Python on your
 system.  To use a different Python version, you can either create a
 virtualenv, activate it and then run cmake.  Or you can set the
 PYTHON_EXECUTABLE variable to specify which Python interpreter should
@@ -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
@@ -571,8 +621,8 @@ The USER-ATC package requires the MANYBODY package also be installed.
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_REAX=yes" and "-D
-PKG_MANYBODY=yes".
+No additional settings are needed besides "-D PKG_USER-ATC=yes"
+and "-D PKG_MANYBODY=yes".
 
 [Traditional make]:
 
@@ -677,6 +727,114 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
+USER-PLUMED package :h4,link(user-plumed)
+
+Before building LAMMPS with this package, you must first build PLUMED.
+PLUMED can be built as part of the LAMMPS build or installed separately
+from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
+:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
+
+PLUMED can be linked into MD codes in three different modes: static,
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
+
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
+
+[CMake build]:
+
+When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
+
+-D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
+-D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
+
+If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG_CONFIG_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
+
+The PLUMED_MODE setting determines the linkage mode for the PLUMED
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
+mode is recommended.
+
+[Traditional make]:
+
+PLUMED needs to be installed before the USER-PLUMED package is installed
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
+
+Download/compilation/configuration of the plumed library can be done
+from the src folder through the following make args:
+
+make lib-plumed                         # print help message
+make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+                                                # /usr/local and use shared linkage mode
+:pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink" are
+created in lib/plumed that point to the location of the PLUMED build to
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
+
+make yes-user-plumed
+make machine :pre
+
+Once this compilation completes you should be able to run LAMMPS in the
+usual way.  For shared linkage mode, libplumed.so must be found by the
+LAMMPS executable, which on many operating systems means, you have to
+set the LD_LIBRARY_PATH environment variable accordingly.
+
+Support for the different linkage modes in LAMMPS varies for different
+operating systems, using the static linkage is expected to be the most
+portable, and thus set to be the default.
+
+If you want to change the linkage mode, you have to re-run "make
+lib-plumed" with the desired settings [and] do a re-install if the
+USER-PLUMED package with "make yes-user-plumed" to update the required
+makefile settings with the changes in the lib/plumed folder.
+
+:line
+
 USER-H5MD package :h4,link(user-h5md)
 
 To build with this package you must have the HDF5 software package
@@ -687,7 +845,7 @@ the HDF5 library.
 
 No additional settings are needed besides "-D PKG_USER-H5MD=yes".
 
-This should autodetect the H5MD library on your system.  Several
+This should auto-detect the H5MD library on your system.  Several
 advanced CMake H5MD options exist if you need to specify where it is
 installed.  Use the ccmake (terminal window) or cmake-gui (graphical)
 tools to see these options and set them interactively from their user
@@ -777,7 +935,7 @@ on your system.
 
 No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
 
-This should autodetect the NETCDF library if it is installed on your
+This should auto-detect the NETCDF library if it is installed on your
 system at standard locations.  Several advanced CMake NETCDF options
 exist if you need to specify where it was installed.  Use the ccmake
 (terminal window) or cmake-gui (graphical) tools to see these options
@@ -834,7 +992,7 @@ 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 +1052,45 @@ 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.
@@ -905,7 +1102,7 @@ Eigen3 is a template library, so you do not need to build it.
 -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location) :pre
 
 If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
-inside the CMake build directory.  If the Eig3n3 library is already on
+inside the CMake build directory.  If the Eigen3 library is already on
 your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
 is the directory the Eigen3++ include file is in.
 
@@ -936,7 +1133,7 @@ your system.
 
 No additional settings are needed besides "-D PKG_USER-VTK=yes".
 
-This should autodetect the VTK library if it is installed on your
+This should auto-detect the VTK library if it is installed on your
 system at standard locations.  Several advanced VTK options exist if
 you need to specify where it was installed.  Use the ccmake (terminal
 window) or cmake-gui (graphical) tools to see these options and set

doc/src/Build_make.txt

@@ -35,16 +35,16 @@ This initial compilation can take a long time, since LAMMPS is a large
 project with many features. If your machine has multiple CPU cores
 (most do these days), using a command like "make -jN mpi" (with N =
 the number of available CPU cores) can be much faster.  If you plan to
-do development on LAMMPS or need to recompile LAMMPS repeatedly, the
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
 installation of the ccache (= Compiler Cache) software may speed up
 compilation even more.
 
 After the initial build, whenever you edit LAMMPS source files, or add
 or remove new files to the source directory (e.g. by installing or
-uninstalling packages), you must recompile and relink the LAMMPS
+uninstalling packages), you must re-compile and relink the LAMMPS
 executable with the same "make" command.  This makefiles dependencies
 should insure that only the subset of files that need to be are
-recompiled.
+re-compiled.
 
 NOTE: When you build LAMMPS for the first time, a long list of *.d
 files will be printed out rapidly.  This is not an error; it is the
@@ -71,8 +71,8 @@ Makefiles you may wish to try include these (some require a package
 first be installed).  Many of these include specific compiler flags
 for optimized performance.  Please note, however, that some of these
 customized machine Makefile are contributed by users.  Since both
-compilers, OS configs, and LAMMPS itself keep changing, their settings
-may become outdated:
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
 
 make mac             # build serial LAMMPS on a Mac
 make mac_mpi         # build parallel LAMMPS on a Mac

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
@@ -73,15 +73,15 @@ 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
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
 to the screen at the end of a run using the "kspace_style
-pppm"_kspace_style.html command.  The "Run output"_doc page gives more
-details.
+pppm"_kspace_style.html command.  The "Run output"_Run_output.html
+doc page gives more details.
 
 FFTW is a fast, portable FFT library that should also work on any
 platform and can be faster than the KISS FFT library.  You can
@@ -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).
@@ -101,7 +101,7 @@ Performing 3d FFTs in parallel can be time consuming due to data
 access and required communication.  This cost can be reduced by
 performing single-precision FFTs instead of double precision.  Single
 precision means the real and imaginary parts of a complex datum are
-4-byte floats.  Double precesion means they are 8-byte doubles.  Note
+4-byte floats.  Double precision means they are 8-byte doubles.  Note
 that Fourier transform and related PPPM operations are somewhat less
 sensitive to floating point truncation errors and thus the resulting
 error is less than the difference in precision. Using the -DFFT_SINGLE
@@ -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)
@@ -193,7 +193,7 @@ Output of JPG, PNG, and movie files :h4,link(graphics)
 
 The "dump image"_dump_image.html command has options to output JPEG or
 PNG image files.  Likewise the "dump movie"_dump_image.html command
-ouputs movie files in MPEG format.  Using these options requires the
+outputs movie files in MPEG format.  Using these options requires the
 following settings:
 
 [CMake variables]:
@@ -206,15 +206,15 @@ following settings:
                           # default = yes if CMake can find ffmpeg, else no :pre
 
 Usually these settings are all that is needed.  If CMake cannot find
-the graphics header, library, executuable files, you can set these
+the graphics header, library, executable files, you can set these
 variables:
 
--D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file 
--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)
@@ -84,7 +84,7 @@ with the cross-compiler environment on Fedora machines.
 Please keep in mind, though, that this only applies to compiling LAMMPS.
 Whether the resulting binaries do work correctly is no tested by the
 LAMMPS developers.  We instead rely on the feedback of the users
-of these precompiled LAMMPS packages for Windows.  We will try to resolve
+of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
 this is subject to time constraints and focus on HPC platforms.
 

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 commmands.
+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 commmands.
 "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 commmands.
 "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 commmands.
 "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
@@ -95,9 +97,9 @@ OPT.
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.htm;,
+"opls (iko)"_dihedral_opls.html,
 "quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
+"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 +26,14 @@ 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,
 "body/nparticle"_pair_body_nparticle.html,
@@ -41,21 +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,
@@ -65,13 +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,
@@ -80,6 +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,
@@ -89,11 +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,
@@ -108,9 +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,
@@ -123,12 +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,
@@ -136,15 +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,
@@ -159,14 +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,
@@ -178,7 +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,
@@ -188,11 +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,
@@ -224,8 +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

@@ -14,7 +14,7 @@ LAMMPS commands are case sensitive.  Command names are lower-case, as
 are specified command arguments.  Upper case letters may be used in
 file names or user-chosen ID strings.
 
-Here are 6 rulse for how each line in the input script is parsed by
+Here are 6 rules for how each line in the input script is parsed by
 LAMMPS:
 
 (1) If the last printable character on the line is a "&" character,
@@ -71,7 +71,7 @@ floating-point value.  The format string is used to output the result
 of the variable expression evaluation.  If a format string is not
 specified a high-precision "%.20g" is used as the default.
 
-This can be useful for formatting print output to a desired precion:
+This can be useful for formatting print output to a desired precision:
 
 print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
 
@@ -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/pair_atm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
+\end{equation}
+
+\end{document}

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

@@ -279,12 +279,6 @@ multibody joint).  The bodies you have defined exceed this limit. :dd
 This is an internal LAMMPS error.  Please report it to the
 developers. :dd
 
-{Atom sorting has bin size = 0.0} :dt
-
-The neighbor cutoff is being used as the bin size, but it is zero.
-Thus you must explicitly list a bin size in the atom_modify sort
-command or turn off sorting. :dd
-
 {Atom style hybrid cannot have hybrid as an argument} :dt
 
 Self-explanatory. :dd
@@ -421,9 +415,9 @@ This is an internal error.  It should normally not occur. :dd
 
 This is an internal error.  It should normally not occur. :dd
 
-{Bad real space Coulomb cutoff in fix tune/kspace} :dt
+{Bad real space Coulombic cutoff in fix tune/kspace} :dt
 
-Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
+Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
 the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd
 
 {Balance command before simulation box is defined} :dt
@@ -460,7 +454,7 @@ compute. :dd
 
 {Big particle in fix srd cannot be point particle} :dt
 
-Big particles must be extended spheriods or ellipsoids. :dd
+Big particles must be extended spheroids or ellipsoids. :dd
 
 {Bigint setting in lmptype.h is invalid} :dt
 
@@ -743,7 +737,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
+{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt
 
 Single precision cannot be used with MSM. :dd
 
@@ -780,7 +774,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd
 
 Self-explanatory. :dd
 
-{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt
+{Cannot change box z boundary to non-periodic for a 2d simulation} :dt
 
 Self-explanatory. :dd
 
@@ -1092,11 +1086,6 @@ 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 +1282,7 @@ are defined. :dd
 You cannot reset the timestep when a fix that keeps track of elapsed
 time is in place. :dd
 
-{Cannot run 2d simulation with nonperiodic Z dimension} :dt
+{Cannot run 2d simulation with non-periodic Z dimension} :dt
 
 Use the boundary command to make the z dimension periodic in order to
 run a 2d simulation. :dd
@@ -1677,10 +1666,6 @@ 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 +2110,29 @@ Self-explanatory. :dd
 Fix setforce cannot be used in this manner.  Use fix addforce
 instead. :dd
 
-{Cannot use nonperiodic boundares with fix ttm} :dt
+{Cannot use non-periodic boundares with fix ttm} :dt
 
 This fix requires a fully periodic simulation box. :dd
 
-{Cannot use nonperiodic boundaries with Ewald} :dt
+{Cannot use non-periodic boundaries with Ewald} :dt
 
 For kspace style ewald, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with EwaldDisp} :dt
+{Cannot use non-periodic boundaries with EwaldDisp} :dt
 
 For kspace style ewald/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
 slab with a non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPM} :dt
+{Cannot use non-periodic boundaries with PPPM} :dt
 
 For kspace style pppm, all 3 dimensions must have periodic boundaries
 unless you use the kspace_modify command to define a 2d slab with a
 non-periodic z dimension. :dd
 
-{Cannot use nonperiodic boundaries with PPPMDisp} :dt
+{Cannot use non-periodic boundaries with PPPMDisp} :dt
 
 For kspace style pppm/disp, all 3 dimensions must have periodic
 boundaries unless you use the kspace_modify command to define a 2d
@@ -2425,10 +2410,6 @@ 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 +3345,21 @@ probably due to errors in the Python code. :dd
 The default minimum order is 2.  This can be reset by the
 kspace_modify minorder command. :dd
 
-{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt
+{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/coul/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt
+{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt
 
 Must use long-range Coulombic interactions. :dd
 
-{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
+{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt
 
-If using a Kspace solver, all Coulomb cutoffs of long pair styles must
+If using a Kspace solver, all Coulombic cutoffs of long pair styles must
 be the same. :dd
 
 {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt
@@ -4074,10 +4055,6 @@ 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 +4356,6 @@ 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
@@ -5078,7 +5010,7 @@ Self-explanatory. :dd
 
 Occurs when number of neighbor atoms for an atom increased too much
 during a run.  Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
 
 {Fix qeq/point requires atom attribute q} :dt
 
@@ -5092,7 +5024,7 @@ Self-explanatory. :dd
 
 Occurs when number of neighbor atoms for an atom increased too much
 during a run.  Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
 
 {Fix qeq/shielded requires atom attribute q} :dt
 
@@ -5110,7 +5042,7 @@ Self-explanatory. :dd
 
 Occurs when number of neighbor atoms for an atom increased too much
 during a run.  Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
 
 {Fix qeq/slater requires atom attribute q} :dt
 
@@ -5541,7 +5473,7 @@ See the package gpu command. :dd
 
 {GPUs are requested but Kokkos has not been compiled for CUDA} :dt
 
-Recompile Kokkos with CUDA support to use GPUs. :dd
+Re-compile Kokkos with CUDA support to use GPUs. :dd
 
 {Ghost velocity forward comm not yet implemented with Kokkos} :dt
 
@@ -6000,9 +5932,9 @@ map command will force an atom map to be created. :dd
 
 Self-explanatory. :dd
 
-{Input line quote not followed by whitespace} :dt
+{Input line quote not followed by white-space} :dt
 
-An end quote must be followed by whitespace. :dd
+An end quote must be followed by white-space. :dd
 
 {Insertion region extends outside simulation box} :dt
 
@@ -7076,7 +7008,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd
 
 {KSpace accuracy too large to estimate G vector} :dt
 
-Reduce the accuracy request or specify gwald explicitly
+Reduce the accuracy request or specify gewald explicitly
 via the kspace_modify command. :dd
 
 {KSpace accuracy too low} :dt
@@ -8076,7 +8008,7 @@ Self-explanatory. :dd
 
 {Package command after simulation box is defined} :dt
 
-The package command cannot be used afer a read_data, read_restart, or
+The package command cannot be used after a read_data, read_restart, or
 create_box command. :dd
 
 {Package gpu command without GPU package installed} :dt
@@ -9260,7 +9192,7 @@ creates one large file for all processors. :dd
 {Restart file byte ordering is not recognized} :dt
 
 The file does not appear to be a LAMMPS restart file since it doesn't
-contain a recognized byte-orderomg flag at the beginning. :dd
+contain a recognized byte-ordering flag at the beginning. :dd
 
 {Restart file byte ordering is swapped} :dt
 
@@ -9472,7 +9404,7 @@ You may also want to boost the page size. :dd
 
 {Small to big integers are not sized correctly} :dt
 
-This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
+This error occurs when the sizes of smallint, imageint, tagint, bigint,
 as defined in src/lmptype.h are not what is expected.  Contact
 the developers if this occurs. :dd
 

doc/src/Errors_warnings.txt

@@ -13,7 +13,7 @@ This is an alphabetic list of the WARNING messages LAMMPS prints out
 and the reason why.  If the explanation here is not sufficient, the
 documentation for the offending command may help.  Warning messages
 also list the source file and line number where the warning was
-generated.  For example, a message lile this:
+generated.  For example, a message like this:
 
 WARNING: Bond atom missing in box size check (domain.cpp:187) :pre
 
@@ -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
@@ -64,11 +64,11 @@ Thermodynamic output, which can be setup via the
 "thermo_style"_thermo_style.html command, often includes pressure
 values.  As explained on the doc page for the
 "thermo_style"_thermo_style.html command, the default pressure is
-setup by the thermo command itself.  It is NOT the presure associated
+setup by the thermo command itself.  It is NOT the pressure associated
 with any barostatting fix you have defined or with any compute you
-have defined that calculates a presure.  The doc pages for the
+have defined that calculates a pressure.  The doc pages for the
 barostatting fixes explain the ID of the pressure compute they create.
-Thus if you want to view these pressurse, you need to specify them
+Thus if you want to view these pressures, you need to specify them
 explicitly via the "thermo_style custom"_thermo_style.html command.
 Or you can use the "thermo_modify"_thermo_modify.html command to
 re-define what pressure compute is used for default thermodynamic

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
@@ -337,7 +337,7 @@ the sphere that surrounds each vertex. The diameter value can be
 different for each body particle. These floating-point values can be
 listed on as many lines as you wish; see the
 "read_data"_read_data.html command for more details.  Because the
-maxmimum vertices per face is hard-coded to be 4
+maximum number of vertices per face is hard-coded to be 4
 (i.e. quadrilaterals), faces with more than 4 vertices need to be
 split into triangles or quadrilaterals.  For triangular faces, the
 last vertex index should be set to -1.

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

@@ -171,21 +171,21 @@ void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
 
 The gather functions collect peratom info of the requested type (atom
 coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor.  The scatter
+same vector of values to each calling processor.  The scatter
 functions do the inverse.  They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
 
 The lammps_gather_atoms() function does this for all N atoms in the
 system, ordered by atom ID, from 1 to N.  The
 lammps_gather_atoms_concat() function does it for all N atoms, but
 simply concatenates the subset of atoms owned by each processor.  The
-resulting vector is not ordered by atom ID.  Atom IDs can be requetsed
+resulting vector is not ordered by atom ID.  Atom IDs can be requested
 by the same function if the caller needs to know the ordering.  The
 lammps_gather_subset() function allows the caller to request values
 for only a subset of atoms (identified by ID).
 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

@@ -73,7 +73,7 @@ that package into your current Python installation.
 cd $LAMMPS_DIR/python
 python install.py :pre
 
-NOTE: Recompiling the shared library requires reinstalling the Python package
+NOTE: Recompiling the shared library requires re-installing the Python package
 
 
 Installation inside of a virtualenv :h5
@@ -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
@@ -159,7 +159,7 @@ ellipsoidal particles:
 
 The advantage of these fixes is that those which thermostat the
 particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting.  The "fix langevin"_fix_langevin
+calculation and thermostatting.  The "fix langevin"_fix_langevin.html
 command can also be used with its {omgea} or {angmom} options to
 thermostat the rotational degrees of freedom for spherical or
 ellipsoidal particles.  Other thermostatting fixes only operate on the
@@ -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

@@ -9,51 +9,51 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Magnetic spins :h3
 
-The magnetic spin simualtions are enabled by the SPIN package, whose
+The magnetic spin simulations are enabled by the SPIN package, whose
 implementation is detailed in "Tranchida"_#Tranchida7.
 
-The model representents the simulation of atomic magnetic spins coupled 
-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 outputed 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

@@ -17,10 +17,11 @@ how to stay current are on the "Install git"_Install_git.html and
 If you prefer to download a tarball, as described on the "Install
 git"_Install_tarball.html doc page, you can stay current by
 downloading "patch files" when new patch releases are made.  A link to
-a patch file is posted on the "bug and feature page"_bug of the
-website, along with a list of changed files and details about what is
-in the new patch release.  This page explains how to apply the patch
-file to your local LAMMPS directory.
+a patch file is posted on the "bug and feature
+page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
+with a list of changed files and details about what is in the new patch
+release.  This page explains how to apply the patch file to your local
+LAMMPS directory.
 
 NOTE: You should not apply patch files to a local Git or SVN repo of
 LAMMPS, only to an unpacked tarball.  Use Git and SVN commands to

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/Intro_overview.txt

@@ -17,7 +17,7 @@ variety of interatomic potentials (force fields) and boundary
 conditions.  It can model 2d or 3d systems with only a few particles
 up to millions or billions.
 
-LAMMPS can be built and run on a laptop or destop machine, but is
+LAMMPS can be built and run on a laptop or desktop machine, but is
 designed for parallel computers.  It will run on any parallel machine
 that supports the "MPI"_mpi message-passing library.  This includes
 shared-memory boxes and distributed-memory clusters and
@@ -45,7 +45,7 @@ nature; some long-range models are included as well.
 LAMMPS uses neighbor lists to keep track of nearby particles.  The
 lists are optimized for systems with particles that are repulsive at
 short distances, so that the local density of particles never becomes
-too large.  This is in contrast to methods used for modeling plasmas
+too large.  This is in contrast to methods used for modeling plasma
 or gravitational bodies (e.g. galaxy formation).
 
 On parallel machines, LAMMPS uses spatial-decomposition techniques to

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Aug 2018 version">
+<META NAME="docnumber" CONTENT="12 Dec 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
-22 Aug 2018 version :c,h2
+12 Dec 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Manual_build.txt

@@ -10,15 +10,16 @@ Section"_Manual.html :c
 
 Building the LAMMPS manual :h2
 
-Depending on how you obtained LAMMPS, the doc directory has 
-2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
+Depending on how you obtained LAMMPS, the doc directory has 2 or 3
+sub-directories and optionally 2 PDF files and 2 e-book format files:
 
 src             # content files for LAMMPS documentation
 html            # HTML version of the LAMMPS manual (see html/Manual.html)
 tools           # tools and settings for building the documentation
 Manual.pdf      # large PDF version of entire manual
 Developer.pdf   # small PDF with info about how LAMMPS is structured
-LAMMPS.epub     # Manual in ePUB format :pre
+LAMMPS.epub     # Manual in ePUB e-book format
+LAMMPS.mobi     # Manual in MOBI e-book format :pre
 
 If you downloaded LAMMPS as a tarball from the web site, all these
 directories and files should be included.
@@ -40,7 +41,7 @@ HTML files already exist.  This requires various tools including
 Sphinx, which the build process will attempt to download and install
 on your system, if not already available.  See more details below.
 
-(c) You can genererate an older, simpler, less-fancy style of HTML
+(c) You can generate an older, simpler, less-fancy style of HTML
 documentation by typing "make old".  This will create an "old"
 directory.  This can be useful if (b) does not work on your box for
 some reason, or you want to quickly view the HTML version of a doc
@@ -60,7 +61,8 @@ 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
 
@@ -68,7 +70,7 @@ make clean-all    # remove entire build folder and any cached data :pre
 
 Installing prerequisites for HTML build :h3
 
-To run the HTML documention build toolchain, Python 3 and virtualenv
+To run the HTML documentation build toolchain, Python 3 and virtualenv
 have to be installed.  Here are instructions for common setups:
 
 Ubuntu :h4
@@ -115,10 +117,8 @@ ePUB :h4
 Same as for HTML. This uses the same tools and configuration
 files as the HTML tree.
 
-For converting the generated ePUB file to a mobi format file
+For converting the generated ePUB file to a MOBI format file
 (for e-book readers like Kindle, that cannot read ePUB), you
 also need to have the 'ebook-convert' tool from the "calibre"
 software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
-You first create the ePUB file with 'make epub' and then do:
-
-ebook-convert LAMMPS.epub LAMMPS.mobi :pre
+You first create the ePUB file and then convert it with 'make mobi'

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_overview.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Overview :h3
 
 The best way to add a new feature to LAMMPS is to find a similar
-featureand look at the corresponding source and header files to figure
+feature and look at the corresponding source and header files to figure
 out what it does.  You will need some knowledge of C++ to be able to
 understand the hi-level structure of LAMMPS and its class
 organization, but functions (class methods) that do actual

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
@@ -297,7 +302,7 @@ lib/gpu/README
 "Section 2.6 -sf gpu"_Run_options.html
 "Section 2.6 -pk gpu"_Run_options.html
 "package gpu"_package.html
-"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
+"Commands all"_lc pages (pair,kspace) for styles followed by (g)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -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
@@ -412,7 +417,7 @@ lib/kokkos/README
 "Section 2.6 -sf kk"_Run_options.html
 "Section 2.6 -pk kokkos"_Run_options.html
 "package kokkos"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -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
@@ -851,7 +877,7 @@ multi-replica simulations in LAMMPS.  Methods in the package include
 nudged elastic band (NEB), parallel replica dynamics (PRD),
 temperature accelerated dynamics (TAD), parallel tempering, and a
 verlet/split algorithm for performing long-range Coulombics on one set
-of processors, and the remainder of the force field calcalation on
+of processors, and the remainder of the force field calculation on
 another set.
 
 [Supporting info:]
@@ -874,7 +900,7 @@ RIGID package :link(PKG-RIGID),h4
 [Contents:]
 
 Fixes which enforce rigid constraints on collections of atoms or
-particles.  This includes SHAKE and RATTLE, as well as varous
+particles.  This includes SHAKE and RATTLE, as well as various
 rigid-body integrators for a few large bodies or many small bodies.
 Also several computes which calculate properties of rigid bodies.
 
@@ -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
@@ -1370,14 +1426,14 @@ which have styles optimized for CPUs and KNLs.
 
 You need to have an Intel compiler, version 14 or higher to take full
 advantage of this package. While compilation with GNU compilers is
-supported, performance will be suboptimal.
+supported, performance will be sub-optimal.
 
 NOTE: the USER-INTEL package contains styles that require using the
 -restrict flag, when compiling with Intel compilers.
 
 [Author:] Mike Brown (Intel).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1392,7 +1448,7 @@ src/USER-INTEL/README
 "Section 2.6 -sf intel"_Run_options.html
 "Section 2.6 -pk intel"_Run_options.html
 "package intel"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
 src/USER-INTEL/TEST
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
@@ -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:]
@@ -1577,13 +1633,11 @@ 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.
 
-:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
-
 To use this package you must have the desired VMD plugins available on
 your system.
 
@@ -1593,14 +1647,14 @@ plugin via the "dump molfile"_dump_molfile.html command.  Plugins can
 be obtained from a VMD installation which has to match the platform
 that you are using to compile LAMMPS for. By adding plugins to VMD,
 support for new file formats can be added to LAMMPS (or VMD or other
-programs that use them) without having to recompile the application
+programs that use them) without having to re-compile the application
 itself.  More information about the VMD molfile plugins can be found
 at
 "http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-[Install:] 
+[Install:]
 
 This package has "specific installation
 instructions"_Build_extras.html#gpu on the "Build
@@ -1631,15 +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(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
@@ -1683,7 +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
@@ -1698,7 +1753,7 @@ src/USER-OMP/README
 "Section 2.6 -sf omp"_Run_options.html
 "Section 2.6 -pk omp"_Run_options.html
 "package omp"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -1722,6 +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:]
@@ -1743,7 +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
@@ -1801,7 +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
@@ -1839,6 +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:]
@@ -1860,7 +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
@@ -1986,7 +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
@@ -1998,3 +2132,5 @@ src/USER-VTK: filenames -> commands
 src/USER-VTK/README
 lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
+
+

doc/src/Packages_standard.txt

@@ -47,7 +47,8 @@ Package, Description, Doc page, Example, Library
 "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
 "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
 "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, n/a, no, no
+"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
 "MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext

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
@@ -58,17 +58,24 @@ Package, Description, Doc page, Example, Library
 "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
 "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
 "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"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

@@ -59,9 +59,9 @@ and callbacks to LAMMPS.
 The "fix python/invoke"_fix_python_invoke.html command can execute
 Python code at selected timesteps during a simulation run.
 
-The "pair_style python"_pair_python command allows you to define
+The "pair_style python"_pair_python.html command allows you to define
 pairwise potentials as python code which encodes a single pairwise
-interaction.  This is useful for rapid-developement and debugging of a
+interaction.  This is useful for rapid development and debugging of a
 new potential.
 
 To use any of these commands, you only need to build LAMMPS with the
@@ -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/Python_head.txt

@@ -62,11 +62,11 @@ library interface provided in src/library.h and src/library.h.  That
 interface is exposed to Python either when calling LAMMPS from Python
 or when calling Python from a LAMMPS input script and then calling
 back to LAMMPS from Python code.  The library interface is designed to
-be easy to add funcionality to.  Thus the Python interface to LAMMPS
+be easy to add functionality to.  Thus the Python interface to LAMMPS
 is also easy to extend as well.
 
 If you create interesting Python scripts that run LAMMPS or
 interesting Python functions that can be called from a LAMMPS input
-script, that you think would be genearlly useful, please post them as
+script, that you think would be generally useful, please post them as
 a pull request to our "GitHub site"_https://github.com/lammps/lammps,
 and they can be added to the LAMMPS distribution or webpage.

doc/src/Python_library.txt

@@ -186,20 +186,20 @@ keyword as a float.
 The get_natoms() method returns the total number of atoms in the
 simulation, as an int.
 
-The set_variable() methosd sets an existing string-style variable to a
+The set_variable() method sets an existing string-style variable to a
 new string value, so that subsequent LAMMPS commands can access the
 variable.
 
-The reset_box() emthods resets the size and shape of the simulation
+The reset_box() method resets the size and shape of the simulation
 box, e.g. as part of restoring a previously extracted and saved state
 of a simulation.
 
 The gather methods collect peratom info of the requested type (atom
 coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor.  The scatter
+same vector of values to each calling processor.  The scatter
 functions do the inverse.  They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
 
 Note that the data returned by the gather methods,
 e.g. gather_atoms("x"), is different from the data structure returned

doc/src/Run_basics.txt

@@ -75,7 +75,7 @@ setenv OMP_NUM_THREADS 2     # csh or tcsh :pre
 This can also be done via the "package"_package.html command or via
 the "-pk command-line switch"_Run_options.html which invokes the
 package command.  See the "package"_package.html command or
-"Speed"_Speed.html doc pages for more details about which accerlarator
+"Speed"_Speed.html doc pages for more details about which accelerator
 packages and which commands support multi-threading.
 
 :line

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

@@ -33,15 +33,15 @@ in parallel, follow these steps.
 
 Download and install a compatible MPI library binary package:
 
-for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
-for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
+for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the
 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_bench.txt

@@ -11,7 +11,7 @@ Benchmarks :h3
 
 Current LAMMPS performance is discussed on the "Benchmarks
 page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
-where timings and parallel efficiencies are listed.  The page has
+where timings and parallel efficiency are listed.  The page has
 several sections, which are briefly described below:
 
 CPU performance on 5 standard problems, strong and weak scaling
@@ -77,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated.
 Performance on a parallel machine can also be predicted from one-core
 or one-node timings if the parallel efficiency can be estimated.  The
 communication bandwidth and latency of a particular parallel machine
-affects the efficiency.  On most machines LAMMPS will give parallel
-efficiencies on these benchmarks above 50% so long as the number of
+affects the efficiency.  On most machines LAMMPS will give a parallel
+efficiency on these benchmarks above 50% so long as the number of
 atoms/core is a few 100 or greater, and closer to 100% for large
 numbers of atoms/core.  This is for all-MPI mode with one MPI task per
 core.  For nodes with accelerator options or hardware (OpenMP, GPU,