Merge pull request #1172 from akohlmey/next-patch-release

Patch release 24 October 2018

.github/CODEOWNERS

@@ -17,6 +17,7 @@ src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
+src/MESSAGE/*         @sjplimp
 src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
@@ -29,19 +30,86 @@ src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
 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

.gitignore

@@ -1,6 +1,7 @@
 *~
 *.o
 *.so
+*.lo
 *.cu_o
 *.ptx
 *_ptx.h
@@ -32,6 +33,7 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 
 #cmake
 /build*

cmake/CMakeLists.txt

@@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT
 
 
 # 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})
 
@@ -43,9 +43,34 @@ 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)
@@ -113,6 +138,7 @@ 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 +147,10 @@ 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 +165,35 @@ 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-PTM USER-QTB USER-REAXC USER-SCAFACOS 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()
+
+# 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)
@@ -183,25 +238,52 @@ 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}))
@@ -215,17 +297,7 @@ 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})
@@ -276,11 +348,14 @@ 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()
 
@@ -400,6 +475,57 @@ if(PKG_LATTE)
   list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
+if(PKG_USER-SCAFACOS)
+  find_package(GSL REQUIRED)
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
+  if(DOWNLOAD_SCAFACOS)
+    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
+                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                               
+                                               FC=${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-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@@ -409,8 +535,8 @@ 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()
 
@@ -427,8 +553,9 @@ if(PKG_USER-SMD)
     set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
     list(APPEND LAMMPS_DEPS Eigen3_build)
   else()
-    find_package(Eigen3)
-    if(NOT Eigen3_FOUND)
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
       message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
     endif()
   endif()
@@ -478,6 +605,40 @@ if(PKG_KIM)
   include_directories(${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)
+
+  if(BUILD_SHARED_LIBS)
+      add_library(cslib SHARED ${cslib_SOURCES})
+  else()
+      add_library(cslib STATIC ${cslib_SOURCES})
+  endif()
+
+  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)
@@ -564,8 +725,8 @@ 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})
@@ -583,8 +744,8 @@ endforeach()
 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})
@@ -598,8 +759,10 @@ 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)
@@ -674,13 +837,16 @@ 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)
 
@@ -880,7 +1046,7 @@ 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")
@@ -893,15 +1059,15 @@ if(PKG_GPU)
 
       set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM 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
@@ -950,7 +1116,7 @@ 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 ${GPU_LIB_CU})
@@ -1008,7 +1174,9 @@ include_directories(${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 +1201,14 @@ 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()
@@ -1056,10 +1224,11 @@ if(BUILD_EXE)
     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 +1243,7 @@ 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 +1296,7 @@ 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)
@@ -1169,7 +1338,7 @@ 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()

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/pkgconfig/liblammps.pc.in

@@ -4,15 +4,15 @@
 # after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
 # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
 
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+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@

doc/Makefile

@@ -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

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

@@ -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
@@ -145,7 +145,7 @@ 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
@@ -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 documention 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

@@ -40,7 +40,7 @@ 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
@@ -50,7 +50,7 @@ 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,
@@ -47,6 +48,7 @@ This is the list of packages that may require additional steps.
 "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)
 
@@ -340,7 +342,7 @@ 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 +363,10 @@ 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
@@ -373,6 +379,35 @@ 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
@@ -470,7 +505,7 @@ 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
@@ -528,9 +563,9 @@ 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]:
 
@@ -687,7 +722,7 @@ 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 +812,7 @@ 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
@@ -894,6 +929,45 @@ 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 +979,7 @@ 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 +1010,7 @@ 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,
@@ -58,6 +59,7 @@ packages:
 "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

@@ -80,8 +80,8 @@ 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
@@ -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
@@ -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]:
@@ -206,7 +206,7 @@ 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 

doc/src/Build_windows.txt

@@ -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_all.txt

@@ -19,7 +19,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 All commands :h3
 
-An alphabetic list of all LAMMPS commmands.
+An alphabetic list of all LAMMPS commands.
 
 "angle_coeff"_angle_coeff.html,
 "angle_style"_angle_style.html,
@@ -71,6 +71,7 @@ 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 +104,7 @@ 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

@@ -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_compute.txt

@@ -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

@@ -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,
@@ -65,13 +67,14 @@ 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,
@@ -104,17 +107,18 @@ OPT.
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,
 "nph/eff"_fix_nh_eff.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
+"nph/sphere (ko)"_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,
@@ -169,26 +173,26 @@ OPT.
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.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 +220,7 @@ 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,

doc/src/Commands_kspace.txt

@@ -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

@@ -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 +196,11 @@ 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,
 "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 +232,8 @@ 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
 

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_messages.txt

@@ -743,7 +743,7 @@ 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
 
@@ -1092,11 +1092,6 @@ correct. :dd
 The specified file cannot be opened.  Check that the path and name are
 correct. :dd
 
-{Cannot open fix ave/spatial file %s} :dt
-
-The specified file cannot be opened.  Check that the path and name are
-correct. :dd
-
 {Cannot open fix ave/time file %s} :dt
 
 The specified file cannot be opened.  Check that the path and name are
@@ -1677,10 +1672,6 @@ provided by an atom map.  An atom map does not exist (by default) for
 non-molecular problems.  Using the atom_modify map command will force
 an atom map to be created. :dd
 
-{Cannot use fix ave/spatial z for 2 dimensional model} :dt
-
-Self-explanatory. :dd
-
 {Cannot use fix bond/break with non-molecular systems} :dt
 
 Only systems with bonds that can be changed can be used.  Atom_style
@@ -2425,10 +2416,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Compute ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Compute ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -4074,10 +4061,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Fix ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Fix ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -4379,51 +4362,6 @@ same style. :dd
 
 Self-explanatory. :dd
 
-{Fix ave/spatial compute does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial compute does not calculate a per-atom vector} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute does not calculate per-atom values} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom vector} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix does not calculate per-atom values} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial for triclinic boxes requires units reduced} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial settings invalid with changing box size} :dt
-
-If the box size changes, only the units reduced option can be
-used. :dd
-
-{Fix ave/spatial variable is not atom-style variable} :dt
-
-A variable used by fix ave/spatial must generate per-atom values. :dd
-
 {Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
 
 One of more of the vector inputs has individual elements which are
@@ -5078,7 +5016,7 @@ 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 +5030,7 @@ 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 +5048,7 @@ 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 +5479,7 @@ 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
 

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

doc/src/Howto.txt

@@ -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

@@ -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_body.txt

@@ -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

@@ -22,7 +22,7 @@ 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
+Here, each of the 4 kinds of chunk-related commands is briefly
 overviewed.  Then some examples are given of how to compute different
 properties with chunk commands.
 
@@ -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 bewteen 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 subsitituted 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_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_library.txt

@@ -171,16 +171,16 @@ 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).

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 Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

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

doc/src/Howto_spherical.txt

@@ -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

doc/src/Howto_spins.txt

@@ -9,10 +9,10 @@ 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 
+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 
@@ -43,7 +43,7 @@ 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 
+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

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 Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

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 Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

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_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="24 Oct 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
+24 Oct 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
@@ -61,6 +62,7 @@ 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 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_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/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 +89,12 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"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-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -297,7 +300,7 @@ 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
@@ -412,7 +415,7 @@ 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 +462,10 @@ 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
@@ -549,10 +552,6 @@ 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 +562,31 @@ 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 +668,9 @@ 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.
@@ -851,7 +875,7 @@ 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 +898,7 @@ 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 +1008,11 @@ 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.
@@ -1370,7 +1394,7 @@ 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.
@@ -1392,7 +1416,7 @@ 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 +1520,7 @@ 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.
@@ -1577,13 +1601,11 @@ 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.
 
@@ -1593,7 +1615,7 @@ 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.
@@ -1631,10 +1653,11 @@ 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).
@@ -1698,7 +1721,7 @@ 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 +1745,25 @@ 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:]
@@ -1839,6 +1881,41 @@ 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-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]
@@ -1998,3 +2075,5 @@ 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

@@ -58,17 +58,20 @@ 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-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-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)

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

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 +354,77 @@ 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
+
+Note that the specified restartfile and/or datafile can have the
+wild-card character "*".  The restartfile can also have the wild-card
+character "%".  The meaning of these characters is explained on the
+"read_restart"_read_restart.html and "write_data"_write_data.html doc
+pages.  The use of "%" means that a parallel restart file can be read.
+Note that a filename such as file.* will need to be enclosed in quotes
+to avoid shell expansion of the "*" character.
+
+Note that following restartfile, the optional word "remap" can be
+used.  This has the effect of adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page.  This is useful if reading the restart file triggers an error
+that atoms have been lost.  In that case, use of the remap flag should
+allow the data file to still be produced.
+
+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 can have wild-card
+characters ("*","%") as explained on the
+"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
+pages.  The use of "%" means that a parallel restart file and/or
+parallel dump file can be read and/or written.  Note that a filename
+such as file.* will need to be enclosed in quotes to avoid shell
+expansion of the "*" character.
+
+Note that following restartfile, the optional word "remap" can be
+used.  This has the effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page.  This is useful if reading the restart file triggers an error
+that atoms have been lost.  In that case, use of the remap flag should
+allow the dump file to still be produced.
+
+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

doc/src/Run_windows.txt

@@ -33,8 +33,8 @@ 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

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,

doc/src/Speed_gpu.txt

@@ -62,7 +62,7 @@ Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-d
 installed. There can be multiple of them for the same or different hardware
 (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
 as 'platforms'.  The GPU library will select the [first] suitable platform,
-but this can be overridded using the device option of the "package"_package.html
+but this can be overridden using the device option of the "package"_package.html
 command. run lammps/lib/gpu/ocl_get_devices to get a list of available
 platforms and devices with a suitable ICD available.
 

doc/src/Speed_intel.txt

@@ -68,7 +68,7 @@ In most molecular dynamics software, parallelization parameters
 to changing the order of operations with finite-precision
 calculations. The USER-INTEL package is deterministic. This means
 that the results should be reproducible from run to run with the
-{same} parallel configurations and when using determinstic
+{same} parallel configurations and when using deterministic
 libraries or library settings (MPI, OpenMP, FFT). However, there
 are differences in the USER-INTEL package that can change the
 order of operations compared to LAMMPS without acceleration:
@@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to
 styles when USER-INTEL styles are not available.
 
 NOTE: For simulations on higher node counts, add "processors * * * 
-grid numa"_processors.html" to the beginning of the input script for
+grid numa"_processors.html to the beginning of the input script for
 better scalability.
 
 When running on many nodes, performance might be better when using
@@ -499,7 +499,7 @@ MPI task.
 When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
 that require skip lists for neighbor builds cannot be offloaded.
 Using "hybrid/overlay"_pair_hybrid.html is allowed.  Only one intel
-accelerated style may be used with hybrid styles.
+accelerated style may be used with hybrid styles when offloading.
 "Special_bonds"_special_bonds.html exclusion lists are not currently
 supported with offload, however, the same effect can often be
 accomplished by setting cutoffs for excluded atom types to 0.  None of

doc/src/Speed_kokkos.txt

@@ -93,12 +93,12 @@ The "t Nt" option specifies how many OpenMP threads per MPI task to
 use with a node. The default is Nt = 1, which is MPI-only mode.  Note
 that the product of MPI tasks * OpenMP threads/task should not exceed
 the physical number of cores (on a node), otherwise performance will
-suffer. If hyperthreading is enabled, then the product of MPI tasks *
-OpenMP threads/task should not exceed the physical number of cores *
-hardware threads.  The "-k on" switch also issues a "package kokkos"
-command (with no additional arguments) which sets various KOKKOS
-options to default values, as discussed on the "package"_package.html
-command doc page.
+suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
+tasks * OpenMP threads/task should not exceed the physical number of
+cores * hardware threads.  The "-k on" switch also issues a
+"package kokkos" command (with no additional arguments) which sets
+various KOKKOS options to default values, as discussed on the
+"package"_package.html command doc page.
 
 The "-sf kk" "command-line switch"_Run_options.html will automatically
 append the "/kk" suffix to styles that support it.  In this manner no
@@ -106,6 +106,11 @@ modification to the input script is needed. Alternatively, one can run
 with the KOKKOS package by editing the input script as described
 below.
 
+NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e. 
+Makefile.kokkos_mpi_only) will give better performance than the OpenMP 
+backend (i.e. Makefile.kokkos_omp) because some of the overhead to make 
+the code thread-safe is removed. 
+
 NOTE: The default for the "package kokkos"_package.html command is to
 use "full" neighbor lists and set the Newton flag to "off" for both
 pairwise and bonded interactions. However, when running on CPUs, it
@@ -122,6 +127,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
 If the "newton"_newton.html command is used in the input
 script, it can also override the Newton flag defaults.
 
+For half neighbor lists and OpenMP, the KOKKOS package uses data 
+duplication (i.e. thread-private arrays) by default to avoid 
+thread-level write conflicts in the force arrays (and other data 
+structures as necessary). Data duplication is typically fastest for 
+small numbers of threads (i.e. 8 or less) but does increase memory 
+footprint and is not scalable to large numbers of threads. An 
+alternative to data duplication is to use thread-level atomics, which 
+don't require duplication. The use of atomics can be forced by compiling 
+with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all 
+Kokkos-enabled pair_styles support data duplication. Alternatively, full 
+neighbor lists avoid the need for duplication or atomics but require 
+more compute operations per atom. When using the Kokkos Serial backend 
+or the OpenMP backend with a single thread, no duplication or atomics are 
+used. For CUDA and half neighbor lists, the KOKKOS package always uses 
+atomics.
+
 [Core and Thread Affinity:]
 
 When using multi-threading, it is important for performance to bind
@@ -149,7 +170,7 @@ Intel Knight's Landing (KNL) Xeon Phi:
 
 KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
 reserved for the OS, and only 64 or 66 cores are used. Each core has 4
-hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
 cores to run on. The product of MPI tasks * OpenMP threads/task should
 not exceed this limit, otherwise performance will suffer. Note that
 with the KOKKOS package you do not need to specify how many KNLs there
@@ -228,7 +249,7 @@ for details and default settings. Experimenting with its options can
 provide a speed-up for specific calculations. For example:
 
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
-mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 
 NOTE: For good performance of the KOKKOS package on GPUs, you must
 have Kepler generation GPUs (or later). The Kokkos library exploits

doc/src/Speed_measure.txt

@@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when
 communication occurs for other processors to catch up.  Thus the
 reported times for "Communication" or "Other" may be higher than they
 really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
 LAMMPS, to obtain synchronized timings.
 

doc/src/Speed_omp.txt

@@ -29,7 +29,7 @@ instructions.
 
 [Run with the USER-OMP package from the command line:]
 
-These example asume one or more 16-core nodes.
+These examples assume one or more 16-core nodes.
 
 env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script           # 1 MPI task, 16 threads according to OMP_NUM_THREADS
 lmp_mpi -sf omp -in in.script                                  # 1 MPI task, no threads, optimized kernels

doc/src/Speed_packages.txt

@@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
 "pair_style lj/cut/opt"_pair_lj.html :ul
 
 To see what accelerate styles are currently available for a particular
-style, find the style name in the "Commands_all"_Commands_all.html
+style, find the style name in the "Commands_all"_lc
 style pages (fix,compute,pair,etc) and see what suffixes are listed
 (g,i,k,o,t) with it.  The doc pages for individual commands
 (e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list

doc/src/USER/atc/man_add_molecule.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_add_species.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_atom_element_map.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_atom_weight.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_atomic_charge.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_boundary.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_boundary_dynamics.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_boundary_faceset.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_boundary_integral.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_consistent_fe_initialization.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_contour_integral.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_control.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_control_momentum.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_control_thermal.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_control_thermal_correction_max_iterations.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_decomposition.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_electron_integration.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_equilibrium_start.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_extrinsic_exchange.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_fe_md_boundary.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_fem_mesh.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_filter_scale.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_filter_type.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_fix_atc.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_fix_flux.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_fix_nodes.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_hardy_computes.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_hardy_fields.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_hardy_gradients.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_hardy_kernel.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>

doc/src/USER/atc/man_hardy_on_the_fly.html

@@ -11,7 +11,7 @@
   <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
   <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
   <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
-  <a href="../../Section_commands.html#comm">Commands</a>
+  <a href="../../Commands_all.html">Commands</a>
 </center>
 
 <hr>