Merge pull request #1198 from akohlmey/next-patch-release

Patch release 9 November 2018

.github/CODEOWNERS

@@ -17,6 +17,7 @@ src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
+src/MESSAGE/*         @sjplimp
 src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
@@ -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

.github/CONTRIBUTING.md

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

.gitignore

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

README

@@ -36,7 +36,14 @@ tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-doc/Manual.html	           the LAMMPS manual
-doc/Section_intro.html	   hi-level introduction to LAMMPS
-doc/Section_start.html	   how to build and use LAMMPS
-doc/Developer.pdf          LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html                # creates HTML pages in doc/html
+% make pdf                 # creates Manual.pdf and Developer.pdf

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 +165,38 @@ set(LAMMPS_LINK_LIBS)
 set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
+  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+  SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
+  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
+  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
+  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
+  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
+  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
+  USER-QUIP USER-QMMM)
+set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(OTHER_PACKAGES CORESHELL QEQ)
+foreach(PKG ${DEFAULT_PACKAGES})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+  enable_language(Fortran)
+endif()
+
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+  enable_language(C)
+endif()
+
+include_directories(${LAMMPS_SOURCE_DIR})
+
+# do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
@@ -183,25 +241,52 @@ 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 +300,7 @@ 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 +351,14 @@ 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()
 
@@ -377,6 +455,9 @@ endif()
 if(PKG_LATTE)
   option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
   if(DOWNLOAD_LATTE)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
     message(STATUS "LATTE not found - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
@@ -397,6 +478,83 @@ 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-PLUMED)
+  find_package(GSL REQUIRED)
+  option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)
+  if(DOWNLOAD_PLUMED)
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz 
+      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> 
+                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                                  )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
+      ${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED plumed REQUIRED)
+    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()
+
 if(PKG_USER-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@@ -406,8 +564,8 @@ 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()
 
@@ -424,8 +582,9 @@ if(PKG_USER-SMD)
     set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
     list(APPEND LAMMPS_DEPS Eigen3_build)
   else()
-    find_package(Eigen3)
-    if(NOT Eigen3_FOUND)
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
       message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
     endif()
   endif()
@@ -475,10 +634,47 @@ if(PKG_KIM)
   include_directories(${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)
   if(DOWNLOAD_MSCG)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR 
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
     include(ExternalProject)
     if(NOT LAPACK_FOUND)
       set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
@@ -558,8 +754,8 @@ RegisterStyles(${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})
@@ -577,8 +773,8 @@ 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})
@@ -592,8 +788,10 @@ 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)
@@ -668,13 +866,16 @@ 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)
 
@@ -704,6 +905,20 @@ if(PKG_USER-OMP)
     include_directories(${USER-OMP_SOURCES_DIR})
 endif()
 
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()
+
 if(PKG_KOKKOS)
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -731,6 +946,11 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+  if(PKG_KSPACE)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+  endif()
+
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
 
   # detects styles which have KOKKOS version
@@ -869,7 +1089,7 @@ 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")
@@ -882,15 +1102,15 @@ 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
@@ -939,7 +1159,7 @@ 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})
@@ -989,7 +1209,6 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
-include_directories(${LAMMPS_SOURCE_DIR})
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
 ######################################
@@ -997,7 +1216,9 @@ 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()
@@ -1022,14 +1243,14 @@ 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()
@@ -1045,10 +1266,11 @@ 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()
 
@@ -1063,7 +1285,7 @@ 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})
 
@@ -1116,7 +1338,7 @@ 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)
@@ -1158,7 +1380,7 @@ 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/README.md

@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BUILD_EXE</code></td>
+  <td>control whether to build LAMMPS executable</td>
+  <td>
+  <dl>
+    <dt><code>on</code> (default)</dt>
+    <dt><code>off</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BUILD_SHARED_LIBS</code></td>
   <td>control whether to build LAMMPS as a shared-library</td>

cmake/pkgconfig/liblammps.pc.in

@@ -1,18 +1,38 @@
 # pkg-config file for lammps
 # https://people.freedesktop.org/~dbn/pkg-config-guide.html
-# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
-# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+
+# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
 # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
 
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+# Use this on commandline with:
+# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp
+
+# Use this in a Makefile:
+# myapp: myapp.cpp
+# 	$(CC) `pkg-config --cflags --libs lammps` -o $@ $<
+
+# Use this in autotools:
+# configure.ac:
+# PKG_CHECK_MODULES([LAMMPS], [lammps])
+# Makefile.am:
+# myapp_CFLAGS = $(LAMMPS_CFLAGS)
+# myapp_LDADD = $(LAMMPS_LIBS)
+
+# Use this in CMake:
+# CMakeLists.txt:
+# find_package(PkgConfig)
+# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
+# target_link_libraries(<lib> PkgConfig::LAMMPS)
+
+prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
 Requires:
-Libs: -L${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

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

cmake/presets/all_on.cmake

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

cmake/presets/manual_selection.cmake

@@ -61,6 +61,7 @@ set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
 set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

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

cmake/presets/std.cmake

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

cmake/presets/std_nolib.cmake

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

cmake/presets/user.cmake

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

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.txt

@@ -1,5 +1,5 @@
 "Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run.html :c
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
@@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
    Build_settings
    Build_package
    Build_extras
+   Build_windows
 
 END_RST -->
 
@@ -39,7 +40,8 @@ END_RST -->
 "Basic build options"_Build_basics.html
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html :all(b)
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

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

@@ -13,12 +13,10 @@ This page is a short summary of how to use CMake to build LAMMPS.
 Details on CMake variables that enable specific LAMMPS build options
 are given on the pages linked to from the "Build"_Build.html doc page.
 
-Richard Berger (Temple U) has also written a more comprehensive guide
+Richard Berger (Temple U) has also written a "more comprehensive
+guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
 for how to use CMake to build LAMMPS.  If you are new to CMake it is a
-good place to start:
-
-"Bulding LAMMPS using
-CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+good place to start.
 
 :line
 
@@ -42,7 +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
@@ -52,7 +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
@@ -81,8 +79,9 @@ directory to un-install all packages.  The purge removes all the *.h
 files auto-generated by make.
 
 You must have CMake version 2.8 or later on your system to build
-LAMMPS.  If you include the GPU or KOKKOS packages, CMake version 3.2
-or later is required.  Installation instructions for CMake are below.
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
 
 After the initial build, if you edit LAMMPS source files, or add your
 own new files to the source directory, you can just re-type make from
@@ -189,7 +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,
@@ -40,6 +41,7 @@ This is the list of packages that may require additional steps.
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
+"USER-PLUMED" _#user-plumed,
 "USER-H5MD"_#user-h5md,
 "USER-INTEL"_#user-intel,
 "USER-MOLFILE"_#user-molfile,
@@ -47,8 +49,9 @@ 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)
+"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
 
 :line
 
@@ -175,8 +178,15 @@ package?" page.
 [CMake build]:
 
 -D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # path to KIM shared library (only needed if a custom location) 
--D KIM_INCLUDE_DIR=path  # path to KIM include directory (only needed if a custom location) :pre
+-D KIM_LIBRARY=path      # KIM library file (only needed if a custom location) 
+-D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
+inside the CMake build directory.  If the KIM library is already on
+your system (in a location CMake cannot find it), KIM_LIBRARY is the
+filename (plus path) of the KIM library file, not the directory the
+library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
+file is in.
 
 [Traditional make]:
 
@@ -296,7 +306,13 @@ library.
 [CMake build]:
 
 -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
--D LATTE_LIBRARY=path      # path to LATTE shared library (only needed if a custom location) :pre
+-D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location) :pre
+
+If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and
+built inside the CMake build directory.  If the LATTE library is
+already on your system (in a location CMake cannot find it),
+LATTE_LIBRARY is the filename (plus path) of the LATTE library file,
+not the directory the library file is in.
 
 [Traditional make]:
 
@@ -327,7 +343,7 @@ 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.
 
@@ -348,6 +364,10 @@ 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
@@ -360,6 +380,35 @@ 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
@@ -371,8 +420,15 @@ lib/mscg/README and MSCG/Install files for more details.
 [CMake build]:
 
 -D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
--D MSCG_LIBRARY=path      # path to MSCG shared library (only needed if a custom location) 
--D MSCG_INCLUDE_DIR=path  # path to MSCG include directory (only needed if a custom location) :pre
+-D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location) 
+-D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
+inside the CMake build directory.  If the MSCG library is already on
+your system (in a location CMake cannot find it), MSCG_LIBRARY is the
+filename (plus path) of the MSCG library file, not the directory the
+library file is in.  MSCG_INCLUDE_DIR is the directory the MSCG
+include file is in.
 
 [Traditional make]:
 
@@ -450,7 +506,7 @@ 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
@@ -508,15 +564,22 @@ file.
 VORONOI package :h4,link(voronoi)
 
 To build with this package, you must download and build the "Voro++
-library"_voro_home.
+library"_voro-home.
 
-:link(voro_home,http://math.lbl.gov/voro++)
+:link(voro-home,http://math.lbl.gov/voro++)
 
 [CMake build]:
 
 -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
--D VORO_LIBRARY=path      # (only needed if at custom location) path to VORO shared library
--D VORO_INCLUDE_DIR=path  # (only needed if at custom location) path to VORO include directory :pre
+-D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location) 
+-D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
+built inside the CMake build directory.  If the Voro++ library is
+already on your system (in a location CMake cannot find it),
+VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in.  VORO_INCLUDE_DIR is the
+directory the Voro++ include file is in.
 
 [Traditional make]:
 
@@ -650,6 +713,62 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
+USER-PLUMED package :h4,link(user-plumed)
+
+[CMake build]:
+
+[Traditional make]:
+
+Before building LAMMPS with this package, you must first build 
+PLUMED.  We recommending building PLUMED separately to LAMMPS using 
+the instructions that can be found at http://plumed.github.io/doc-master/user-doc/html/_installation.html.
+Before compiling LAMMPS you can then install the fix plumed command
+and compile LAMMPS in the usual manner:
+
+make yes-user-plumed 
+make machine :pre
+
+Once this compilation completes you should be able to run LAMMPS in the usual
+way.  When running LAMMPS with an input script that contains a fix
+plumed command LAMMPS will try to call the PLUMED runtime library.  PLUMED
+must therefore be available in your path if LAMMPS is compiled in this way.
+
+On some machines it is not possible to call runtime libraries in the way described
+above.  When compiling on these machines it is thus better to statically link
+PLUMED when compiling LAMMPS.  To do this you must either download a PLUMED
+tarball from http://www.plumed.org/get-it or clone it using
+git clone https://github.com/plumed/plumed2.git.  If you download the tarball
+unpack it in the /lib/plumed directory.  Similarly if you clone 
+it clone it to the /lib/plumed directory as if there is a version of PLUMED within
+this directory LAMMPS will always try to statically link the version of PLUMED
+that this directory contains instead of dynamically linking the library.
+
+Once you have downloaded PLUMED into /lib/plumed you must again build the code
+here by following the instructions that can be found at
+http://plumed.github.io/doc-master/user-doc/html/_installation.html.
+
+You can statically link PLUMED manually and if you want to access the full
+range of PLUMED functionalities this is what you should do.  If you only want the
+basic range of functionalities, however, (i.e. no user contributed modules) then
+you can download and compile PLUMED in one step from the lammps/src dir, using a
+command like like those below:
+
+make lib-plumed                       # print help message
+make lib-plumed  args="-b"            # download and build the latest stable version of PLUMED
+
+These commands will simply invoke the lib/plumed/Install.py script with
+args specified.  Furthermore, once the script has completed you should
+have a compiled version of PLUMED.  With this built you can install/un-install
+PLUMED and build LAMMPS in the usual manner:
+
+make yes-user-plumed
+make machine :pre
+
+make no-user-plumed
+make machine :pre
+
+:line
+
 USER-H5MD package :h4,link(user-h5md)
 
 To build with this package you must have the HDF5 software package
@@ -660,7 +779,7 @@ 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
@@ -750,7 +869,7 @@ 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
@@ -867,6 +986,45 @@ 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.
@@ -877,7 +1035,10 @@ Eigen3 is a template library, so you do not need to build it.
 -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
 -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location) :pre
 
-Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library.
+If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
+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.
 
 [Traditional make]:
 
@@ -906,7 +1067,7 @@ 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,
@@ -58,8 +59,9 @@ 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)
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
 
 The mechanism for including packages is simple but different for CMake
 versus make.

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

@@ -0,0 +1,97 @@
+"Higher level section"_Build.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
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.  
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or 
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested. 
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+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 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.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.

doc/src/Commands.txt

@@ -1,4 +1,4 @@
-"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
 "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
 Section"_Packages.html :c
 

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,
@@ -91,6 +94,7 @@ OPT.
 "lineforce"_fix_lineforce.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso"_fix_meso.html,
+"meso/move"_fix_meso_move.html,
 "meso/stationary"_fix_meso_stationary.html,
 "momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
@@ -104,17 +108,18 @@ 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,
@@ -168,27 +173,28 @@ OPT.
 "restrain"_fix_restrain.html,
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.html,
+"rigid/meso"_fix_rigid_meso.html,
 "rigid/nph (o)"_fix_rigid.html,
+"rigid/nph/small"_fix_rigid.html,
 "rigid/npt (o)"_fix_rigid.html,
+"rigid/npt/small"_fix_rigid.html,
 "rigid/nve (o)"_fix_rigid.html,
+"rigid/nve/small"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
+"rigid/nvt/small"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
 "rx (k)"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "shardlow (k)"_fix_shardlow.html,
 "smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/adjust_dt"_fix_smd_adjust_dt.html,
+"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
+"smd/wall_surface"_fix_smd_wall_surface.html,
 "spring"_fix_spring.html,
 "spring/chunk"_fix_spring_chunk.html,
 "spring/rg"_fix_spring_rg.html,
@@ -216,7 +222,7 @@ 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 +196,12 @@ OPT.
 "quip"_pair_quip.html,
 "reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
-"rebo (oi)"_pair_airebo.html,
+"rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html,
 "smd/ulsph"_pair_smd_ulsph.html,
 "smtbq"_pair_smtbq.html,
 "snap (k)"_pair_snap.html,
@@ -224,8 +233,8 @@ OPT.
 "tip4p/long/soft (o)"_pair_lj_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
+"vashishta (gko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
+"yukawa (gko)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
+"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Commands_parse.txt

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

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

@@ -8,27 +8,44 @@ Section"_Examples.html :c
 
 :line
 
-How to discussions :h2
+Howto discussions :h2
 
 These doc pages describe how to perform various tasks with LAMMPS,
 both for users and developers.  The
 "glossary"_http://lammps.sandia.gov website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.
-
-The example input scripts included in the examples dir of the LAMMPS
+terminology with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the examples dir of the LAMMPS
 distribution and highlighted on the "Examples"_Examples.html doc page
 also show how to setup and run various kinds of simulations.
 
+Tutorials howto :h3
+
 <!-- RST
 
 .. toctree::
+   :name: tutorials
    :maxdepth: 1
 
    Howto_github
    Howto_pylammps
    Howto_bash
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+General howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: general
    :maxdepth: 1
 
    Howto_restart
@@ -37,36 +54,89 @@ also show how to setup and run various kinds of simulations.
    Howto_replica
    Howto_library
    Howto_couple
+   Howto_client_server
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"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
+"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Settings howto :h3
+
+<!-- RST
 
 .. toctree::
-   :maxdepth: 1
-
-   Howto_output
-   Howto_chunk
-
-.. toctree::
+   :name: settings
    :maxdepth: 1
 
    Howto_2d
    Howto_triclinic
-   Howto_walls
-   Howto_nemd
-   Howto_granular
-   Howto_spherical
-   Howto_dispersion
-
-.. toctree::
-   :maxdepth: 1
-
-   Howto_temperature
    Howto_thermostat
    Howto_barostat
+   Howto_walls
+   Howto_nemd
+   Howto_dispersion
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+
+Analysis howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: analysis
+   :maxdepth: 1
+
+   Howto_output
+   Howto_chunk
+   Howto_temperature
    Howto_elastic
    Howto_kappa
    Howto_viscosity
    Howto_diffusion
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+"Calculate temperature"_Howto_temperature.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Force fields howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: force
    :maxdepth: 1
 
    Howto_bioFF
@@ -74,9 +144,27 @@ also show how to setup and run various kinds of simulations.
    Howto_tip4p
    Howto_spc
 
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Packages howto :h3
+
+<!-- RST
+
 .. toctree::
+   :name: packages
    :maxdepth: 1
 
+   Howto_spherical
+   Howto_granular
    Howto_body
    Howto_polarizable
    Howto_coreshell
@@ -87,43 +175,11 @@ also show how to setup and run various kinds of simulations.
 
 END_RST -->
 
+
 <!-- HTML_ONLY -->
 
-"Using GitHub with LAMMPS"_Howto_github.html
-"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
-
-"Restart a simulation"_Howto_restart.html
-"Visualize LAMMPS snapshots"_Howto_viz.html
-"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)
-
-"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
-"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
-
-"2d simulations"_Howto_2d.html
-"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
-"Walls"_Howto_walls.html
-"NEMD simulations"_Howto_nemd.html
-"Granular models"_Howto_granular.html
 "Finite-size spherical and aspherical particles"_Howto_spherical.html
-"Long-range dispersion settings"_Howto_dispersion.html :all(b)
-
-"Calculate temperature"_Howto_temperature.html
-"Thermostats"_Howto_thermostat.html
-"Barostats"_Howto_barostat.html
-"Calculate elastic constants"_Howto_elastic.html
-"Calculate thermal conductivity"_Howto_kappa.html
-"Calculate viscosity"_Howto_viscosity.html
-"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
-
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
-"TIP3P water model"_Howto_tip3p.html
-"TIP4P water model"_Howto_tip4p.html
-"SPC water model"_Howto_spc.html :all(b)
-
+"Granular models"_Howto_granular.html
 "Body style particles"_Howto_body.html
 "Polarizable models"_Howto_polarizable.html
 "Adiabatic core/shell model"_Howto_coreshell.html

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_diffusion.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Calculate a diffusion coefficient :h3
+Calculate diffusion coefficients :h3
 
 The diffusion coefficient D of a material can be measured in at least
 2 ways using various options in LAMMPS.  See the examples/DIFFUSE

doc/src/Howto_dispersion.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Long-raage dispersion settings :h3
+Long-range dispersion settings :h3
 
 The PPPM method computes interactions by splitting the pair potential
 into two parts, one of which is computed in a normal pairwise fashion,

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_temperature.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-Calcalate temperature :h3
+Calculate temperature :h3
 
 Temperature is computed as kinetic energy divided by some number of
 degrees of freedom (and the Boltzmann constant).  Since kinetic energy

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_authors.txt

@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-LAMMPS authors :h3
+Authors of LAMMPS :h3
 
 The primary LAMMPS developers are at Sandia National Labs and Temple
 University:
@@ -15,7 +15,8 @@ University:
 "Steve Plimpton"_sjp, sjplimp at sandia.gov
 Aidan Thompson, athomps at sandia.gov
 Stan Moore, stamoor at sandia.gov
-Axel Kohlmeyer, akohlmey at gmail.com :ul
+Axel Kohlmeyer, akohlmey at gmail.com
+Richard Berger, richard.berger at temple.edu :ul
 
 :link(sjp,http://www.cs.sandia.gov/~sjplimp)
 
@@ -24,26 +25,31 @@ and Ray Shan, now at Materials Design.
 
 :line
 
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort.  Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
+The "Authors page"_http://lammps.sandia.gov/authors.html of the
+"LAMMPS website"_lws has a comprehensive list of all the individuals
+who have contributed code for a new feature or command or tool to
+LAMMPS.
 
-Richard Berger (Temple U), Python interface, GitHub site, Sphinx doc pages
+:line
+
+The following folks deserve special recognition.  Many of the packages
+they have written are unique for an MD code and LAMMPS would not be as
+general-purpose as it is without their expertise and efforts.
+
+Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF
+Mike Brown (Intel), GPU and USER-INTEL packages
+Colin Denniston (U Western Ontario), USER-LB package
+Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages
+Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
+Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
+Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
+Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
+Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
+Mike Parks (Sandia), PERI package for Peridynamics
 Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
-Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
+Christian Trott (Sandia), USER-CUDA and KOKKOS packages
+Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
+Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
 
 :line
 
@@ -58,322 +64,3 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
 Steve Lustig (Dupont)
 Jim Belak and Roy Pollock (LLNL) :ul
 
-:line
-
-Here is a timeline for when various individuals contributed to a new
-feature or command or tool added to LAMMPS:
-
-Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U)
-Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
-Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
-Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
-May18 : fix bond/react : Jake Gissinger (CU Boulder)
-Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
-Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U) 
-Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
-Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
-Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
-Dec17 : fix python/move : Richard Berger (Temple U)
-Nov17 : pair extep : Jaap Kroes (Radboud U)
-Oct17 : USER-UEF package : David Nicholson (MIT)
-Oct17 : fix rhok : Ulf Pederson (Roskilde U)
-Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
-Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
-Sep17 : fix latte : Christian Negre (LANL)
-Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
-Aug17 : USER-MESO package : Zhen Li (Brown University)
-Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
-Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
-Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
-Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
-Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
-Jun17 : compute cnp/atom : Paulo Branicio (USC)
-May17 : fix python and pair python : Richard Berger (Temple U)
-May17 : pair edip/multi : Chao Jiang (U Wisconsin)
-May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
-Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
-Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
-Mar17 : fix filter/corotate : Lukas Fath (KIT)
-Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
-Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
-Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
-Jan17 : fix mscg : Lauren Abbott (Sandia)
-Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
-Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
-Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
-Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
-Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
-Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
-Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
-Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
-Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
-Sep16 : kspace pppm/kk : Stan Moore (Sandia)
-Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
-Aug16 : fix controller : Aidan Thompson (Sandia)
-Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
-Jul16 : dihedral spherical : Andrew Jewett
-Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
-Jun16 : fix orient/bcc : Tegar Wicaksono (UBC) 
-Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
-Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
-May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
-Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
-Apr16 : bond write : Axel Kohlmeyer (Temple U)
-Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
-Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
-Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
-Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
-Dec15 : fix qeq/fire : Ray Shan (Sandia)
-Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
-Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
-Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
-Oct15 : displace_atoms variable option : Reese Jones (Sandia)
-Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
-Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
-Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
-Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
-Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
-Aug15 : timer command : Axel Kohlmeyer (Temple U)
-Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
-Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
-Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
-Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
-Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
-Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
-Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
-Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
-Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
-Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
-Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
-Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
-Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
-Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
-Feb15 : fix tfmc : Kristof Bal (U of Antwerp) 
-Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
-Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
-Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
-Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
-Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF) 
-Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
-Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
-Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
-Aug14 : USER-INTEL package : Mike Brown (Intel)
-May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
-May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
-Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
-Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
-Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
-Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
-Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
-Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
-Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
-Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
-Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
-Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
-Sep13 : xmgrace tool : Vikas Varshney
-Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
-Aug13 : pair nm and variants : Julien Devemy (ICCF)
-Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
-Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
-Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
-Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
-Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
-Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia) 
-Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
-Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
-Jun13 : fix tune/kspace : Paul Crozier (Sandia)
-Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
-May13 : compute msd/nongauss : Rob Hoy
-May13 : pair list : Axel Kohlmeyer (Temple U)
-May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
-Apr13 : dump_modify nfile and fileper : Christopher Knight
-Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
-Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
-Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
-Feb13 : fix species : Ray Shan (Sandia)
-Jan13 : compute voronoi/atom : Daniel Schwen
-Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
-Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
-Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
-Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
-Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
-Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
-Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
-Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
-Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
-Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
-Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
-Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
-Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
-Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
-Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
-May12 : read_dump : Tim Sirk (ARL)
-May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
-May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
-Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
-Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
-Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
-Feb12 : pair_style beck : Jon Zimmerman (Sandia)
-Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
-Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
-Jan12 : dihedral_style table : Andrew Jewett (UCSB)
-Jan12 : angle_style dipole : Mario Orsi
-Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
-Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
-Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
-Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
-Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
-Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
-Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
-Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
-Sep11 : pair_style edip : Luca Ferraro (CASPUR)
-Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
-Aug11 : fix restrain : Craig Tenney (Sandia)
-Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
-Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
-Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
-Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
-Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
-Aug11 : pair_style dipole/sf : Mario Orsi
-Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
-Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \
-  Axel Kohlmeyer (Temple U)
-Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
-  Chandra Veer Singh (Cornell)
-Jun11 : Windows build option via Microsoft Visual Studio : \
-  Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : dump image : Nathan Fabian (Sandia)
-May11 : pppm GPU single and double : Mike Brown (ORNL)
-May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
-2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
-- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
-- : fix adapt and compute ti for thermodynamic integration for \
-  free energies : Sai Jayaraman (Sandia)
-- : pair_style born and gauss : Sai Jayaraman (Sandia)
-- : stochastic rotation dynamics (SRD) via fix srd : \
-  Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
-- : ipp Perl script tool : Reese Jones (Sandia)
-- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
-- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
-- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
-- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
-- : fix ave/correlate :  Benoit Leblanc, Dave Rigby, \
-  Paul Saxe (Materials Design) and Reese Jones (Sandia)
-- : pair_style peri/lps : Mike Parks (Sandia)
-- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
-- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U) 
-- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
-- : public SVN & Git repositories for LAMMPS : \
-  Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
-- : compute heat/flux : German Samolyuk (ORNL) and \
-  Mario Pinto (Computational Research Lab, Pune, India)
-- : pair_style yukawa/colloid : Randy Schunk (Sandia)
-- : fix wall/colloid : Jeremy Lechman (Sandia)
-2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
-- : concentration-dependent EAM potential : \
-  Alexander Stukowski (Technical University of Darmstadt)
-- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
-- : min_style hftn : Todd Plantenga (Sandia)
-- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
-- : dump cfg : Liang Wan (Chinese Academy of Sciences)
-- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
-- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
-- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
-- : fix langevin tally : Carolyn Phillips (U Michigan)
-- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
-  Philip Howell (Siemens), Vikas Varsney (AFRL)
-- : region cone : Pim Schravendijk
-- : pair_style born/coul/long : Ahmed Ismail (Sandia)
-- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
-- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
-- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
-- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
-2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
-- : peridynamics : Mike Parks (Sandia)
-- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
-- : GROMACS pair potentials : Mark Stevens (Sandia)
-- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
-- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
-- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
-- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
-- : pair_style lubricate : Randy Schunk (Sandia)
-- : compute ackland/atom : Gerolf Ziegenhain
-- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
-  Pieter in 't Veld (Sandia)
-- : AI-REBO bond-order potential : Ase Henry (MIT)
-- : making LAMMPS a true "object" that can be instantiated \
-  multiple times, e.g. as a library : Ben FrantzDale (RPI)
-- : pymol_asphere viz tool : Mike Brown (Sandia)
-2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
-- : tensile and shear deformations : Pieter in 't Veld (Sandia)
-- : GayBerne potential : Mike Brown (Sandia)
-- : ellipsoidal particles : Mike Brown (Sandia)
-- : colloid potentials : Pieter in 't Veld (Sandia)
-- : fix heat : Paul Crozier and Ed Webb (Sandia)
-- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
-- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
-- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
-- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
-- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
-- : MEAM potential : Greg Wagner (Sandia)
-- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
-  James Fischer (High Performance Technologies), \
-  David Richie and Vincent Natoli (Stone Ridge Technologies)
-2006 : fix wall/lj126 : Mark Stevens (Sandia)
-- : Stillinger-Weber and Tersoff potentials : \
-  Aidan Thompson and Xiaowang Zhou (Sandia)
-- : region prism : Pieter in 't Veld (Sandia)
-- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : OPLS dihedral potential: Mark Stevens (Sandia)
-- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
-- : faster pair hybrid potential: James Fischer \
-    (High Performance Technologies, Inc), Vincent Natoli and \
-    David Richie (Stone Ridge Technology)
-- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
-- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
-- : grain boundary orientation fix : Koenraad Janssens and \
-  David Olmsted (Sandia)
-- : pair_style lj/smooth potential : Craig Maloney (UCSB) 
-- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
-  (Johns Hopkins U) and Paul Crozier (Sandia)
-- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
-- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
-    Mark Stevens (Sandia)
-- : Finnis/Sinclair EAM: Tim Lau (MIT)
-- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
-    Frank van Swol (Sandia)
-- : TIP4P potential (4-site water): Ahmed Ismail and \
-  Amalie Frischknecht (Sandia)
-2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
-- : compressed dump files: Erik Luijten (U Illinois)
-- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
-- : electric field fix: Christina Payne (Vanderbilt U)
-- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
-  Vikas Varshney (U Akron)
-- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
-- : Morse bond potential: Jeff Greathouse (Sandia)
-- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
-- : force tables for long-range Coulombics: Paul Crozier (Sandia)
-2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
-  Christian Burisch (Bochum University, Germany)
-- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
-- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
-    Andrey Kalinichev (Sandia)
-- : parallel tempering: Mark Sears (Sandia)
-earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
-- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
-- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
-- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
-- : HTFN energy minimizer: Todd Plantenga (Sandia)
-- : class 2 force fields: Eric Simon (Cray)
-- : NVT/NPT integrators: Mark Stevens (Sandia)
-- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
-- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)

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="16 Aug 2018 version">
+<META NAME="docnumber" CONTENT="9 Nov 2018 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-16 Aug 2018 version :c,h2
+9 Nov 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 
@@ -66,7 +66,7 @@ every LAMMPS command.
 
 .. toctree::
    :maxdepth: 2
-   :numbered:
+   :numbered: 3
    :caption: User Documentation
    :name: userdoc
    :includehidden:
@@ -74,7 +74,7 @@ every LAMMPS command.
    Intro
    Install
    Build
-   Run
+   Run_head
    Commands
    Packages
    Speed
@@ -112,7 +112,7 @@ END_RST -->
 "Introduction"_Intro.html :olb,l
 "Install LAMMPS"_Install.html :l
 "Build LAMMPS"_Build.html :l
-"Run LAMMPS"_Run.html :l
+"Run LAMMPS"_Run_head.html :l
 "Commands"_Commands.html :l
 "Optional packages"_Packages.html :l
 "Accelerate performance"_Speed.html :l

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
@@ -81,7 +83,7 @@ sudo yum install python3-virtualenv :pre
 
 Fedora (since version 22) :h4
 
-sudo dnf install python3-virtualenv pre
+sudo dnf install python3-virtualenv :pre
 
 MacOS X :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 +89,13 @@ 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-SDPD"_#PKG-USER-SDPD,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -297,7 +301,7 @@ 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
@@ -382,6 +386,11 @@ switches"_Run_options.html.  Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
 have styles optimized for CPUs, KNLs, and GPUs.
 
 You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
 
 [Authors:] The KOKKOS package was created primarily by Christian Trott
 and Stan Moore (Sandia), with contributions from other folks as well.
@@ -407,7 +416,7 @@ 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
@@ -454,10 +463,10 @@ 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
@@ -544,10 +553,6 @@ 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
@@ -558,6 +563,31 @@ 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:]
@@ -639,9 +669,9 @@ 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.
@@ -846,7 +876,7 @@ 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:]
@@ -869,7 +899,7 @@ 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.
 
@@ -979,11 +1009,11 @@ 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.
@@ -1171,6 +1201,34 @@ examples/USER/colvars :ul
 
 :line
 
+USER-PLUMED package :link(USER-PLUMED),h4
+
+[Contents:]
+
+The fix plumed command allows you to use the plugin for molecular
+dynamics PLUMED to analyse and bias your LAMMPS trajectory on the fly.
+In practise PLUMED is called from within the lammps input script by using
+the "fix plumed _fix_plumed.html command.
+
+[Authors:] The PLUMED library is written and maintained by
+Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and
+Gareth Tribello. 
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-PLUMED/README
+lib/plumed/README
+"fix plumed "_fix_plumed.html
+examples/USER/plumed :ul
+
+:line
+
 USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
 
 [Contents:]
@@ -1365,7 +1423,7 @@ 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.
@@ -1387,7 +1445,7 @@ 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
 
@@ -1491,7 +1549,7 @@ 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.
@@ -1572,13 +1630,11 @@ 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.
 
@@ -1588,7 +1644,7 @@ 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.
@@ -1626,10 +1682,11 @@ 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).
@@ -1693,7 +1750,7 @@ 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
@@ -1717,6 +1774,25 @@ 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:]
@@ -1834,6 +1910,66 @@ examples/reax :ul
 
 :line
 
+USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
+
+[Contents:]
+
+A KSpace style which wraps the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de to compute long-range Coulombic
+interactions.
+
+To use this package you must have the ScaFaCoS library available on
+your system.
+
+[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS itself was developed by a consortium of German research
+facilities with a BMBF (German Ministry of Science and Education)
+funded project in 2009-2012. Participants of the consortium were the
+Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
+the Forschungszentrum Juelich.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-scafacos on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-SCAFACOS: filenames -> commands
+src/USER-SCAFACOS/README
+"kspace_style scafacos"_kspace_style.html
+"kspace_modify"_kspace_modify.html
+examples/USER/scafacos :ul
+
+:line
+
+USER-SDPD package :link(PKG-USER-SDPD),h4
+
+[Contents:]
+
+A pair style for smoothed dissipative particle dynamics (SDPD), which
+is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
+where thermal fluctuations are important (see the
+"USER-SPH package"_#PKG-USER-SPH).
+Also two fixes for moving and rigid body integration of SPH/SDPD particles
+(particles of atom_style meso).
+
+[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
+Sciences, Iran).
+
+[Supporting info:]
+
+src/USER-SDPD: filenames -> commands
+src/USER-SDPD/README
+"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
+"fix meso/move"_fix_meso_move.html
+"fix rigid/meso"_fix_rigid_meso.html
+examples/USER/sdpd :ul
+
+:line
+
 USER-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]
@@ -1993,3 +2129,5 @@ src/USER-VTK: filenames -> commands
 src/USER-VTK/README
 lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
+
+

doc/src/Packages_standard.txt

@@ -25,42 +25,43 @@ refers to the examples/USER/atc directory.  The "Library" column
 indicates whether an extra library is needed to build and use the
 package:
 
-dash = no library
+no  = no library
 sys = system library: you likely have it on your machine
 int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
-"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
-"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
-"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
-"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no
+"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no
+"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no
+"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no
+"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys
+"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no
+"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no
 "GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no
 "KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no
 "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"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, -, -, -
-"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
-"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"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
-"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
 "REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
-"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
-"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
+"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
+"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
+"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
+"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no
+"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no
+"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no
+"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l)

doc/src/Packages_user.txt

@@ -32,7 +32,7 @@ refers to the examples/USER/atc directory.  The "Library" column
 indicates whether an extra library is needed to build and use the
 package:
 
-dash = no library
+no  = no library
 sys = system library: you likely have it on your machine
 int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
@@ -40,35 +40,39 @@ ext = external library: you will need to download and install it on your machine
 Package, Description, Doc page, Example, Library
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
+"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
+"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
 "USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
-"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"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, -
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no
+"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no
+"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no
+"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no
+"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no
+"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext
+"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
+"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
+"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
+"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
+"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"_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, -
+"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, -
+"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
+"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
+"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal, USER/sdpd, no
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+"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

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
@@ -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

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
@@ -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_output.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)

doc/src/Run_windows.txt

@@ -1,4 +1,4 @@
-"Higher level section"_Run.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS
 Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
@@ -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_compare.txt

@@ -9,65 +9,108 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Comparison of various accelerator packages :h3
 
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
 The next section compares and contrasts the various accelerator
 options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
+run on GPUs, optimize for vector units on CPUs and run on Intel
+Xeon Phi (co-)processors.
 
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
+All of these packages can accelerate a LAMMPS calculation taking
+advantage of hardware features, but they do it in different ways
+and acceleration is not always guaranteed.
 
 As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other.  We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine.  See the benchmarking
+one package may be faster than the other.  We give some guidelines
+below, but the best way to determine which package is faster for your
+input script is to try multiple of them on your machine and experiment
+with available performance tuning settings.  See the benchmarking
 section below for examples where this has been done.
 
 [Guidelines for using each package optimally:]
 
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
+Both, the GPU and the KOKKOS package allows you to assign multiple
+MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
+can lead to a speedup through better utilization of the GPU (by
+overlapping computation and data transfer) and more efficient
+computation of the non-GPU accelerated parts of LAMMPS through MPI
+parallelization, as all system data is maintained and updated on
+the host. For KOKKOS, there is less to no benefit from this, due
+to its different memory management model, which tries to retain
+data on the GPU.
+ :ulb,l
 
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep.  The
-KOKKOS/CUDA package only does this on timesteps when a CPU calculation
-is required (e.g. to invoke a fix or compute that is non-GPU-ized).
-Hence, if you can formulate your input script to only use GPU-ized
-fixes and computes, and avoid doing I/O too often (thermo output, dump
-file snapshots, restart files), then the data transfer cost of the
-KOKKOS/CUDA package can be very low, causing it to run faster than the
-GPU package. :l
+The GPU package moves per-atom data (coordinates, forces, and
+(optionally) neighbor list data, if not computed on the GPU) between
+the CPU and GPU at every timestep.  The KOKKOS/CUDA package only does
+this on timesteps when a CPU calculation is required (e.g. to invoke
+a fix or compute that is non-GPU-ized). Hence, if you can formulate
+your input script to only use GPU-ized fixes and computes, and avoid
+doing I/O too often (thermo output, dump file snapshots, restart files),
+then the data transfer cost of the KOKKOS/CUDA package can be very low,
+causing it to run faster than the GPU package. :l
 
-The GPU package is often faster than the KOKKOS/CUDA package, if the
-number of atoms per GPU is smaller.  The crossover point, in terms of
-atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
-strongly on the pair style.  For example, for a simple Lennard Jones
+The GPU package is often faster than the KOKKOS/CUDA package, when the
+number of atoms per GPU is on the smaller side.  The crossover point,
+in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
+depends strongly on the pair style.  For example, for a simple Lennard Jones
 system the crossover (in single precision) is often about 50K-100K
 atoms per GPU.  When performing double precision calculations the
 crossover point can be significantly smaller. :l
 
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU.  If the GPU package is running with several MPI processes
+Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
+etc) on the CPU.  If the GPU package is running with several MPI processes
 assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
+spread across more CPUs and hence the GPU package can run faster in these
+cases. :l
 
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU.  Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU.  In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l
+When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
+performance depends to some extent on the available bandwidth between
+the CPUs and the GPU. This can differ significantly based on the
+available bus technology, capability of the host CPU and mainboard,
+the wiring of the buses and whether switches are used to increase the
+number of available bus slots, or if GPUs are housed in an external
+enclosure.  This can become quite complex. :l
+
+To achieve significant acceleration through GPUs, both KOKKOS and GPU
+package require capable GPUs with fast on-device memory and efficient
+data transfer rates. This requests capable upper mid-level to high-end
+(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
+result in a slowdown instead. :l
+
+For the GPU package, specifically when running in parallel with MPI,
+if it often more efficient to exclude the PPPM kspace style from GPU
+acceleration and instead run it - concurrently with a GPU accelerated
+pair style - on the CPU. This can often be easily achieved with placing
+a {suffix off} command before and a {suffix on} command after the
+{kspace_style pppm} command. :l
+
+The KOKKOS/OpenMP and USER-OMP package have different thread management
+strategies, which should result in USER-OMP being more efficient for a
+small number of threads with increasing overhead as the number of threads
+per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
+case, but have lower performance with few threads. :l
+
+The USER-INTEL package contains many options and settings for achieving
+additional performance on Intel hardware (CPU and accelerator cards), but
+to unlock this potential, an Intel compiler is required. The package code
+will compile with GNU gcc, but it will not be as efficient. :l
 :ule
 
-[Differences between the two packages:]
+[Differences between the GPU and KOKKOS packages:]
 
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations. :ulb,l
+The GPU package accelerates only pair force, neighbor list, and (parts
+of) PPPM calculations. The KOKKOS package attempts to run most of the
+calculation on the GPU, but can transparently support non-accelerated
+code (with a performance penalty due to having data transfers between
+host and GPU). :ulb,l
 
 The GPU package requires neighbor lists to be built on the CPU when using
 exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+
+The GPU package can be compiled for CUDA or OpenCL and thus supports
+both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
+resulting in equal or better performance over OpenCL. :l
+
+OpenCL in the GPU package does theoretically also support Intel CPUs or
+Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
+is superior. :l
 :ule

doc/src/Speed_gpu.txt

@@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 GPU package :h3
 
-The GPU package was developed by Mike Brown at ORNL and his
-collaborators, particularly Trung Nguyen (ORNL).  It provides GPU
-versions of many pair styles, including the 3-body Stillinger-Weber
-pair style, and for "kspace_style pppm"_kspace_style.html for
-long-range Coulombics.  It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+"kspace_style pppm"_kspace_style.html for long-range Coulombics.
+It has the following general features:
 
 It is designed to exploit common GPU hardware configurations where one
 or more GPUs are coupled to many cores of one or more multi-core CPUs,
 e.g. within a node of a parallel machine. :ulb,l
 
-Atom-based data (e.g. coordinates, forces) moves back-and-forth
+Atom-based data (e.g. coordinates, forces) are moved back-and-forth
 between the CPU(s) and GPU every timestep. :l
 
 Neighbor lists can be built on the CPU or on the GPU :l
@@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
 run on the GPU.  The FFT portion, which requires MPI communication
 between processors, runs on the CPU. :l
 
-Asynchronous force computations can be performed simultaneously on the
-CPU(s) and GPU. :l
+Force computations of different style (pair vs. bond/angle/dihedral/improper)
+can be performed concurrently on the GPU and CPU(s), respectively. :l
 
 It allows for GPU computations to be performed in single or double
 precision, or in mixed-mode precision, where pairwise forces are
@@ -39,21 +39,32 @@ force vectors. :l
 LAMMPS-specific code is in the GPU package.  It makes calls to a
 generic GPU library in the lib/gpu directory.  This library provides
 NVIDIA support as well as more general OpenCL support, so that the
-same functionality can eventually be supported on a variety of GPU
-hardware. :l
+same functionality is supported on a variety of hardware. :l
 :ule
 
 [Required hardware/software:]
 
-To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA CUDA software on your system:
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
 
-Check if you have an NVIDIA GPU: cat
-/proc/driver/nvidia/gpus/0/information Go to
-http://www.nvidia.com/object/cuda_get.html Install a driver and
-toolkit appropriate for your system (SDK is not necessary) Run
-lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
-below) to list supported devices and properties :ul
+Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
+Go to http://www.nvidia.com/object/cuda_get.html :l
+Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
+Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
+list supported devices and properties :ule,l
+
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
+Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
+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 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.
 
 [Building LAMMPS with the GPU package:]
 
@@ -120,7 +131,10 @@ GPUs/node to use, as well as other options.
 
 The performance of a GPU versus a multi-core CPU is a function of your
 hardware, which pair style is used, the number of atoms/GPU, and the
-precision used on the GPU (double, single, mixed).
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
 
 See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
 LAMMPS web site for performance of the GPU package on various
@@ -146,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
 performance.  Neighbor lists can be built on the GPU or CPU.  Force
 calculations can be dynamically balanced across the CPU cores and
 GPUs.  GPU-specific settings can be made which can be optimized
-for different hardware.  See the "packakge"_package.html command
+for different hardware.  See the "package"_package.html command
 doc page for details. :l
 
 As described by the "package gpu"_package.html command, GPU

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/Tools.txt

@@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
 reside in that directory.  Most of them are larger packages in their
 own sub-directories with their own Makefiles and/or README files.
 
-"amber2lmp"_#amber
-"binary2txt"_#binary
-"ch2lmp"_#charmm
-"chain"_#chain
-"colvars"_#colvars
-"createatoms"_#createatoms
-"doxygen"_#doxygen
-"drude"_#drude
-"eam database"_#eamdb
-"eam generate"_#eamgn
-"eff"_#eff
-"emacs"_#emacs
-"fep"_#fep
-"i-pi"_#ipi
-"ipp"_#ipp
-"kate"_#kate
-"lmp2arc"_#arc
-"lmp2cfg"_#cfg
-"matlab"_#matlab
-"micelle2d"_#micelle
-"moltemplate"_#moltemplate
-"msi2lmp"_#msi
-"phonon"_#phonon
-"polybond"_#polybond
-"pymol_asphere"_#pymol
-"python"_#pythontools
-"reax"_#reax_tool
-"smd"_#smd
-"vim"_#vim
-"xmgrace"_#xmgrace :ul
+:line
+
+Pre-processing tools :h3
+
+"amber2lmp"_#amber,
+"ch2lmp"_#charmm,
+"chain"_#chain,
+"createatoms"_#createatoms,
+"drude"_#drude,
+"eam database"_#eamdb,
+"eam generate"_#eamgn,
+"eff"_#eff,
+"ipp"_#ipp,
+"micelle2d"_#micelle,
+"moltemplate"_#moltemplate,
+"msi2lmp"_#msi,
+"polybond"_#polybond :tb(c=6,ea=c,a=l)
+
+Post-processing tools :h3
+
+"amber2lmp"_#amber,
+"binary2txt"_#binary,
+"ch2lmp"_#charmm,
+"colvars"_#colvars,
+"eff"_#eff,
+"fep"_#fep,
+"lmp2arc"_#arc,
+"lmp2cfg"_#cfg,
+"matlab"_#matlab,
+"phonon"_#phonon,
+"pymol_asphere"_#pymol,
+"python"_#pythontools,
+"reax"_#reax_tool,
+"smd"_#smd,
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+
+Miscellaneous tools :h3
+
+"doxygen"_#doxygen,
+"emacs"_#emacs,
+"i-pi"_#ipi,
+"kate"_#kate,
+"vim"_#vim :tb(c=5,ea=c,a=l)
 
 :line
 
-amber2lmp tool :h3,link(amber)
+Tool descriptions :h3
+
+amber2lmp tool :h4,link(amber)
 
 The amber2lmp sub-directory contains two Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
@@ -91,7 +106,7 @@ necessary modifications yourself.
 
 :line
 
-binary2txt tool :h3,link(binary)
+binary2txt tool :h4,link(binary)
 
 The file binary2txt.cpp converts one or more binary LAMMPS dump file
 into ASCII text files.  The syntax for running the tool is
@@ -104,7 +119,7 @@ since binary files are not compatible across all platforms.
 
 :line
 
-ch2lmp tool :h3,link(charmm)
+ch2lmp tool :h4,link(charmm)
 
 The ch2lmp sub-directory contains tools for converting files
 back-and-forth between the CHARMM MD code and LAMMPS.
@@ -129,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
 
 :line
 
-chain tool :h3,link(chain)
+chain tool :h4,link(chain)
 
 The file chain.f creates a LAMMPS data file containing bead-spring
 polymer chains and/or monomer solvent atoms.  It uses a text file
@@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.html.
 
 :line
 
-colvars tools :h3,link(colvars)
+colvars tools :h4,link(colvars)
 
 The colvars directory contains a collection of tools for postprocessing
 data produced by the colvars collective variable library.
@@ -168,7 +183,7 @@ gmail.com) at ICTP, Italy.
 
 :line
 
-createatoms tool :h3,link(createatoms)
+createatoms tool :h4,link(createatoms)
 
 The tools/createatoms directory contains a Fortran program called
 createAtoms.f which can generate a variety of interesting crystal
@@ -181,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
 
 :line
 
-doxygen tool :h3,link(doxygen)
+doxygen tool :h4,link(doxygen)
 
 The tools/doxygen directory contains a shell script called
 doxygen.sh which can generate a call graph and API lists using
@@ -193,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
 
 :line
 
-drude tool :h3,link(drude)
+drude tool :h4,link(drude)
 
 The tools/drude directory contains a Python script called
 polarizer.py which can add Drude oscillators to a LAMMPS
@@ -206,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
 
 :line
 
-eam database tool :h3,link(eamdb)
+eam database tool :h4,link(eamdb)
 
 The tools/eam_database directory contains a Fortran program that will
 generate EAM alloy setfl potential files for any combination of 16
@@ -222,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
 
 :line
 
-eam generate tool :h3,link(eamgn)
+eam generate tool :h4,link(eamgn)
 
 The tools/eam_generate directory contains several one-file C programs
 that convert an analytic formula into a tabulated "embedded atom
@@ -235,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
 
 :line
 
-eff tool :h3,link(eff)
+eff tool :h4,link(eff)
 
 The tools/eff directory contains various scripts for generating
 structures and post-processing output for simulations using the
@@ -246,7 +261,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
 
 :line
 
-emacs tool :h3,link(emacs)
+emacs tool :h4,link(emacs)
 
 The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs 
 that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -257,7 +272,7 @@ These tools were provided by Aidan Thompson at Sandia
 
 :line
 
-fep tool :h3,link(fep)
+fep tool :h4,link(fep)
 
 The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
@@ -270,7 +285,7 @@ See README file in the tools/fep directory.
 
 :line
 
-i-pi tool :h3,link(ipi)
+i-pi tool :h4,link(ipi)
 
 The tools/i-pi directory contains a version of the i-PI package, with
 all the LAMMPS-unrelated files removed.  It is provided so that it can
@@ -287,7 +302,7 @@ calculations with LAMMPS.
 
 :line
 
-ipp tool :h3,link(ipp)
+ipp tool :h4,link(ipp)
 
 The tools/ipp directory contains a Perl script ipp which can be used
 to facilitate the creation of a complicated file (say, a lammps input
@@ -301,7 +316,7 @@ tools/createatoms tool's input file.
 
 :line
 
-kate tool :h3,link(kate)
+kate tool :h4,link(kate)
 
 The file in the tools/kate directory is an add-on to the Kate editor
 in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -312,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio
 
 :line
 
-lmp2arc tool :h3,link(arc)
+lmp2arc tool :h4,link(arc)
 
 The lmp2arc sub-directory contains a tool for converting LAMMPS output
 files to the format for Accelrys' Insight MD code (formerly
@@ -328,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
 
 :line
 
-lmp2cfg tool :h3,link(cfg)
+lmp2cfg tool :h4,link(cfg)
 
 The lmp2cfg sub-directory contains a tool for converting LAMMPS output
 files into a series of *.cfg files which can be read into the
@@ -339,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 :line
 
-matlab tool :h3,link(matlab)
+matlab tool :h4,link(matlab)
 
 The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
 post-processing LAMMPS output.  The scripts include readers for log
@@ -357,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
 
 :line
 
-micelle2d tool :h3,link(micelle)
+micelle2d tool :h4,link(micelle)
 
 The file micelle2d.f creates a LAMMPS data file containing short lipid
 chains in a monomer solution.  It uses a text file containing lipid
@@ -374,7 +389,7 @@ definition file.  This tool was used to create the system for the
 
 :line
 
-moltemplate tool :h3,link(moltemplate)
+moltemplate tool :h4,link(moltemplate)
 
 The moltemplate sub-directory contains a Python-based tool for
 building molecular systems based on a text-file description, and
@@ -388,7 +403,7 @@ supports it.  It has its own WWW page at
 
 :line
 
-msi2lmp tool :h3,link(msi)
+msi2lmp tool :h4,link(msi)
 
 The msi2lmp sub-directory contains a tool for creating LAMMPS template
 input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -405,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information.
 
 :line
 
-phonon tool :h3,link(phonon)
+phonon tool :h4,link(phonon)
 
 The phonon sub-directory contains a post-processing tool useful for
 analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -420,7 +435,7 @@ University.
 
 :line
 
-polybond tool :h3,link(polybond)
+polybond tool :h4,link(polybond)
 
 The polybond sub-directory contains a Python-based tool useful for
 performing "programmable polymer bonding".  The Python file
@@ -434,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
 
 :line
 
-pymol_asphere tool :h3,link(pymol)
+pymol_asphere tool :h4,link(pymol)
 
 The pymol_asphere sub-directory contains a tool for converting a
 LAMMPS dump file that contains orientation info for ellipsoidal
@@ -452,7 +467,7 @@ This tool was written by Mike Brown at Sandia.
 
 :line
 
-python tool :h3,link(pythontools)
+python tool :h4,link(pythontools)
 
 The python sub-directory contains several Python scripts
 that perform common LAMMPS post-processing tasks, such as:
@@ -468,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts.
 
 :line
 
-reax tool :h3,link(reax_tool)
+reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alond codes that can
 post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -479,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia.
 
 :line
 
-smd tool :h3,link(smd)
+smd tool :h4,link(smd)
 
 The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
 Makefile which can be compiled and used to convert triangle output
@@ -495,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 
 :line
 
-vim tool :h3,link(vim)
+vim tool :h4,link(vim)
 
 The files in the tools/vim directory are add-ons to the VIM editor
 that allow easier editing of LAMMPS input scripts.  See the README.txt
@@ -506,7 +521,7 @@ ziegenhain.com)
 
 :line
 
-xmgrace tool :h3,link(xmgrace)
+xmgrace tool :h4,link(xmgrace)
 
 The files in the tools/xmgrace directory can be used to plot the
 thermodynamic data in LAMMPS log files via the xmgrace plotting

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>