Merge pull request #2899 from akohlmey/next_patch_release

Step version strings for the next patch release

.github/CODEOWNERS

@@ -22,42 +22,42 @@ src/MESSAGE/*         @sjplimp
 src/MLIAP/*           @athomps
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
-src/BROWNIAN/*   @samueljmcameron
-src/CG-DNA/*      @ohenrich
-src/CG-SDK/*      @akohlmey
-src/COLVARS/*    @giacomofiorin
-src/DIELECTRIC/* @ndtrung81
-src/FEP/*        @agiliopadua
-src/ML-HDNNP/*      @singraber
-src/INTEL/*      @wmbrownintel
-src/MANIFOLD/*   @Pakketeretet2
-src/MDI/*        @taylor-a-barnes
-src/MEAM/*      @martok
-src/MESONT/*     @iafoss
-src/MOFFF/*      @hheenen
-src/MOLFILE/*    @akohlmey
-src/NETCDF/*     @pastewka
-src/ML-PACE/*       @yury-lysogorskiy
-src/PLUMED/*     @gtribello
-src/PHONON/*     @lingtikong
-src/PTM/*        @pmla
-src/OPENMP/*        @akohlmey
-src/QMMM/*       @akohlmey
-src/REAXFF/*      @hasanmetin
-src/REACTION/*   @jrgissing
-src/SCAFACOS/*   @rhalver
-src/TALLY/*      @akohlmey
-src/UEF/*        @danicholson
-src/VTK/*        @rbberger
-
+src/BROWNIAN/*        @samueljmcameron
+src/CG-DNA/*          @ohenrich
+src/CG-SDK/*          @akohlmey
+src/COLVARS/*         @giacomofiorin
+src/DIELECTRIC/*      @ndtrung81
+src/FEP/*             @agiliopadua
+src/ML-HDNNP/*        @singraber
+src/INTEL/*           @wmbrownintel
+src/MANIFOLD/*        @Pakketeretet2
+src/MDI/*             @taylor-a-barnes
+src/MEAM/*            @martok
+src/MESONT/*          @iafoss
+src/MOFFF/*           @hheenen
+src/MOLFILE/*         @akohlmey
+src/NETCDF/*          @pastewka
+src/ML-PACE/*         @yury-lysogorskiy
+src/PLUMED/*          @gtribello
+src/PHONON/*          @lingtikong
+src/PTM/*             @pmla
+src/OPENMP/*          @akohlmey
+src/QMMM/*            @akohlmey
+src/REAXFF/*          @hasanmetin @stanmoore1
+src/REACTION/*        @jrgissing
+src/SCAFACOS/*        @rhalver
+src/TALLY/*           @akohlmey
+src/UEF/*             @danicholson
+src/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/*_grem.*              @dstelter92
-src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+src/REPLICA/*_grem.*                @dstelter92
+src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/MISC/*_tracker.*                @jtclemm
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -81,6 +81,7 @@ src/kspace.*              @sjplimp
 src/lmptyp.h              @sjplimp
 src/library.*             @sjplimp
 src/main.cpp              @sjplimp
+src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
 src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
@@ -109,7 +110,6 @@ 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
@@ -122,13 +122,14 @@ src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
+src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
-tools/code_standard/* @rbberger
+tools/coding_standard/* @rbberger
 tools/valgrind/*      @akohlmey
 tools/swig/*          @akohlmey
 tools/offline/*       @rbberger

.gitignore

@@ -44,6 +44,8 @@ Thumbs.db
 /build*
 /CMakeCache.txt
 /CMakeFiles/
+/Testing
 /Makefile
+/Testing
 /cmake_install.cmake
 /lmp

cmake/.coveragerc.in

@@ -0,0 +1,10 @@
+[run]
+source = @LAMMPS_PYTHON_DIR@
+parallel=True
+branch=True
+omit=*/install.py
+     */setup.py
+
+[paths]
+sources = python
+          @LAMMPS_PYTHON_DIR@

cmake/CMakeLists.txt

@@ -77,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
     set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@@ -161,9 +161,15 @@ set(STANDARD_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
   FEP
   GRANULAR
   H5MD
+  INTERLAYER
   KIM
   KSPACE
   LATBOLTZ
@@ -190,6 +196,7 @@ set(STANDARD_PACKAGES
   MPIIO
   MSCG
   NETCDF
+  ORIENT
   PERI
   PHONON
   PLUGIN
@@ -212,7 +219,6 @@ set(STANDARD_PACKAGES
   SRD
   TALLY
   UEF
-  USER-MISC
   VORONOI
   VTK
   YAFF)
@@ -238,15 +244,16 @@ if(PKG_ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
@@ -305,6 +312,9 @@ pkg_depends(LATBOLTZ MPI)
 pkg_depends(PHONON KSPACE)
 pkg_depends(SCAFACOS MPI)
 pkg_depends(DIELECTRIC KSPACE)
+pkg_depends(DIELECTRIC EXTRA-PAIR)
+pkg_depends(CG-DNA MOLECULE)
+pkg_depends(CG-DNA ASPHERE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -360,6 +370,8 @@ if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
   endif()
 endif()
 
+# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
+set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
@@ -757,6 +769,13 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
+find_package(ClangFormat 8.0)
+
+if(ClangFormat_FOUND)
+  add_custom_target(format-src
+    COMMAND ${ClangFormat_EXECUTABLE} --verbose -i -style=file *.cpp *.h */*.cpp */*.h
+    WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
+endif()
 
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)

cmake/Modules/CodeCoverage.cmake

@@ -54,6 +54,8 @@ if(ENABLE_COVERAGE)
 
     if(COVERAGE_FOUND)
         set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
+        configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
+
         add_custom_command(
             OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
             COMMAND ${COVERAGE_BINARY} combine
@@ -63,16 +65,16 @@ if(ENABLE_COVERAGE)
 
         add_custom_target(
             gen_python_coverage_html
-            COMMAND ${COVERAGE_BINARY} html -d ${PYTHON_COVERAGE_HTML_DIR}
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
             COMMENT "Generating HTML Python coverage report..."
         )
 
         add_custom_target(
             gen_python_coverage_xml
-            COMMAND ${COVERAGE_BINARY} xml -o ${CMAKE_BINARY_DIR}/python_coverage.xml
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
             COMMENT "Generating XML Python coverage report..."
         )

cmake/Modules/FindFFTW3.cmake

@@ -38,7 +38,7 @@ if(FFTW3_FOUND)
       add_library(FFTW3::FFTW3_OMP UNKNOWN IMPORTED)
       set_target_properties(FFTW3::FFTW3_OMP PROPERTIES
         IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-	IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
+        IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
         INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
     endif()
   endif()

cmake/Modules/FindFFTW3F.cmake

@@ -37,7 +37,7 @@ if(FFTW3F_FOUND)
       add_library(FFTW3F::FFTW3F_OMP UNKNOWN IMPORTED)
       set_target_properties(FFTW3F::FFTW3F_OMP PROPERTIES
         IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-	IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
+        IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
         INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
     endif()
   endif()

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/Packages/INTEL.cmake

@@ -3,7 +3,7 @@ if(NOT FOUND_IMMINTRIN)
   message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
 endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
+target_compile_definitions(lammps PRIVATE -DLMP_INTEL)
 
 set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by INTEL (cpu or knl)")
 set(INTEL_ARCH_VALUES cpu knl)

cmake/Modules/Packages/KOKKOS.cmake

@@ -74,11 +74,12 @@ else()
   target_link_libraries(lammps PRIVATE kokkos)
   target_link_libraries(lmp PRIVATE kokkos)
 endif()
-target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
+target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_KOKKOS>)
 
 set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
 set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
@@ -126,4 +127,4 @@ endif()
 get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
 
 target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
-target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${KOKKOS_PKG_SOURCES_DIR}>)

cmake/Modules/Packages/MACHDYN.cmake

@@ -7,8 +7,8 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
-  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
-  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
@@ -30,3 +30,8 @@ else()
   endif()
   target_link_libraries(lammps PRIVATE Eigen3::Eigen)
 endif()
+
+# PGI/Nvidia compiler internals collide with vector intrinsics support in Eigen3
+if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+  target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
+endif()

cmake/Modules/Packages/MDI.cmake

@@ -114,5 +114,5 @@ else()
   target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
 endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
-target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)
+target_compile_definitions(lammps PRIVATE -DLMP_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_MDI)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -1,3 +1,70 @@
 enable_language(Fortran)
-find_package(QUIP REQUIRED)
-target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
+find_package(QUIP QUIET)
+
+if(QUIP_FOUND)
+  set(DOWNLOAD_QUIP_DEFAULT OFF)
+else()
+  set(DOWNLOAD_QUIP_DEFAULT ON)
+endif()
+option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT})
+if(DOWNLOAD_QUIP)
+  string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+  set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n")
+  set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n")
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
+    set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
+  elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
+    set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
+  else()
+    message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
+  endif()
+  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}MATH_LINKOPTS=")
+  foreach(flag ${BLAS_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  foreach(flag ${LAPACK_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  set(temp "${temp}\n")
+  set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
+  set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
+  set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
+  set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
+  set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
+  set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
+  file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
+
+  message(STATUS "QUIP download via git requested - we will build our own")
+  # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
+  # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
+  include(ExternalProject)
+  ExternalProject_Add(quip_build
+    GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
+    GIT_TAG origin/public
+    GIT_SHALLOW YES
+    GIT_PROGRESS YES
+    PATCH_COMMAND cp ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
+    CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
+    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    INSTALL_COMMAND ""
+    BUILD_IN_SOURCE YES
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
+  )
+  ExternalProject_get_property(quip_build SOURCE_DIR)
+  add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::QUIP PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
+  target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
+  add_dependencies(LAMMPS::QUIP quip_build)
+else()
+  find_package(QUIP REQUIRED)
+  target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/OPENMP.cmake

@@ -5,7 +5,7 @@
                        ${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp
                        ${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
                        ${OPENMP_SOURCES_DIR}/domain_omp.cpp)
-  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
+  target_compile_definitions(lammps PRIVATE -DLMP_OPENMP)
   set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}")
 
   # detects styles which have OPENMP version
@@ -25,15 +25,15 @@
   endif()
 
   if(PKG_REAXFF)
-    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
   endif()
 
   target_sources(lammps PRIVATE ${OPENMP_SOURCES})

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
@@ -72,7 +72,6 @@ if(DOWNLOAD_PLUMED)
                                              ${PLUMED_CONFIG_OMP}
                                              CXX=${PLUMED_CONFIG_CXX}
                                              CC=${PLUMED_CONFIG_CC}
-    PATCH_COMMAND sed -i "/^#include <algorithm>/a #include <limits>" <SOURCE_DIR>/src/lepton/Operation.h
     BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
   )
   ExternalProject_get_property(plumed_build INSTALL_DIR)

cmake/Modules/Tools.cmake

@@ -9,14 +9,16 @@ if(BUILD_TOOLS)
     check_language(Fortran)
     if(CMAKE_Fortran_COMPILER)
       enable_language(Fortran)
-      add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
+      add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f90)
       target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-      install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+      add_executable(micelle2d.x ${LAMMPS_TOOLS_DIR}/micelle2d.f90)
+      target_link_libraries(micelle2d.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+      install(TARGETS chain.x micelle2d.x DESTINATION ${CMAKE_INSTALL_BINDIR})
     else()
-      message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
+      message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x' and 'micelle2d.x'")
     endif()
   else()
-    message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
+    message(WARNING "CMake build doesn't support Fortran, skipping build of 'chain.x' and 'micelle2d.x'")
   endif()
 
   enable_language(C)

cmake/presets/all_off.cmake

@@ -25,11 +25,17 @@ set(ALL_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
   FEP
   GPU
   GRANULAR
   H5MD
   INTEL
+  INTERLAYER
   KIM
   KOKKOS
   KSPACE
@@ -59,6 +65,7 @@ set(ALL_PACKAGES
   NETCDF
   OPENMP
   OPT
+  ORIENT
   PERI
   PHONON
   PLUGIN
@@ -81,7 +88,6 @@ set(ALL_PACKAGES
   SRD
   TALLY
   UEF
-  USER-MISC
   VORONOI
   VTK
   YAFF)

cmake/presets/all_on.cmake

@@ -27,11 +27,17 @@ set(ALL_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
   FEP
   GPU
   GRANULAR
   H5MD
   INTEL
+  INTERLAYER
   KIM
   KOKKOS
   KSPACE
@@ -61,6 +67,7 @@ set(ALL_PACKAGES
   NETCDF
   OPENMP
   OPT
+  ORIENT
   PERI
   PHONON
   PLUGIN
@@ -83,7 +90,6 @@ set(ALL_PACKAGES
   SRD
   TALLY
   UEF
-  USER-MISC
   VORONOI
   VTK
   YAFF)

cmake/presets/clang.cmake

@@ -10,9 +10,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f95" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

cmake/presets/gcc.cmake

@@ -1,4 +1,4 @@
-# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
+# preset that will explicitly request gcc/g++ compilers with support for MPI and OpenMP
 
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
@@ -15,9 +15,9 @@ set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
 set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
 set(OpenMP_C "gcc" CACHE STRING "" FORCE)

cmake/presets/hip.cmake

@@ -1,12 +1,26 @@
-# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable hipcc plus gcc/gfortran with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER gfortran CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
-set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
+set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -21,10 +21,16 @@ set(WIN_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
   FEP
   GPU
   GRANULAR
   INTEL
+  INTERLAYER
   KSPACE
   LATTE
   MACHDYN
@@ -39,11 +45,13 @@ set(WIN_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-SNAP
+  ML-RANN
   MOFFF
   MOLECULE
   MOLFILE
   OPENMP
   OPT
+  ORIENT
   PERI
   PHONON
   POEMS
@@ -61,7 +69,6 @@ set(WIN_PACKAGES
   SRD
   TALLY
   UEF
-  USER-MISC
   VORONOI
   YAFF)
 

cmake/presets/most.cmake

@@ -23,8 +23,13 @@ set(ALL_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  EXTRA-COMPUTE
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
   FEP
   GRANULAR
+  INTERLAYER
   KSPACE
   MACHDYN
   MANYBODY
@@ -37,6 +42,7 @@ set(ALL_PACKAGES
   MOLECULE
   OPENMP
   OPT
+  ORIENT
   PERI
   PHONON
   PLUGIN
@@ -51,8 +57,8 @@ set(ALL_PACKAGES
   SPH
   SPIN
   SRD
+  TALLY
   UEF
-  USER-MISC
   VORONOI
   YAFF)
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "2 July 2021" "2021-07-2"
+.TH LAMMPS "31 August 2021" "2021-08-31"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Bibliography.rst

@@ -191,7 +191,7 @@ Bibliography
    A.\  Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
 
 **(Campana)**
-   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
+   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
 
 **(Cao1)**
    J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@@ -767,7 +767,7 @@ Bibliography
    Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
 
 **(Moustafa)**
-   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
 
 **(Muller-Plathe1)**
    Muller-Plathe, J Chem Phys, 106, 6082 (1997).

doc/src/Build.rst

@@ -22,4 +22,5 @@ page.
    Build_extras
    Build_manual
    Build_windows
+   Build_diskspace
    Build_development

doc/src/Build_development.rst

@@ -1,15 +1,15 @@
-Development build options (CMake only)
-======================================
+Development build options
+=========================
 
-The CMake build procedure of LAMMPS offers a few extra options which are
+The build procedures in LAMMPS offers a few extra options which are
 useful during development, testing or debugging.
 
 ----------
 
 .. _compilation:
 
-Monitor compilation flags
--------------------------
+Monitor compilation flags (CMake only)
+--------------------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
@@ -30,8 +30,8 @@ variable VERBOSE set to 1:
 
 .. _clang-tidy:
 
-Enable static code analysis with clang-tidy
--------------------------------------------
+Enable static code analysis with clang-tidy (CMake only)
+--------------------------------------------------------
 
 The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
 static code analysis tool to diagnose (and potentially fix) typical
@@ -52,8 +52,8 @@ significantly more time consuming than the compilation itself.
 
 .. _iwyu_processing:
 
-Report missing and unneeded '#include' statements
--------------------------------------------------
+Report missing and unneeded '#include' statements (CMake only)
+--------------------------------------------------------------
 
 The conventions for how and when to use and order include statements in
 LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
@@ -86,8 +86,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support
----------------------------------------------------------
+Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
+----------------------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
 which use different sanitizer libraries to detect problems in the code
@@ -116,8 +116,8 @@ compilation and linking stages.  This is done through setting the
 
 .. _testing:
 
-Code Coverage and Unit Testing
-------------------------------
+Code Coverage and Unit Testing (CMake only)
+-------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
 during development: integration testing (i.e. whether the code compiles
@@ -464,7 +464,8 @@ Coding style utilities
 
 To aid with enforcing some of the coding style conventions in LAMMPS
 some additional build targets have been added. These require Python 3.5
-or later and will only work on Unix-like operating and file systems.
+or later and will only work properly on Unix-like operating and file systems.
+
 The following options are available.
 
 .. code-block:: bash
@@ -476,17 +477,43 @@ The following options are available.
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
 
+These should help to replace all TAB characters with blanks and remove
+any trailing whitespace.  Also all LAMMPS homepage URL references can be
+updated to the location change from Sandia to the lammps.org domain.
+And the permission check can remove executable permissions from non-executable
+files (like source code).
+
+Clang-format support
+--------------------
+
 For the code in the ``unittest`` and ``src`` trees we are transitioning
 to use the `clang-format` tool to assist with having a consistent source
-code style.  The `clang-format` command bundled with Clang version 8.0
-or later is required.  The configuration is in files ``.clang-format``
-in the respective folders.  Since the modifications from `clang-format`
-can be significant and - especially for "legacy style code" - also is
-not always improving readability, a large number of files currently have
-a ``// clang-format off`` at the top, which will disable the processing.
-Over time, files will be refactored and updated to that `clang-format`
-may be applied to them (at least in part).
+code formatting style.  The `clang-format` command bundled with Clang
+version 8.0 or later is required.  The configuration is in files called
+``.clang-format`` in the respective folders.  Since the modifications
+from `clang-format` can be significant and - especially for "legacy
+style code" - they are not always improving readability, a large number
+of files currently have a ``// clang-format off`` at the top, which will
+disable the processing.  As of fall 2021 all files have been either
+"protected" this way or are enabled for full or partial `clang-format`
+processing.  Over time, the "protected" files will be refactored and
+updated so that `clang-format` may be applied to them as well.
 
-If `clang-format` is available, the source code files in the ``unittest``
-tree can be updated to conform to the formatting settings using
-``make format-tests`` and the files in ``src`` with ``make format-src``.
+It is recommended for all newly contributed files to use the clang-format
+processing while writing the code or do the coding style processing
+(including the scripts mentioned in the previous paragraph)
+
+If `clang-format` is available, files can be updated individually with
+commands like the following:
+
+.. code-block:: bash
+
+   $ clang-format -i some_file.cpp
+
+
+The following target are available for both, GNU make and CMake:
+
+.. code-block:: bash
+
+   make format-src       # apply clang-format to all files in src and the package folders
+   make format-tests     # apply clang-format to all files in the unittest tree

doc/src/Build_diskspace.rst

@@ -0,0 +1,45 @@
+Notes for saving disk space when building LAMMPS from source
+------------------------------------------------------------
+
+LAMMPS is a large software project with a large number of source files,
+extensive documentation, and a large collection of example files.
+When downloading LAMMPS by cloning the
+`git repository from GitHub <https://github.com/lammps/lammps>`_ this
+will by default also download the entire commit history since September 2006.
+Compiling LAMMPS will add the storage requirements of the compiled object
+files and libraries to the tally.
+
+In a user account on an HPC cluster with filesystem quotas or in other
+environments with restricted disk space capacity it may be needed to
+reduce the storage requirements. Here are some suggestions:
+
+- Create a so-called shallow repository by cloning only the last commit
+  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
+  This reduces the downloaded size to about half.  With ``--depth=1`` it is not possible to check out different
+  versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
+  extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).
+
+- Download a tar archive from either the `download section on the LAMMPS homepage <https://www.lammps.org/download.html>`_
+  or from the `LAMMPS releases page on GitHub <https://github.com/lammps/lammps/releases>`_ these will not
+  contain the git history at all.
+
+- Build LAMMPS without the debug flag (remove ``-g`` from the machine makefile or use ``-DCMAKE_BUILD_TYPE=Release``)
+  or use the ``strip`` command on the LAMMPS executable when no more debugging would be needed.  The strip command
+  may also be applied to the LAMMPS shared library. The static library may be deleted entirely.
+
+- Delete compiled object files and libraries after copying the LAMMPS executable to a permanent location.
+  When using the traditional build process, one may use ``make clean-<machine>`` or ``make clean-all``
+  to delete object files in the src folder.  For CMake based builds, one may use ``make clean`` or just
+  delete the entire build folder.
+
+- The folders containing the documentation tree (doc), the examples (examples) are not needed to build and
+  run LAMMPS and can be safely deleted.  Some files in the potentials folder are large and may be deleted,
+  if not needed.  The largest of those files (occupying about 120 MBytes combined) will only be downloaded on
+  demand, when the corresponding package is installed.
+
+- When using the CMake build procedure, the compilation can be done on a (local) scratch storage that will not
+  count toward the quota.  A local scratch file system may offer the additional benefit of speeding up creating
+  object files and linking with libraries compared to a networked file system.  Also with CMake (and unlike with
+  the traditional make) it is possible to compile LAMMPS executables with different settings and packages included
+  from the same source tree since all the configuration information is stored in the build folder.  So it is
+  not necessary to have multiple copies of LAMMPS.

doc/src/Build_extras.rst

@@ -31,36 +31,36 @@ This is the list of packages that may require additional steps.
 .. table_from_list::
    :columns: 6
 
-   * :ref:`COMPRESS <compress>`
-   * :ref:`GPU <gpu>`
-   * :ref:`KIM <kim>`
-   * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
-   * :ref:`MESSAGE <message>`
-   * :ref:`ML-IAP <mliap>`
-   * :ref:`MSCG <mscg>`
-   * :ref:`OPT <opt>`
-   * :ref:`POEMS <poems>`
-   * :ref:`PYTHON <python>`
-   * :ref:`VORONOI <voronoi>`
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
    * :ref:`COLVARS <colvars>`
+   * :ref:`COMPRESS <compress>`
+   * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
-   * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`INTEL <intel>`
+   * :ref:`KIM <kim>`
+   * :ref:`KOKKOS <kokkos>`
+   * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
    * :ref:`MESONT <mesont>`
-   * :ref:`MOLFILE <molfile>`
-   * :ref:`NETCDF <netcdf>`
+   * :ref:`MESSAGE <message>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
-   * :ref:`PLUMED <plumed>`
-   * :ref:`OPENMP <openmp>`
-   * :ref:`QMMM <qmmm>`
    * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
+   * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
+   * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
+   * :ref:`POEMS <poems>`
+   * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
    * :ref:`SCAFACOS <scafacos>`
-   * :ref:`MACHDYN <machdyn>`
+   * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
 
 ----------
@@ -74,7 +74,8 @@ To build with this package you must have the `zlib compression library
 <https://zlib.net>`_ available on your system to build dump styles with
 a '/gz' suffix.  There are also styles using the
 `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
-'/zstd' suffix.
+'/zstd' suffix.  The zstd library version must be at least 1.4.  Older
+versions use an incompatible API and thus LAMMPS will fail to compile.
 
 .. tabs::
 
@@ -1856,8 +1857,8 @@ ML-QUIP package
 To build with this package, you must download and build the QUIP
 library.  It can be obtained from GitHub.  For support of GAP
 potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  See step 1 and step 1.1 in the
-``lib/quip/README`` file for details on how to do this.
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
 
 .. tabs::
 
@@ -1865,11 +1866,14 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
       .. code-block:: bash
 
+         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
          -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
-      CMake will **not** download and build the QUIP library.  But once you have
-      done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should
-      work.  Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
+      CMake will try to download and build the QUIP library from GitHub, if it is not
+      found on the local machine. This requires to have git installed. It will use the same compilers
+      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      and installed QUIP library and CMake cannot find it.
 
    .. tab:: Traditional make
 

doc/src/Build_manual.rst

@@ -204,9 +204,9 @@ be multiple tests run automatically:
 
   .. parsed-literal::
 
-     Found 74 packages
-     Standard package NEWPACKAGE missing in Packages_standard.rst
-     Standard package NEWPACKAGE missing in Packages_details.rst
+     Found 88 packages
+     Package NEWPACKAGE missing in Packages_list.rst
+     Package NEWPACKAGE missing in Packages_details.rst
 
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and

doc/src/Commands_category.rst

@@ -2,7 +2,7 @@ Commands by category
 ====================
 
 This page lists most of the LAMMPS commands, grouped by category.  The
-:doc:`General commands <Commands_all>` doc page lists all general commands
+:doc:`General commands <Commands_all>` page lists all general commands
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 

doc/src/Commands_compute.rst

@@ -72,6 +72,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
    * :doc:`heat/flux <compute_heat_flux>`
    * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`heat/flux/virial/tally <compute_tally>`
    * :doc:`hexorder/atom <compute_hexorder_atom>`
    * :doc:`hma <compute_hma>`
    * :doc:`improper <compute_improper>`
@@ -151,7 +152,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`temp/chunk <compute_temp_chunk>`
    * :doc:`temp/com <compute_temp_com>`
    * :doc:`temp/cs <compute_temp_cs>`
-   * :doc:`temp/deform <compute_temp_deform>`
+   * :doc:`temp/deform (k) <compute_temp_deform>`
    * :doc:`temp/deform/eff <compute_temp_deform_eff>`
    * :doc:`temp/drude <compute_temp_drude>`
    * :doc:`temp/eff <compute_temp_eff>`

doc/src/Commands_fix.rst

@@ -148,7 +148,7 @@ OPT.
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`
    * :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
-   * :doc:`nvt/sllod (io) <fix_nvt_sllod>`
+   * :doc:`nvt/sllod (iko) <fix_nvt_sllod>`
    * :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
    * :doc:`nvt/sphere (o) <fix_nvt_sphere>`
    * :doc:`nvt/uef <fix_nh_uef>`
@@ -157,6 +157,7 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
@@ -178,14 +179,14 @@ OPT.
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
-   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
    * :doc:`rattle <fix_shake>`
-   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
-   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
+   * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rhok <fix_rhok>`
@@ -235,6 +236,7 @@ OPT.
    * :doc:`ti/spring <fix_ti_spring>`
    * :doc:`tmd <fix_tmd>`
    * :doc:`ttm <fix_ttm>`
+   * :doc:`ttm/grid <fix_ttm>`
    * :doc:`ttm/mod <fix_ttm>`
    * :doc:`tune/kspace <fix_tune_kspace>`
    * :doc:`vector <fix_vector>`

doc/src/Commands_input.rst

@@ -50,6 +50,6 @@ values are not desired, the :doc:`processors <processors>` and
 tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.

doc/src/Commands_kspace.rst

@@ -24,6 +24,7 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/disp/dipole <kspace_style>`
    * :doc:`ewald/dipole <kspace_style>`
    * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
@@ -33,8 +34,10 @@ OPT.
    * :doc:`pppm/cg (o) <kspace_style>`
    * :doc:`pppm/dipole <kspace_style>`
    * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/disp (io) <kspace_style>`
    * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/disp/dielectric <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`pppm/dielectric <kspace_style>`

doc/src/Commands_pair.rst

@@ -29,7 +29,7 @@ OPT.
    * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
-   *
+   * :doc:`tracker <pair_tracker>`
    *
    *
    *
@@ -75,6 +75,7 @@ OPT.
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
    * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/exclude <pair_coul>`
    * :doc:`coul/long (gko) <pair_coul>`
    * :doc:`coul/long/cs (g) <pair_cs>`
    * :doc:`coul/long/dielectric <pair_dielectric>`
@@ -235,7 +236,7 @@ OPT.
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`rann <pair_rann>`
-   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Commands_parse.rst

@@ -47,7 +47,7 @@ LAMMPS:
    named "x" followed by an "x" character.
 
    How the variable is converted to a text string depends on what style
-   of variable it is; see the :doc:`variable <variable>` doc page for
+   of variable it is; see the :doc:`variable <variable>` page for
    details.  It can be a variable that stores multiple text strings, and
    return one of them.  The returned text string can be multiple "words"
    (space separated) which will then be interpreted as multiple

doc/src/Developer_org.rst

@@ -17,7 +17,7 @@ currently supports building with :doc:`conventional makefiles
 differ in how packages are enabled or disabled for inclusion into a
 LAMMPS binary so they cannot be mixed.  The source files for each
 package are in all-uppercase sub-directories of the ``src`` folder, for
-example ``src/MOLECULE`` or ``src/USER-MISC``.  The ``src/STUBS``
+example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
 sub-directory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
 directory and its sub-directories contain makefiles with settings and

doc/src/Developer_utils.rst

@@ -334,10 +334,11 @@ arguments of commands in LAMMPS are parsed and to make abstractions of
 repetitive tasks.
 
 The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
-for parsing references to compute or fix styles or variables. These
-would start with a "c\_", "f\_", "v\_" followed by the ID or name of
-than instance and may be postfixed with one or two array indices
-"[<number>]" with numbers > 0.
+for parsing references to compute or fix styles, variables or custom
+integer or double properties handled by :doc:`fix property/atom <fix_property_atom>`.
+These would start with a "c\_", "f\_", "v\_", "d\_", "d2\_", "i\_", or "i2\_"
+followed by the ID or name of than instance and may be postfixed with
+one or two array indices "[<number>]" with numbers > 0.
 
 A typical code segment would look like this:
 

doc/src/Errors_bugs.rst

@@ -17,8 +17,9 @@ the steps outlined below:
    if your issue has already been reported and if it is still open.
  * Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
    to see if there is already a fix for your bug pending.
- * Check the `mailing list archives <https://www.lammps.org/mail.html>`_
-   to see if the issue has been discussed before.
+ * Check the `mailing list archives <https://www.lammps.org/mail.html>`_ or
+   the `LAMMPS forum <https://www.lammps.org/forum.html>`_ to see if the
+   issue has been discussed before.
 
 If none of these steps yields any useful information, please file a new
 bug report on the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_.

doc/src/Errors_messages.rst

@@ -570,10 +570,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    See the region prism command for details.
 
 *Can only use -plog with multiple partitions*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Can only use -pscreen with multiple partitions*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Can only use Kokkos supported regions with Kokkos package*
    Self-explanatory.
@@ -1154,7 +1154,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Cannot use -reorder after -partition*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Cannot use Ewald with 2d simulation*
    The kspace style ewald cannot be used in 2d simulations.  You can use
@@ -2347,14 +2347,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Compute used in variable between runs is not current*
    Computes cannot be invoked by a variable in between runs.  Thus they
    must have been evaluated on the last timestep of the previous run in
-   order for their value(s) to be accessed.  See the doc page for the
+   order for their value(s) to be accessed.  See the page for the
    variable command for more info.
 
 *Compute used in variable thermo keyword between runs is not current*
    Some thermo keywords rely on a compute to calculate their value(s).
    Computes cannot be invoked by a variable in between runs.  Thus they
    must have been evaluated on the last timestep of the previous run in
-   order for their value(s) to be accessed.  See the doc page for the
+   order for their value(s) to be accessed.  See the page for the
    variable command for more info.
 
 *Compute vcm/chunk does not use chunk/atom compute*
@@ -3126,7 +3126,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Energy was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied energy, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Epsilon or sigma reference not set by pair style in PPPMDisp*
    Self-explanatory.
@@ -4535,10 +4535,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    particles.
 
 *Incorrect # of floating-point values in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect # of integer values in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect %s format in data file*
    A section of the data file being read by fix property/atom does
@@ -4573,7 +4573,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    The number of fields per line is not what expected.
 
 *Incorrect bonus data format in data file*
-   See the read_data doc page for a description of how various kinds of
+   See the read_data page for a description of how various kinds of
    bonus data must be formatted for certain atom styles.
 
 *Incorrect boundaries with slab Ewald*
@@ -4641,7 +4641,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Incorrect number of words per line in the potential file.
 
 *Incorrect integer value in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect multiplicity arg for dihedral coefficients*
    Self-explanatory.  Check the input script or data file.
@@ -5996,7 +5996,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Needed bonus data not in data file*
-   Some atom styles require bonus data.  See the read_data doc page for
+   Some atom styles require bonus data.  See the read_data page for
    details.
 
 *Needed molecular topology not in data file*
@@ -6198,7 +6198,7 @@ keyword to allow for additional bonds to be formed
 
 *One or more atom IDs is too big*
    The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-   setting in your LAMMPS build.  See the :doc:`Build settings <Build_settings>` doc page for more info.
+   setting in your LAMMPS build.  See the :doc:`Build settings <Build_settings>` page for more info.
 
 *One or more atom IDs is zero*
    Either all atoms IDs must be zero or none of them.
@@ -6593,7 +6593,7 @@ keyword to allow for additional bonds to be formed
 
 *Pair style bop requires comm ghost cutoff at least 3x larger than %g*
    Use the communicate ghost command to set this.  See the pair bop
-   doc page for more details.
+   page for more details.
 
 *Pair style born/coul/long requires atom attribute q*
    An atom style that defines this attribute must be used.
@@ -6913,7 +6913,7 @@ keyword to allow for additional bonds to be formed
 *Per-atom energy was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied energy, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Per-atom fix in equal-style variable formula*
    Equal-style variables cannot use per-atom quantities.
@@ -6921,7 +6921,7 @@ keyword to allow for additional bonds to be formed
 *Per-atom virial was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to have
    tallied the virial, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Per-processor system is too big*
    The number of owned atoms plus ghost atoms on a single
@@ -8408,7 +8408,7 @@ keyword to allow for additional bonds to be formed
 *Virial was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied the virial, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Voro++ error: narea and neigh have a different size*
    This error is returned by the Voro++ library.

doc/src/Errors_warnings.rst

@@ -213,7 +213,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    in unexpected behavior.
 
 *Fix bond/swap will ignore defined angles*
-   See the doc page for fix bond/swap for more info on this
+   See the page for fix bond/swap for more info on this
    restriction.
 
 *Fix deposit near setting < possible overlap separation %g*
@@ -514,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations.
    will integrate the body motion, but it would be more efficient to use
    fix rigid.
 
-*Not using real units with pair reax*
+*Not using real units with pair reaxff*
    This is most likely an error, unless you have created your own ReaxFF
    parameter file in a different set of units.
 
@@ -805,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations.
 *Using pair tail corrections with pair_modify compute no*
    The tail corrections will thus not be computed.
 
-*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
-   Self-explanatory.

doc/src/Examples.rst

@@ -150,6 +150,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | threebody   | regression test input for a variety of manybody potentials       |
 +-------------+------------------------------------------------------------------+
+| tracker     | track interactions in LJ melt                                    |
++-------------+------------------------------------------------------------------+
 | vashishta   | use of the Vashishta potential                                   |
 +-------------+------------------------------------------------------------------+
 | voronoi     | Voronoi tesselation via compute voronoi/atom command             |
@@ -172,10 +174,10 @@ web site.
 If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
 script a series of JPG images will be produced by the run (assuming
 you built LAMMPS with JPG support; see the
-:doc:`Build_settings <Build_settings>` doc page for details).  These can
+:doc:`Build_settings <Build_settings>` page for details).  These can
 be viewed individually or turned into a movie or animated by tools
 like ImageMagick or QuickTime or various Windows-based tools.  See the
-:doc:`dump image <dump_image>` doc page for more details.  E.g. this
+:doc:`dump image <dump_image>` page for more details.  E.g. this
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.
 
@@ -205,14 +207,12 @@ Uppercase directories
 +------------+--------------------------------------------------------------------------------------------------+
 | MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
 +------------+--------------------------------------------------------------------------------------------------+
-| PACKAGES   | examples for specific packages and contributed commands in USER-MISC                             |
+| PACKAGES   | examples for specific packages and contributed commands                                          |
 +------------+--------------------------------------------------------------------------------------------------+
 | SPIN       | examples for features of the SPIN package                                                        |
 +------------+--------------------------------------------------------------------------------------------------+
 | UNITS      | examples that run the same simulation in lj, real, metal units                                   |
 +------------+--------------------------------------------------------------------------------------------------+
-| USER-MISC  | examples for commands in the USER-MISC packages                                                  |
-+------------+--------------------------------------------------------------------------------------------------+
 | VISCOSITY  | compute viscosity via several methods                                                            |
 +------------+--------------------------------------------------------------------------------------------------+
 
@@ -226,7 +226,4 @@ of the sub-directories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
 page for more info on specific packages.
 
-Similarly the USER-MISC directory has sub-directories for examples
-corresponding to individual commands or styles in the USER-MISC package.
-
 .. _openkim: https://openkim.org

doc/src/Howto.rst

@@ -54,6 +54,7 @@ Analysis howto
    Howto_kappa
    Howto_viscosity
    Howto_diffusion
+   Howto_structured_data
 
 Force fields howto
 ==================

doc/src/Howto_barostat.rst

@@ -50,7 +50,7 @@ a temperature or pressure compute to a barostatting fix.
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes pressure
-values.  As explained on the doc page for the
+values.  As explained on the page for the
 :doc:`thermo_style <thermo_style>` command, the default pressure is
 setup by the thermo command itself.  It is NOT the pressure associated
 with any barostatting fix you have defined or with any compute you

doc/src/Howto_bioFF.rst

@@ -49,7 +49,7 @@ command's documentation for the formula it computes.
 COMPASS is a general force field for atomistic simulation of common
 organic molecules, inorganic small molecules, and polymers which was
 developed using ab initio and empirical parameterization techniques.
-See the :doc:`Tools <Tools>` doc page for the msi2lmp tool for creating
+See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
 LAMMPS template input and data files from BIOVIA's Materials Studio
 files.  Please note that the msi2lmp tool is very old and largely
 unmaintained, so it does not support all features of Materials Studio

doc/src/Howto_body.rst

@@ -10,7 +10,7 @@ deformable objects, etc.  Note that other kinds of finite-size
 spherical and aspherical particles are also supported by LAMMPS, such
 as spheres, ellipsoids, line segments, and triangles, but they are
 simpler entities than body particles.  See the :doc:`Howto spherical
-<Howto_spherical>` doc page for a general overview of all these
+<Howto_spherical>` page for a general overview of all these
 particle types.
 
 Body particles are used via the :doc:`atom_style body <atom_style>`
@@ -170,14 +170,14 @@ with this body style to compute body/body and body/non-body interactions.
 The *rounded/polygon* body style represents body particles as a 2d
 polygon with a variable number of N vertices.  This style can only be
 used for 2d models; see the :doc:`boundary <boundary>` command.  See the
-"pair_style body/rounded/polygon" doc page for a diagram of two
+"pair_style body/rounded/polygon" page for a diagram of two
 squares with rounded circles at the vertices.  Special cases for N = 1
 (circle) and N = 2 (rod with rounded ends) can also be specified.
 
 One use of this body style is for 2d discrete element models, as
 described in :ref:`Fraige <body-Fraige>`.
 
-Similar to body style *nparticle*\ , the atom_style body command for
+Similar to body style *nparticle*, the atom_style body command for
 this body style takes two additional arguments:
 
 .. parsed-literal::
@@ -284,7 +284,7 @@ The *rounded/polyhedron* body style represents body particles as a 3d
 polyhedron with a variable number of N vertices, E edges and F faces.
 This style can only be used for 3d models; see the
 :doc:`boundary <boundary>` command.  See the "pair_style
-body/rounded/polygon" doc page for a diagram of a two 2d squares with
+body/rounded/polygon" page for a diagram of a two 2d squares with
 rounded circles at the vertices.  A 3d cube with rounded spheres at
 the 8 vertices and 12 rounded edges would be similar.  Special cases
 for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be
@@ -293,7 +293,7 @@ specified.
 This body style is for 3d discrete element models, as described in
 :ref:`Wang <body-Wang>`.
 
-Similar to body style *rounded/polygon*\ , the atom_style body command
+Similar to body style *rounded/polygon*, the atom_style body command
 for this body style takes two additional arguments:
 
 .. parsed-literal::

doc/src/Howto_chunk.rst

@@ -51,7 +51,7 @@ scales the floating point value to spread it across multiple integers.
 Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
 pencils, 3d bins = boxes, spherical bins, cylindrical bins.
 
-This compute also calculates the number of chunks *Nchunk*\ , which is
+This compute also calculates the number of chunks *Nchunk*, which is
 used by other commands to tally per-chunk data.  *Nchunk* can be a
 static value or change over time (e.g. the number of clusters).  The
 chunk ID for an individual atom can also be static (e.g. a molecule

doc/src/Howto_client_server.rst

@@ -119,7 +119,7 @@ server code.  Another code could be substituted for either.
 
 The examples below show launching both codes from the same window (or
 batch script), using the "&" character to launch the first code in the
-background.  For all modes except *mpi/one*\ , you could also launch the
+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.
 
@@ -132,7 +132,7 @@ 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:
+For message exchange in *file*, *zmq*, or *mpi/two* modes:
 
 .. code-block:: bash
 

doc/src/Howto_cmake.rst

@@ -362,7 +362,7 @@ have to be enabled to be included into a LAMMPS executable.  Packages
 are enabled through setting variables of the kind ``PKG_<NAME>`` to
 ``on`` and disabled by setting them to ``off`` (or using ``yes``,
 ``no``, ``1``, ``0`` correspondingly).  ``<NAME>`` has to be replaced by
-the name of the package, e.g. ``MOLECULE`` or ``USER-MISC``.
+the name of the package, e.g. ``MOLECULE`` or ``EXTRA-PAIR``.
 
 
 Using presets

doc/src/Howto_coreshell.rst

@@ -5,7 +5,7 @@ The adiabatic core-shell model by :ref:`Mitchell and Fincham <MitchellFincham>`
 to a system.  In order to mimic the electron shell of an ion, a
 satellite particle is attached to it. This way the ions are split into
 a core and a shell where the latter is meant to react to the
-electrostatic environment inducing polarizability.  See the :doc:`Howto polarizable <Howto_polarizable>` doc page for a discussion of all
+electrostatic environment inducing polarizability.  See the :doc:`Howto polarizable <Howto_polarizable>` page for a discussion of all
 the polarizable models available in LAMMPS.
 
 Technically, shells are attached to the cores by a spring force f =
@@ -78,7 +78,7 @@ satellite particle if desired.
 Since the core/shell model permits distances of r = 0.0 between the
 core and shell, a pair style with a "cs" suffix needs to be used to
 implement a valid long-range Coulombic correction.  Several such pair
-styles are provided in the CORESHELL package.  See :doc:`this doc page <pair_cs>` for details.  All of the core/shell enabled pair
+styles are provided in the CORESHELL package.  See :doc:`this page <pair_cs>` for details.  All of the core/shell enabled pair
 styles require the use of a long-range Coulombic solver, as specified
 by the :doc:`kspace_style <kspace_style>` command.  Either the PPPM or
 Ewald solvers can be used.

doc/src/Howto_couple.rst

@@ -42,7 +42,7 @@ context of your application.
    stand-alone code could communicate with LAMMPS through files that the
    command writes and reads.
 
-   See the :doc:`Modify command <Modify_command>` doc page for info on how
+   See the :doc:`Modify command <Modify_command>` page for info on how
    to add a new command to LAMMPS.
 
 .. spacer

doc/src/Howto_drude2.rst

@@ -91,7 +91,7 @@ DRUDE package) to convert a non-polarizable data file (here
 
 This will automatically insert the new atoms and bonds.
 The masses and charges of DCs and DPs are computed
-from *phenol.dff*\ , as well as the DC-DP bond constants.  The file
+from *phenol.dff*, as well as the DC-DP bond constants.  The file
 *phenol.dff* contains the polarizabilities of the atom types
 and the mass of the Drude particles, for instance:
 
@@ -106,7 +106,7 @@ and the mass of the Drude particles, for instance:
 
 The hydrogen atoms are absent from this file, so they will be treated
 as non-polarizable atoms.  In the non-polarizable data file
-*data.102494.lmp*\ , atom names corresponding to the atom type numbers
+*data.102494.lmp*, atom names corresponding to the atom type numbers
 have to be specified as comments at the end of lines of the *Masses*
 section.  You probably need to edit it to add these names. It should
 look like
@@ -125,7 +125,7 @@ look like
 
 **Basic input file**
 
-The atom style should be set to (or derive from) *full*\ , so that you
+The atom style should be set to (or derive from) *full*, so that you
 can define atomic charges and molecular bonds, angles, dihedrals...
 
 The *polarizer* tool also outputs certain lines related to the input
@@ -143,7 +143,7 @@ and N for non-polarizable atoms.  Here the atom types 1 to 3 (C and O
 atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
 the atom types 6 to 8 are the newly created DPs.
 
-By recognizing the fix *drude*\ , LAMMPS will find and store matching
+By recognizing the fix *drude*, LAMMPS will find and store matching
 DC-DP pairs and will treat DP as equivalent to their DC in the
 *special bonds* relations.  It may be necessary to extend the space
 for storing such special relations.  In this case extra space should
@@ -340,11 +340,11 @@ For the *thole* pair style the coefficients are
 The special neighbors have charge-charge and charge-dipole
 interactions screened by the *coul* factors of the *special_bonds*
 command (0.0, 0.0, and 0.5 in the example above).  Without using the
-pair_style *thole*\ , dipole-dipole interactions are screened by the
-same factor.  By using the pair_style *thole*\ , dipole-dipole
+pair_style *thole*, dipole-dipole interactions are screened by the
+same factor.  By using the pair_style *thole*, dipole-dipole
 interactions are screened by Thole's function, whatever their special
 relationship (except within each DC-DP pair of course).  Consider for
-example 1-2 neighbors: using the pair_style *thole*\ , their dipoles
+example 1-2 neighbors: using the pair_style *thole*, their dipoles
 will see each other (despite the *coul* factor being 0.) and the
 interactions between these dipoles will be damped by Thole's function.
 
@@ -384,7 +384,7 @@ For our phenol example, the groups would be defined as
    group CORES  type 1 2 3     # DCs
    group DRUDES type 6 7 8     # DPs
 
-Note that with the fixes *drude/transform*\ , it is not required to
+Note that with the fixes *drude/transform*, it is not required to
 specify *comm_modify vel yes* because the fixes do it anyway (several
 times and for the forces also).
 

doc/src/Howto_github.rst

@@ -140,8 +140,8 @@ After everything is done, add the files to the branch and commit them:
    flag) will automatically include **all** modified **and** new files
    and that is rarely the behavior you want.  It can easily lead to
    accidentally adding unrelated and unwanted changes into the
-   repository.  Instead it is preferable to explicitly use *git add*\ ,
-   *git rm*\ , *git mv* for adding, removing, renaming individual files,
+   repository.  Instead it is preferable to explicitly use *git add*,
+   *git rm*, *git mv* for adding, removing, renaming individual files,
    respectively, and then *git commit* to finalize the commit.
    Carefully check all pending changes with *git status* before
    committing them.  If you find doing this on the command line too

doc/src/Howto_kappa.rst

@@ -4,7 +4,7 @@ Calculate thermal conductivity
 The thermal conductivity kappa of a material can be measured in at
 least 4 ways using various options in LAMMPS.  See the examples/KAPPA
 directory for scripts that implement the 4 methods discussed here for
-a simple Lennard-Jones fluid model.  Also, see the :doc:`Howto viscosity <Howto_viscosity>` doc page for an analogous discussion
+a simple Lennard-Jones fluid model.  Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion
 for viscosity.
 
 The thermal conductivity tensor kappa is a measure of the propensity
@@ -58,7 +58,7 @@ between hot and cold regions of the simulation box.
 The :doc:`compute heat/flux <compute_heat_flux>` command can calculate
 the needed heat flux and describes how to implement the Green_Kubo
 formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate <fix_ave_correlate>` command to calculate the needed
-auto-correlation.  See the doc page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
+auto-correlation.  See the page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
 that calculates the thermal conductivity of solid Ar via the GK
 formalism.
 

doc/src/Howto_manifold.rst

@@ -3,7 +3,7 @@ Manifolds (surfaces)
 
 **Overview:**
 
-This doc page is not about a LAMMPS input script command, but about
+This page is not about a LAMMPS input script command, but about
 manifolds, which are generalized surfaces, as defined and used by the
 MANIFOLD package, to track particle motion on the manifolds.  See
 the src/MANIFOLD/README file for more details about the package

doc/src/Howto_mdi.rst

@@ -3,7 +3,7 @@ Using LAMMPS with the MDI library for code coupling
 
 .. note::
 
-  This Howto doc page will eventually replace the
+  This Howto page will eventually replace the
   :doc:`Howto client/server <Howto_client_server>` doc page.
 
 Client/server coupling of two codes is where one code is the "client"
@@ -120,7 +120,7 @@ input script will continue.  After finishing execution of the input
 script, the instance of LAMMPS will be destroyed.
 
 LAMMPS supports the full set of MD-appropriate engine commands defined
-by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` doc page for
+by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` page for
 a list of these.
 
 If those commands are not sufficient for a user-developed driver to use

doc/src/Howto_output.rst

@@ -268,7 +268,7 @@ Computes that generate values to output
 Every :doc:`compute <compute>` in LAMMPS produces either global or
 per-atom or local values.  The values can be scalars or vectors or
 arrays of data.  These values can be output using the other commands
-described in this section.  The doc page for each compute command
+described in this section.  The page for each compute command
 describes what it produces.  Computes that produce per-atom or local
 values have the word "atom" or "local" in their style name.  Computes
 without the word "atom" or "local" produce global values.
@@ -281,7 +281,7 @@ Fixes that generate values to output
 Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
 local values which can be accessed by other commands.  The values can
 be scalars or vectors or arrays of data.  These values can be output
-using the other commands described in this section.  The doc page for
+using the other commands described in this section.  The page for
 each fix command tells whether it produces any output quantities and
 describes them.
 

doc/src/Howto_replica.rst

@@ -8,34 +8,33 @@ periodically.
 
 These are the relevant commands:
 
-* :doc:`neb <neb>` for nudged elastic band calculations
+* :doc:`hyper <hyper>` for bond boost hyperdynamics (HD)
+* :doc:`neb <neb>` for nudged elastic band calculations (NEB)
 * :doc:`neb_spin <neb_spin>` for magnetic nudged elastic band calculations
-* :doc:`prd <prd>` for parallel replica dynamics
-* :doc:`tad <tad>` for temperature accelerated dynamics
-* :doc:`temper <temper>` for parallel tempering
+* :doc:`prd <prd>` for parallel replica dynamics (PRD)
+* :doc:`tad <tad>` for temperature accelerated dynamics (TAD)
+* :doc:`temper <temper>` for parallel tempering with fixed volume
+* :doc:`temper/npt <temper_npt>` for parallel tempering extended for NPT
+* :doc:`temper/grem <temper_grem>` for parallel tempering with generalized replica exchange (gREM)
 * :doc:`fix pimd <fix_pimd>` for path-integral molecular dynamics (PIMD)
 
-NEB is a method for finding transition states and barrier energies.
-PRD and TAD are methods for performing accelerated dynamics to find
-and perform infrequent events.  Parallel tempering or replica exchange
-runs different replicas at a series of temperature to facilitate
-rare-event sampling.
+NEB is a method for finding transition states and barrier potential energies.
+HD, PRD, and TAD are methods for performing accelerated dynamics to find and
+perform infrequent events.  Parallel tempering or replica exchange runs
+different replicas at a series of temperature to facilitate rare-event
+sampling.  PIMD runs different replicas whose individual particles in different
+replicas are coupled together by springs to model a system of ring-polymers which
+can represent the quantum nature of atom cores.
 
 These commands can only be used if LAMMPS was built with the REPLICA
-package.  See the :doc:`Build package <Build_package>` doc page for more
-info.
-
-PIMD runs different replicas whose individual particles are coupled
-together by springs to model a system or ring-polymers.
-
-This commands can only be used if LAMMPS was built with the USER-MISC
-package.  See the :doc:`Build package <Build_package>` doc page for more
+package.  See the :doc:`Build package <Build_package>` page for more
 info.
 
 In all these cases, you must run with one or more processors per
 replica.  The processors assigned to each replica are determined at
-run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
-which in this context are the same as replicas.  E.g.  these commands:
+run-time by using the :doc:`-partition command-line switch
+<Run_options>` to launch LAMMPS on multiple partitions, which in this
+context are the same as replicas.  E.g.  these commands:
 
 .. code-block:: bash
 
@@ -46,9 +45,11 @@ would each run 8 replicas, on either 16 or 8 processors.  Note the use
 of the :doc:`-in command-line switch <Run_options>` to specify the input
 script which is required when running in multi-replica mode.
 
-Also note that with MPI installed on a machine (e.g. your desktop),
-you can run on more (virtual) processors than you have physical
-processors.  Thus the above commands could be run on a
-single-processor (or few-processor) desktop so that you can run
-a multi-replica simulation on more replicas than you have
-physical processors.
+Also note that with MPI installed on a machine (e.g. your desktop), you
+can run on more (virtual) processors than you have physical processors.
+Thus the above commands could be run on a single-processor (or
+few-processor) desktop so that you can run a multi-replica simulation on
+more replicas than you have physical processors. This is useful for
+testing and debugging, since with most modern processors and MPI
+libraries the efficiency of a calculation can severely diminish when
+oversubscribing processors.

doc/src/Howto_structured_data.rst

@@ -0,0 +1,154 @@
+Output structured data from LAMMPS
+##################################
+
+LAMMPS can output structured data with the :doc:`print <print>` and :doc:`fix
+print <fix_print>` command.  This gives you flexibility since you can build
+custom data formats that contain system properties, thermo data, and variables
+values. This output can be directed to the screen and/or to a file for post
+processing.
+
+Writing the current system state, thermo data, variable values
+==============================================================
+
+Use the :doc:`print <print>` command to output the current system state, which
+can include system properties, thermo data and variable values.
+
+YAML
+----
+
+.. code-block:: LAMMPS
+
+   print """---
+   timestep: $(step)
+   pe: $(pe)
+   ke: $(ke)""" file current_state.yaml screen no
+
+.. code-block:: yaml
+   :caption: current_state.yaml
+
+   ---
+   timestep: 250
+   pe: -4.7774327356321810711
+   ke: 2.4962152903997174569
+
+JSON
+----
+
+.. code-block:: LAMMPS
+
+   print """{
+     "timestep": $(step),
+     "pe": $(pe),
+     "ke": $(ke)
+   }""" file current_state.json screen no
+
+.. code-block:: JSON
+   :caption: current_state.json
+
+   {
+     "timestep": 250,
+     "pe": -4.7774327356321810711,
+     "ke": 2.4962152903997174569
+   }
+
+
+Writing continuous data during a simulation
+===========================================
+
+The :doc:`fix print <fix_print>` command allows you to output an arbitrary string at defined times during a simulation run.
+
+YAML
+----
+
+.. code-block:: LAMMPS
+
+   fix extra all print 50 """
+   - timestep: $(step)
+     pe: $(pe)
+     ke: $(ke)""" file output.yaml screen no
+
+.. code-block:: yaml
+   :caption: output.yaml
+
+   # Fix print output for fix extra
+   - timestep: 0
+     pe: -6.77336805325924729
+     ke: 4.4988750000000026219
+
+   - timestep: 50
+     pe: -4.8082494418323200591
+     ke: 2.5257981827119797558
+
+   - timestep: 100
+     pe: -4.7875608875581505686
+     ke: 2.5062598821985102582
+
+   - timestep: 150
+     pe: -4.7471033686005483787
+     ke: 2.466095925545450207
+
+   - timestep: 200
+     pe: -4.7509052858544134068
+     ke: 2.4701136792591693592
+
+   - timestep: 250
+     pe: -4.7774327356321810711
+     ke: 2.4962152903997174569
+
+Post-processing of YAML files can be easily be done with Python and other
+scripting languages. In case of Python the `yaml` package allows you to load the
+data files and obtain a list of dictionaries.
+
+.. code-block:: python
+
+   import yaml
+
+   with open("output.yaml") as f:
+      data = yaml.load(f, Loader=yaml.FullLoader)
+
+   print(data)
+
+.. code-block::
+
+   [{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
+
+Line Delimited JSON (LD-JSON)
+-----------------------------
+
+The JSON format itself is very strict when it comes to delimiters. For continuous
+output/streaming data it is beneficial use the *line delimited JSON* format.
+Each line represents one JSON object.
+
+.. code-block:: LAMMPS
+
+   fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no
+
+.. code-block:: json
+   :caption: output.json
+
+   {"timestep": 0, "pe": -6.77336805325924729, "ke": 4.4988750000000026219}
+   {"timestep": 50, "pe": -4.8082494418323200591, "ke": 2.5257981827119797558}
+   {"timestep": 100, "pe": -4.7875608875581505686, "ke": 2.5062598821985102582}
+   {"timestep": 150, "pe": -4.7471033686005483787, "ke": 2.466095925545450207}
+   {"timestep": 200, "pe": -4.7509052858544134068, "ke": 2.4701136792591693592}
+   {"timestep": 250, "pe": -4.7774327356321810711, "ke": 2.4962152903997174569}
+
+One simple way to load this data into a Python script is to use the `pandas`
+package. It can directly load these files into a data frame:
+
+.. code-block:: python
+
+   import pandas as pd
+
+   data = pd.read_json('output.json', lines=True)
+   print(data)
+
+.. code-block:: bash
+
+      timestep        pe        ke
+   0         0 -6.773368  4.498875
+   1        50 -4.808249  2.525798
+   2       100 -4.787561  2.506260
+   3       150 -4.747103  2.466096
+   4       200 -4.750905  2.470114
+   5       250 -4.777433  2.496215

doc/src/Howto_thermostat.rst

@@ -28,7 +28,7 @@ can be invoked via the *dpd/tstat* pair style:
 :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
 particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
 that it subtracts out a velocity bias due to a deforming box and
-integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` doc page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
+integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
 velocities but also rotational velocities for spherical and aspherical
 particles.
 
@@ -88,7 +88,7 @@ Below is a list of some custom temperature computes that can be used like that:
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes temperature
-values.  As explained on the doc page for the
+values.  As explained on the page for the
 :doc:`thermo_style <thermo_style>` command, the default temperature is
 setup by the thermo command itself.  It is NOT the temperature
 associated with any thermostatting fix you have defined or with any

doc/src/Howto_triclinic.rst

@@ -23,21 +23,21 @@ origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
 and are called "tilt factors" because they are the amount of
 displacement applied to faces of an originally orthogonal box to
 transform it into the parallelepiped.  In LAMMPS the triclinic
-simulation box edge vectors **a**\ , **b**\ , and **c** cannot be arbitrary
+simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary
 vectors.  As indicated, **a** must lie on the positive x axis.  **b** must
 lie in the xy plane, with strictly positive y component. **c** may have
 any orientation with strictly positive z component.  The requirement
-that **a**\ , **b**\ , and **c** have strictly positive x, y, and z components,
-respectively, ensures that **a**\ , **b**\ , and **c** form a complete
+that **a**, **b**, and **c** have strictly positive x, y, and z components,
+respectively, ensures that **a**, **b**, and **c** form a complete
 right-handed basis.  These restrictions impose no loss of generality,
 since it is possible to rotate/invert any set of 3 crystal basis
 vectors so that they conform to the restrictions.
 
-For example, assume that the 3 vectors **A**\ ,\ **B**\ ,\ **C** are the edge
+For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge
 vectors of a general parallelepiped, where there is no restriction on
-**A**\ ,\ **B**\ ,\ **C** other than they form a complete right-handed basis i.e.
-**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**\ ,\ **b**\ ,\ **c** are a linear
-rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
+**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e.
+**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear
+rotation of **A**, **B**, and **C** and can be computed as follows:
 
 .. math::
 
@@ -57,9 +57,9 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
 where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
 indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
 between the vectors described below. Note that by construction,
-**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively.
+**a**, **b**, and **c** have strictly positive x, y, and z components, respectively.
 If it should happen that
-**A**\ , **B**\ , and **C** form a left-handed basis, then the above equations
+**A**, **B**, and **C** form a left-handed basis, then the above equations
 are not valid for **c**\ . In this case, it is necessary
 to first apply an inversion. This can be achieved
 by interchanging two basis vectors or by changing the sign of one of them.
@@ -95,7 +95,7 @@ for details.
 The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
 time the simulation box is created.  This happens in one of 3 ways.
 If the :doc:`create_box <create_box>` command is used with a region of
-style *prism*\ , then a triclinic box is setup.  See the
+style *prism*, then a triclinic box is setup.  See the
 :doc:`region <region>` command for details.  If the
 :doc:`read_data <read_data>` command is used to define the simulation
 box, and the header of the data file contains a line with the "xy xz
@@ -135,7 +135,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
 ... are geometrically all equivalent.  If the box tilt exceeds this
 limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
 command), then the box is "flipped" to an equivalent shape with a tilt
-factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` doc page for further details.
+factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` page for further details.
 
 One exception to this rule is if the first dimension in the tilt
 factor (x for xy) is non-periodic.  In that case, the limits on the
@@ -160,10 +160,10 @@ For extreme values of tilt, LAMMPS may also lose atoms and generate an
 error.
 
 Triclinic crystal structures are often defined using three lattice
-constants *a*\ , *b*\ , and *c*\ , and three angles :math:`\alpha`,
+constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
 :math:`\beta`, and :math:`\gamma`. Note that in this nomenclature,
 the a, b, and c lattice constants are the scalar lengths of the edge
-vectors **a**\ , **b**\ , and **c** defined above.  The relationship
+vectors **a**, **b**, and **c** defined above.  The relationship
 between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`,
 :math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) =
 (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
@@ -188,10 +188,10 @@ The inverse relationship can be written as follows:
   {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
   {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
 
-The values of *a*\ , *b*\ , *c* , :math:`\alpha` , :math:`\beta`, and
+The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the
 :doc:`thermo_style custom <thermo_style>` keywords
-*cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ ,
+*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*,
 respectively.
 
 As discussed on the :doc:`dump <dump>` command doc page, when the BOX

doc/src/Howto_viscosity.rst

@@ -42,7 +42,7 @@ command, which determines grad(Vstream) in the equation above.
 E.g. the derivative in the y-direction of the Vx component of fluid
 motion or grad(Vstream) = dVx/dy.  The Pxy off-diagonal component of
 the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
-is the J term in the equation above.  See the :doc:`Howto nemd <Howto_nemd>` doc page for details on NEMD simulations.
+is the J term in the equation above.  See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
 
 The third method is to perform a reverse non-equilibrium MD simulation
 using the :doc:`fix viscosity <fix_viscosity>` command which implements

doc/src/Howto_viz.rst

@@ -13,7 +13,7 @@ by several popular visualization tools. The :doc:`dump image <dump_image>` and :
 output internally rendered images and convert a sequence of them to a
 movie during the MD run.  Several programs included with LAMMPS as
 auxiliary tools can convert between LAMMPS format files and other
-formats.  See the :doc:`Tools <Tools>` doc page for details.
+formats.  See the :doc:`Tools <Tools>` page for details.
 
 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
@@ -25,7 +25,7 @@ RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
 snapshots.
 
-.. _pizza: https://pizza.sandia.gov
+.. _pizza: https://lammps.github.io/pizza
 
 .. _ensight: https://www.ansys.com/products/fluids/ansys-ensight
 

doc/src/Howto_walls.rst

@@ -53,7 +53,7 @@ granular particles; all the other commands create smooth walls.
 * :doc:`fix wall/region <fix_wall_region>` - use region surface as wall
 * :doc:`fix wall/gran <fix_wall_gran>` - flat or curved walls with :doc:`pair_style granular <pair_gran>` potential
 
-The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all
+The *lj93*, *lj126*, *colloid*, *harmonic*, and *morse* styles all
 allow the flat walls to move with a constant velocity, or oscillate in
 time.  The :doc:`fix wall/region <fix_wall_region>` command offers the
 most generality, since the region surface is treated as a wall, and

doc/src/Intro_authors.rst

@@ -29,7 +29,7 @@ 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), REAXFF package for C version of ReaxFF
+* Metin Aktulga (MSU), REAXFF package for C/C++ version of ReaxFF
 * Mike Brown (Intel), GPU and INTEL packages
 * Colin Denniston (U Western Ontario), LATBOLTZ package
 * Georg Ganzenmuller (EMI), MACHDYN and SPH packages
@@ -37,9 +37,10 @@ general-purpose as it is without their expertise and efforts.
 * Reese Jones (Sandia) and colleagues, 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
+* Trung Ngyuen (Northwestern U), GPU, RIGID, BODY, and DIELECTRIC packages
 * Mike Parks (Sandia), PERI package for Peridynamics
 * Roy Pollock (LLNL), Ewald and PPPM solvers
+* Julien Tranchida (Sandia), SPIN package
 * Christian Trott (Sandia), CUDA and KOKKOS packages
 * Ilya Valuev (JIHT), AWPMD package for wave packet MD
 * Greg Wagner (Northwestern U), MEAM package for MEAM potential

doc/src/Intro_features.rst

@@ -24,18 +24,22 @@ General features
 ^^^^^^^^^^^^^^^^
 
 * runs on a single processor or in parallel
-* distributed-memory message-passing parallelism (MPI)
-* spatial-decomposition of simulation domain for parallelism
-* open-source distribution
-* highly portable C++
-* optional libraries used: MPI and single-processor FFT
-* GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+* distributed memory message-passing parallelism (MPI)
+* shared memory multi-threading parallelism (OpenMP)
+* spatial decomposition of simulation domain for MPI parallelism
+* particle decomposition inside of spatial decomposition for OpenMP and GPU parallelism
+* GPLv2 licensed open-source distribution
+* highly portable C++-11
+* modular code with most functionality in optional packages
+* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
+* other libraries are optional and only required for specific packages
+* GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP support for many code features
 * easy to extend with new features and functionality
 * runs from an input script
 * syntax for defining and using variables and formulas
 * syntax for looping over runs and breaking out of loops
 * run one or multiple simulations simultaneously (in parallel) from one script
-* build as library, invoke LAMMPS through library interface or provided Python wrapper
+* build as library, invoke LAMMPS through library interface or provided Python wrapper or SWIG based wrappers
 * couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
 
 .. _particle:
@@ -53,9 +57,11 @@ Particle and model types
 * granular materials
 * coarse-grained mesoscale models
 * finite-size spherical and ellipsoidal particles
-* finite-size  line segment (2d) and triangle (3d) particles
+* finite-size line segment (2d) and triangle (3d) particles
+* finite-size rounded polygons (2d) and polyhedra (3d) particles
 * point dipole particles
-* rigid collections of particles
+* particles with magnetic spin
+* rigid collections of n particles
 * hybrid combinations of these
 
 .. _ff:
@@ -68,26 +74,30 @@ Interatomic potentials (force fields)
 :doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
 commands)
 
-* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins,     Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
+* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
 * charged pairwise potentials: Coulombic, point-dipole
-* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff,     REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
-* long-range interactions for charge, point-dipoles, and LJ dispersion:     Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
+* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
+* machine learning potentials: SNAP, GAP, ACE, N2P2, RANN, AGNI
+* long-range interactions for charge, point-dipoles, and LJ dispersion:  Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM
 * polarization models: :doc:`QEq <fix_qeq>`,     :doc:`core/shell model <Howto_coreshell>`,     :doc:`Drude dipole model <Howto_drude>`
 * charge equilibration (QEq via dynamic, point, shielded, Slater methods)
 * coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
-* mesoscopic potentials: granular, Peridynamics, SPH
+* mesoscopic potentials: granular, Peridynamics, SPH, mesoscopic tubular potential (MESONT)
+* semi-empirical potentials: multi-ion generalized pseudopotential theory (MGPT), second moment tight binding + QEq (SMTB-Q), density functional tight-binding (LATTE)
 * electron force field (eFF, AWPMD)
-* bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)
-* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic,     class 2 (COMPASS)
-* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS
-* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
+* bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), tabulated
+* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS), tabulated
+* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, tabulated
+* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS), tabulated
 * polymer potentials: all-atom, united-atom, bead-spring, breakable
-* water potentials: TIP3P, TIP4P, SPC
+* water potentials: TIP3P, TIP4P, SPC, SPC/E and variants
+* interlayer potentials for graphene and analogues
+* metal-organic framework potentials (QuickFF, MO-FF)
 * implicit solvent potentials: hydrodynamic lubrication, Debye
-* force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
+* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
 * access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim command <kim_commands>`
-* hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
-* overlaid potentials: superposition of multiple pair potentials
+* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
+* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
 
 .. _create:
 
@@ -120,9 +130,10 @@ Ensembles, constraints, and boundary conditions
 * harmonic (umbrella) constraint forces
 * rigid body constraints
 * SHAKE bond and angle constraints
-* Monte Carlo bond breaking, formation, swapping
+* motion constraints to manifold surfaces
+* Monte Carlo bond breaking, formation, swapping, template based reaction modeling
 * atom/molecule insertion and deletion
-* walls of various kinds
+* walls of various kinds, static and moving
 * non-equilibrium molecular dynamics (NEMD)
 * variety of additional boundary conditions and constraints
 
@@ -146,6 +157,7 @@ Diagnostics
 ^^^^^^^^^^^
 
 * see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
+* introspection command for system, simulation, and compile time settings and configurations
 
 .. _output:
 
@@ -160,8 +172,9 @@ Output
 * parallel I/O of dump and restart files
 * per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
 * user-defined system-wide (log file) or per-atom (dump file) calculations
-* spatial and time averaging of per-atom quantities
-* time averaging of system-wide quantities
+* custom partitioning (chunks) for binning, and static or dynamic grouping of atoms for analysis
+* spatial, time, and per-chunk averaging of per-atom quantities
+* time averaging and histogramming of system-wide quantities
 * atom snapshots in native, XYZ, XTC, DCD, CFG formats
 
 .. _replica1:
@@ -170,9 +183,12 @@ Multi-replica models
 ^^^^^^^^^^^^^^^^^^^^
 
 * :doc:`nudged elastic band <neb>`
+* :doc:`hyperdynamics <hyper>`
 * :doc:`parallel replica dynamics <prd>`
 * :doc:`temperature accelerated dynamics <tad>`
 * :doc:`parallel tempering <temper>`
+* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
+* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
 
 .. _prepost:
 
@@ -187,7 +203,7 @@ Pre- and post-processing
   plotting, and visualization for LAMMPS simulations.  Pizza.py is
   written in `Python <python_>`_ and is available for download from `the Pizza.py WWW site <pizza_>`_.
 
-.. _pizza: https://pizza.sandia.gov
+.. _pizza: https://lammps.github.io/pizza
 
 .. _python: http://www.python.org
 
@@ -203,11 +219,12 @@ page for details.
 These are LAMMPS capabilities which you may not think of as typical
 classical MD options:
 
-* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`
+* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`, optional with recursive bisectioning decomposition
 * :doc:`generalized aspherical particles <Howto_body>`
 * :doc:`stochastic rotation dynamics (SRD) <fix_srd>`
-* :doc:`real-time visualization and interactive MD <fix_imd>`
+* :doc:`real-time visualization and interactive MD <fix_imd>`, :doc:`built-in renderer for images and movies <dump_image>`
 * calculate :doc:`virtual diffraction patterns <compute_xrd>`
+* calculate :doc:`finite temperature phonon dispersion <fix_phonon>` and the :doc:`dynamical matrix of minimized structures <dynamical_matrix>`
 * :doc:`atom-to-continuum coupling <fix_atc>` with finite elements
 * coupled rigid body integration via the :doc:`POEMS <fix_poems>` library
 * :doc:`QM/MM coupling <fix_qmmm>`

doc/src/Intro_nonfeatures.rst

@@ -32,7 +32,7 @@ Here are suggestions on how to perform these tasks:
   are simple programs that will build simple molecular systems, such as
   linear bead-spring polymer chains.  The moltemplate program is a true
   molecular builder that will generate complex molecular models.  See
-  the :doc:`Tools <Tools>` doc page for details on tools packaged with
+  the :doc:`Tools <Tools>` page for details on tools packaged with
   LAMMPS.  The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
   describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
@@ -49,7 +49,7 @@ Here are suggestions on how to perform these tasks:
 * **Simulation analysis:** If you want to perform analysis on-the-fly as
   your simulation runs, see the :doc:`compute <compute>` and
   :doc:`fix <fix>` doc pages, which list commands that can be used in a
-  LAMMPS input script.  Also see the :doc:`Modify <Modify>` doc page for
+  LAMMPS input script.  Also see the :doc:`Modify <Modify>` page for
   info on how to add your own analysis code or algorithms to LAMMPS.
   For post-processing, LAMMPS output such as :doc:`dump file snapshots <dump>` can be converted into formats used by other MD or
   post-processing codes.  To some degree, that conversion can be done
@@ -61,7 +61,7 @@ Here are suggestions on how to perform these tasks:
   LAMMPS will do these conversions.  Scripts provided in the
   tools/python directory can extract and massage data in dump files to
   make it easier to import into other programs.  See the
-  :doc:`Tools <Tools>` doc page for details on these various options.
+  :doc:`Tools <Tools>` page for details on these various options.
 * **Visualization:** LAMMPS can produce NETPBM, JPG or PNG snapshot images
   on-the-fly via its :doc:`dump image <dump_image>` command and pass
   them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
@@ -71,13 +71,13 @@ Here are suggestions on how to perform these tasks:
   LAMMPS website for
   visualization packages that can process LAMMPS output data.
 * **Plotting:** See the next bullet about Pizza.py as well as the
-  :doc:`Python <Python_head>` doc page for examples of plotting LAMMPS
+  :doc:`Python <Python_head>` page for examples of plotting LAMMPS
   output.  Scripts provided with the *python* tool in the tools
   directory will extract and massage data in log and dump files to make
   it easier to analyze and plot.  See the :doc:`Tools <Tools>` doc page
   for more discussion of the various tools.
 * **Pizza.py:** Our group has also written a separate toolkit called
-  `Pizza.py <https://pizza.sandia.gov>`_ which can do certain kinds of
+  `Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
   setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
   simulations.  It thus provides some functionality for several of the
   above bullets.  Pizza.py is written in `Python <http://www.python.org>`_

doc/src/Intro_opensource.rst

@@ -1,40 +1,61 @@
 LAMMPS open-source license
 --------------------------
 
-LAMMPS is a freely-available open-source code, distributed under the
-terms of the `GNU Public License Version 2 <gpl_>`_, which means you can
-use or modify the code however you wish for your own purposes, but have
-to adhere to certain rules when redistributing it or software derived
+GPL version of LAMMPS
+^^^^^^^^^^^^^^^^^^^^^
+
+LAMMPS is an open-source code, available free-of-charge, and distributed
+under the terms of the `GNU Public License Version 2 <gpl_>`_ (GPLv2),
+which means you can use or modify the code however you wish for your own
+purposes, but have to adhere to certain rules when redistributing it -
+specifically in binary form - or are distributing software derived
 from it or that includes parts of it.
 
-LAMMPS comes with no warranty of any kind.  As each source file states
-in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the `GNU Public License Version 2 <gpl_>`_
-(GPLv2).  This is often referred to as open-source distribution - see
-`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The
-legal text of the GPL is in the LICENSE file included in the LAMMPS
-distribution.
+LAMMPS comes with no warranty of any kind.
+
+As each source file states in its header, it is a copyrighted code, and
+thus not in the public domain. For more information about open-source
+software and open-source distribution, see `www.gnu.org <gnuorg_>`_
+or `www.opensource.org <opensource_>`_.  The legal text of the GPL as it
+applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
 .. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
 
+.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
+
 .. _gnuorg: http://www.gnu.org
 
 .. _opensource: http://www.opensource.org
 
-Here is a summary of what the GPL means for LAMMPS users:
+Here is a more specific summary of what the GPL means for LAMMPS users:
 
-(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+(1) Anyone is free to use, copy, modify, or extend LAMMPS in any way they
 choose, including for commercial purposes.
 
 (2) If you **distribute** a modified version of LAMMPS, it must remain
-open-source, meaning you distribute **all** of it under the terms of
-the GPL.  You should clearly annotate such a code as a derivative version
-of LAMMPS.
+open-source, meaning you are required to distribute **all** of it under
+the terms of the GPL.  You should clearly annotate such a modified code
+as a derivative version of LAMMPS.
 
 (3) If you release any code that includes or uses LAMMPS source code,
 then it must also be open-sourced, meaning you distribute it under
-the terms of the GPL.
+the terms of the GPL.  You may write code that interfaces LAMMPS to
+a differently licensed library.  In that case the code that provides
+the interface must be licensed GPL, but not necessarily that library
+unless you are distributing binaries that require the library to run.
 
 (4) If you give LAMMPS files to someone else, the GPL LICENSE file and
 source file headers (including the copyright and GPL notices) should
 remain part of the code.
+
+
+LGPL version of LAMMPS
+^^^^^^^^^^^^^^^^^^^^^^
+
+We occasionally make stable LAMMPS releases available under the `GNU
+Lesser Public License v2.1 <lgpl_>`_.  This is on request only and with
+non-LGPL compliant files removed.  This allows uses linking non-GPL
+compatible software with the (otherwise unmodified) LAMMPS library
+or loading it dynamically at runtime.  Any **modifications** to
+the LAMMPS code however, even with the LGPL licensed version, must still
+be made available under the same open source terms as LAMMPS itself.

doc/src/Intro_overview.rst

@@ -10,23 +10,26 @@ 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 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
-supercomputers.
+designed for parallel computers.  It will run in serial and on any
+parallel machine that supports the `MPI <mpi_>`_ message-passing
+library.  This includes shared-memory boxes and distributed-memory
+clusters and supercomputers. Parts of LAMMPS also support
+`OpenMP multi-threading <omp_>`_, vectorization and GPU acceleration.
 
 .. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
 .. _lws: https://www.lammps.org
+.. _omp: https://www.openmp.org
 
-LAMMPS is written in C++.  Earlier versions were written in F77 and
-F90.  See the `History page <https://www.lammps.org/history.html>`_ of
-the website for details.  All versions can be downloaded from the
-`LAMMPS website <lws_>`_.
+LAMMPS is written in C++ and requires a compiler that is at least
+compatible with the C++-11 standard.  Earlier versions were written in
+F77, F90, and C++-98.  See the `History page
+<https://www.lammps.org/history.html>`_ of the website for details.  All
+versions can be downloaded as source code from the `LAMMPS website
+<lws_>`_.
 
-LAMMPS is designed to be easy to modify or extend with new
-capabilities, such as new force fields, atom types, boundary
-conditions, or diagnostics.  See the :doc:`Modify <Modify>` doc page for
-more details.
+LAMMPS is designed to be easy to modify or extend with new capabilities,
+such as new force fields, atom types, boundary conditions, or
+diagnostics.  See the :doc:`Modify <Modify>` page for more details.
 
 In the most general sense, LAMMPS integrates Newton's equations of
 motion for a collection of interacting particles.  A single particle
@@ -41,8 +44,10 @@ short distances, so that the local density of particles never becomes
 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
-partition the simulation domain into small sub-domains of equal
-computational cost, one of which is assigned to each processor.
-Processors communicate and store "ghost" atom information for atoms
-that border their sub-domain.
+On parallel machines, LAMMPS uses spatial-decomposition techniques with
+MPI parallelization to partition the simulation domain into small
+sub-domains of equal computational cost, one of which is assigned to
+each processor.  Processors communicate and store "ghost" atom
+information for atoms that border their sub-domain.  Multi-threading
+parallelization and GPU acceleration with with particle-decomposition
+can be used in addition.

doc/src/Intro_website.rst

@@ -20,7 +20,8 @@ available online are listed below.
 * `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
 * `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
 * `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
-* `Mail list <https://www.lammps.org/mail.html>`_
+* `Mailing list <https://www.lammps.org/mail.html>`_
+* `LAMMPS forum <https://www.lammps.org/forum.html>`_
 * `Workshops <https://www.lammps.org/workshops.html>`_
 * `Tutorials <https://www.lammps.org/tutorials.html>`_
 

doc/src/Library_scatter.rst

@@ -17,6 +17,7 @@ It documents the following functions:
 - :cpp:func:`lammps_gather_atoms_subset`
 - :cpp:func:`lammps_scatter_atoms`
 - :cpp:func:`lammps_scatter_atoms_subset`
+- :cpp:func:`lammps_gather_bonds`
 - :cpp:func:`lammps_gather`
 - :cpp:func:`lammps_gather_concat`
 - :cpp:func:`lammps_gather_subset`
@@ -51,6 +52,11 @@ It documents the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_gather_bonds
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_gather
    :project: progguide
 

doc/src/Library_utility.rst

@@ -8,7 +8,11 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_decode_image_flags`
 - :cpp:func:`lammps_set_fix_external_callback`
 - :cpp:func:`lammps_fix_external_set_energy_global`
+- :cpp:func:`lammps_fix_external_set_energy_peratom`
 - :cpp:func:`lammps_fix_external_set_virial_global`
+- :cpp:func:`lammps_fix_external_set_virial_peratom`
+- :cpp:func:`lammps_fix_external_set_vector_length`
+- :cpp:func:`lammps_fix_external_set_vector`
 - :cpp:func:`lammps_free`
 - :cpp:func:`lammps_is_running`
 - :cpp:func:`lammps_force_timeout`
@@ -33,7 +37,7 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
-.. doxygenfunction:: lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*)
+.. doxygenfunction:: lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void*)
    :project: progguide
 
 -----------------------
@@ -43,11 +47,31 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
+.. doxygenfunction:: lammps_fix_external_set_energy_peratom
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_fix_external_set_virial_global
    :project: progguide
 
 -----------------------
 
+.. doxygenfunction:: lammps_fix_external_set_virial_peratom
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_fix_external_set_vector_length
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_fix_external_set_vector
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_free
    :project: progguide
 

doc/src/Manual_version.rst

@@ -2,12 +2,21 @@ What does a LAMMPS version mean
 -------------------------------
 
 The LAMMPS "version" is the date when it was released, such as 1 May
-2014. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it in the next *patch* release, which are
-typically made every couple of weeks.  Info on patch releases are on
-`this website page <https://www.lammps.org/bug.html>`_. Every few
-months, the latest patch release is subjected to more thorough testing
-and labeled as a *stable* version.
+2014.  LAMMPS is updated continuously and we aim to keep it working
+correctly and reliably at all times.  You can follow its development
+in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
+
+Whenever we fix a bug or update or add a feature, it will be merged into
+the `master` branch of the git repository.  When a sufficient number of
+changes have accumulated *and* the software passes a set of automated
+tests, we release it in the next *patch* release, which are made every
+few weeks.  Info on patch releases are on `this website page
+<https://www.lammps.org/bug.html>`_.
+
+Once or twice a year, only bug fixes and small, non-intrusive changes are
+included for a period of time, and the code is subjected to more detailed
+and thorough testing than the default automated testing.  The latest
+patch release after such a period is then labeled as a *stable* version.
 
 Each version of LAMMPS contains all the features and bug-fixes up to
 and including its version date.

doc/src/Modify_body.rst

@@ -6,7 +6,7 @@ Body particles can represent complex entities, such as surface meshes
 of discrete points, collections of sub-particles, deformable objects,
 etc.
 
-See the :doc:`Howto body <Howto_body>` doc page for an overview of using
+See the :doc:`Howto body <Howto_body>` page for an overview of using
 body particles and the various body styles LAMMPS supports.  New
 styles can be created to add new kinds of body particles to LAMMPS.
 

doc/src/Modify_contribute.rst

@@ -25,13 +25,16 @@ the work of others (and possibly get scooped by them) or have your work
 duplicated by others.
 
 For informal communication with (some of) the LAMMPS developers you may
-ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
-This slack work space is by invitation only. Thus for access, please
-send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
-you are working on.  Only discussions related to LAMMPS development are
-tolerated, so this is **NOT** for people that look for help with compiling,
-installing, or using LAMMPS. Please contact the `lammps-users mailing
-list <https://www.lammps.org/mail.html>`_ for those purposes instead.
+ask to join the `LAMMPS developers on Slack
+<https://lammps.slack.com>`_.  This slack work space is by invitation
+only. Thus for access, please send an e-mail to ``slack@lammps.org``
+explaining what part of LAMMPS you are working on.  Only discussions
+related to LAMMPS development are tolerated, so this is **NOT** for
+people that look for help with compiling, installing, or using
+LAMMPS. Please contact the
+`lammps-users mailing list <https://www.lammps.org/mail.html>`_ or the
+`LAMMPS forum <https://www.lammps.org/forum.html>`_ for those purposes
+instead.
 
 How quickly your contribution will be integrated depends largely on how
 much effort it will cause to integrate and test it, how many and what
@@ -49,11 +52,9 @@ with gzip.  Please only use gzip compression, as this works well and is
 available on all platforms.
 
 If the new features/files are broadly useful we may add them as core
-files to LAMMPS or as part of a :doc:`package <Packages_list>`.  The
-USER-MISC package is simply a collection of (mostly) unrelated single
-files, which is the simplest way to have your contribution quickly added
-to the LAMMPS distribution.  All packages are listed and described
-on the :doc:`Packages details <Packages_details>` doc page.
+files to LAMMPS or as part of a :doc:`package <Packages_list>`.  All
+packages are listed and described on the :doc:`Packages details
+<Packages_details>` doc page.
 
 Note that by providing us files to release, you are agreeing to make
 them open-source, i.e. we can release them under the terms of the GPL
@@ -61,7 +62,7 @@ them open-source, i.e. we can release them under the terms of the GPL
 a LGPL (version 2.1) distribution that we make available to developers
 on request only and with files that are authorized for that kind of
 distribution removed (e.g. interface to FFTW).  See the
-:doc:`LAMMPS license <Intro_opensource>` doc page for details.
+:doc:`LAMMPS license <Intro_opensource>` page for details.
 
 .. note::
 
@@ -79,7 +80,7 @@ distribution removed (e.g. interface to FFTW).  See the
 
 .. _lws: https://www.lammps.org
 
-The previous sections of this doc page describe how to add new "style"
+The previous sections of this page describe how to add new "style"
 files of various kinds to LAMMPS.  Packages are simply collections of
 one or more new class files which are invoked as a new style within a
 LAMMPS input script.  If designed correctly, these additions typically
@@ -92,7 +93,7 @@ trivial change is making a parent-class method "virtual" when you derive
 a new child class from it.
 
 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
+or package for our consideration.  Following these steps will save
 both you and us time. Please have a look at the existing files in
 packages in the src directory for examples. If you are uncertain, please ask.
 
@@ -106,7 +107,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
   your contribution(s) to be added to main LAMMPS code or one of its
   standard packages, it needs to be written in a style compatible with
   other LAMMPS source files. This means: 2-character indentation per
-  level, **no tabs**\ , no lines over 100 characters. I/O is done via
+  level, **no tabs**, no lines over 100 characters. I/O is done via
   the C-style stdio library (mixing of stdio and iostreams is generally
   discouraged), class header files should not import any system headers
   outside of <cstdio>, STL containers should be avoided in headers,
@@ -150,37 +151,40 @@ packages in the src directory for examples. If you are uncertain, please ask.
   You may also use ``// clang-format on/off`` throughout your file
   to protect sections of the file from being reformatted.
 
-* If you want your contribution to be added as a user-contributed
-  feature, and it's a single file (actually a \*.cpp and \*.h file) it can
-  rapidly be added to the USER-MISC directory.  Send us the one-line
-  entry to add to the USER-MISC/README file in that dir, along with the
-  2 source files.  You can do this multiple times if you wish to
-  contribute several individual features.
+* Please review the list of :doc:`available Packages <Packages_details>`
+  to see if your contribution could be added to be added to one of them.
+  It should fit into the general purposed of that package.  If it does not
+  fit well, it can be added to one of the EXTRA- packages or the MISC package.
 
-* If you want your contribution to be added and it has several related
-  features or is dependent on an external or bundled library, it is best
-  to make it a package directory with a name like FOO.  In addition to
-  your new files, the directory should contain a README text file.  The
-  README should contain your name and contact information and a brief
-  description of what your new package does.  If your files depend on
-  other LAMMPS style files also being installed (e.g. because your file
-  is a derived class from the other LAMMPS class), then an Install.sh
-  file is also needed to check for those dependencies.  See other README
-  and Install.sh files in other directories as examples.  Submit a pull
-  request on GitHub or send us a tarball of this FOO directory.  Pull
-  requests are strongly encouraged since the greatly reduce the effort
-  to integrate a contribution and simplify the process of adjusting the
-  contributed code to cleanly integrate into the LAMMPS distribution.
+* If your contribution has several related features that are not covered
+  by one of the existing packages or is dependent on a library (bundled
+  or external), it is best to make it a package directory with a name
+  like FOO.  In addition to your new files, the directory should contain
+  a README text file.  The README should contain your name and contact
+  information and a brief description of what your new package does.  If
+  your files depend on other LAMMPS style files also being installed
+  (e.g. because your file is a derived class from the other LAMMPS
+  class), then an Install.sh file is also needed to check for those
+  dependencies and modifications to src/Depend.sh to trigger the checks.
+  See other README and Install.sh files in other directories as examples.
+  Similarly for CMake support changes need to be made to cmake/CMakeLists.txt,
+  the files in cmake/presets, and possibly a file to cmake/Modules/Packages/
+  added.  Please check out how this is handled for existing packages and
+  ask the LAMMPS developers if you need assistance.  Please submit a pull
+  request on GitHub or send us a tarball of this FOO directory and all
+  modified files.  Pull requests are strongly encouraged since they greatly
+  reduce the effort required to integrate a contribution and simplify the
+  process of adjusting the contributed code to cleanly fit into the
+  LAMMPS distribution.
 
 * Your new source files need to have the LAMMPS copyright, GPL notice,
   and your name and email address at the top, like other
   user-contributed LAMMPS source files.  They need to create a class
-  that is inside the LAMMPS namespace.  If the file is for one of the
-  USER packages, including USER-MISC, then we are not as picky about the
-  coding style (see above).  I.e. the files do not need to be in the
-  same stylistic format and syntax as other LAMMPS files, though that
-  would be nice for developers as well as users who try to read your
-  code.
+  that is inside the LAMMPS namespace.  To simplify maintenance, we
+  may ask to adjust the programming style and formatting style to closer
+  match the rest of LAMMPS.  We bundle a clang-format configuration file
+  that can help with adjusting the formatting, although this is not a
+  strict requirement.
 
 * You **must** also create a **documentation** file for each new command
   or style you are adding to LAMMPS.  For simplicity and convenience,
@@ -199,13 +203,13 @@ packages in the src directory for examples. If you are uncertain, please ask.
   pdf" in the doc folder.  As appropriate, the text files can include
   inline mathematical expression or figures (see doc/JPG for examples).
   Additional PDF files with further details (see doc/PDF for examples)
-  may also be included.  The doc page should also include literature
+  may also be included.  The page should also include literature
   citations as appropriate; see the bottom of doc/fix_nh.rst for
   examples and the earlier part of the same file for how to format the
   cite itself.  Citation labels must be unique across all .rst files.
-  The "Restrictions" section of the doc page should indicate if your
+  The "Restrictions" section of the page should indicate if your
   command is only available if LAMMPS is built with the appropriate
-  USER-MISC or FOO package.  See other package doc files for examples of
+  FOO package.  See other package doc files for examples of
   how to do this.  Please run at least "make html" and "make spelling"
   and carefully inspect and proofread the resulting HTML format doc page
   before submitting your code.  Upon submission of a pull request,

doc/src/Modify_fix.rst

@@ -129,7 +129,7 @@ derived class.  See fix.h for details.
 Typically, only a small fraction of these methods are defined for a
 particular fix.  Setmask is mandatory, as it determines when the fix
 will be invoked during the timestep.  Fixes that perform time
-integration (\ *nve*\ , *nvt*\ , *npt*\ ) implement initial_integrate() and
+integration (\ *nve*, *nvt*, *npt*\ ) implement initial_integrate() and
 final_integrate() to perform velocity Verlet updates.  Fixes that
 constrain forces implement post_force().
 

doc/src/Packages.rst

@@ -7,7 +7,7 @@ specific set of features.  For example, force fields for molecular
 systems or rigid-body constraints are in packages.  You can see the
 list of all packages and "make" commands to manage them by typing
 "make package" from within the src directory of the LAMMPS
-distribution.  The :doc:`Build package <Build_package>` doc page gives
+distribution.  The :doc:`Build package <Build_package>` page gives
 general info on how to install and un-install packages as part of the
 LAMMPS build process.
 

doc/src/Packages_details.rst

@@ -49,11 +49,17 @@ page gives those details.
    * :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>`
    * :ref:`DRUDE <PKG-DRUDE>`
    * :ref:`EFF <PKG-EFF>`
+   * :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
+   * :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
+   * :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
+   * :ref:`EXTRA-MOLECULE <PKG-EXTRA-MOLECULE>`
+   * :ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>`
    * :ref:`FEP <PKG-FEP>`
    * :ref:`GPU <PKG-GPU>`
    * :ref:`GRANULAR <PKG-GRANULAR>`
    * :ref:`H5MD <PKG-H5MD>`
    * :ref:`INTEL <PKG-INTEL>`
+   * :ref:`INTERLAYER <PKG-INTERLAYER>`
    * :ref:`KIM <PKG-KIM>`
    * :ref:`KOKKOS <PKG-KOKKOS>`
    * :ref:`KSPACE <PKG-KSPACE>`
@@ -83,6 +89,7 @@ page gives those details.
    * :ref:`NETCDF <PKG-NETCDF>`
    * :ref:`OPENMP <PKG-OPENMP>`
    * :ref:`OPT <PKG-OPT>`
+   * :ref:`ORIENT <PKG-ORIENT>`
    * :ref:`PERI <PKG-PERI>`
    * :ref:`PHONON <PKG-PHONON>`
    * :ref:`PLUGIN <PKG-PLUGIN>`
@@ -108,7 +115,6 @@ page gives those details.
    * :ref:`VORONOI <PKG-VORONOI>`
    * :ref:`VTK <PKG-VTK>`
    * :ref:`YAFF <PKG-YAFF>`
-   * :ref:`USER-MISC <PKG-USER-MISC>`
 
 ----------
 
@@ -183,6 +189,7 @@ atomic information to continuum fields.
 **Install:**
 
 This package has :ref:`specific installation instructions <atc>` on the :doc:`Build extras <Build_extras>` page.
+The ATC package requires that also the `MANYBODY <PKG-MANYBODY>`_ package is installed.
 
 **Supporting info:**
 
@@ -311,6 +318,11 @@ rigid-body integrators with improved stability.
 
 **Author:** Oliver Henrich (University of Strathclyde, Glasgow).
 
+**Install:**
+
+The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
+`ASPHERE <PKG-ASPHERE>`_ packages are installed.
+
 **Supporting info:**
 
 * src/CG-DNA: filenames -> commands
@@ -507,6 +519,11 @@ compute for simulating systems using boundary element solvers for
 computing the induced charges at the interface between two media with
 different dielectric constants.
 
+**Install:**
+
+To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
+:ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>` packages need to be installed.
+
 **Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
 
 **Supporting info:**
@@ -557,6 +574,7 @@ short-range or long-range interactions.
 * :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
 * :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
 * :doc:`pair_style lj/long/dipole/long <pair_dipole>`
+* :doc: `angle_style dipole <angle_dipole>`
 * examples/dipole
 
 ----------
@@ -750,6 +768,86 @@ tools/eff; see its README file.
 * tools/eff
 * https://www.lammps.org/movies.html#eff
 
+-------------------
+
+.. _PKG-EXTRA-COMPUTE:
+
+EXTRA-COMPUTE package
+---------------------
+
+**Contents:**
+
+Additional compute styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-COMPUTE: filenames -> commands
+* :doc:`compute <compute>`
+
+----------
+
+.. _PKG-EXTRA-DUMP:
+
+EXTRA-DUMP package
+------------------
+
+**Contents:**
+
+Additional dump styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-DUMP: filenames -> commands
+* :doc:`dump <dump>`
+
+----------
+
+.. _PKG-EXTRA-FIX:
+
+EXTRA-FIX package
+-----------------
+
+**Contents:**
+
+Additional fix styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-FIX: filenames -> commands
+* :doc:`fix <fix>`
+
+----------
+
+.. _PKG-EXTRA-MOLECULE:
+
+EXTRA-MOLECULE package
+----------------------
+
+**Contents:**
+
+Additional bond, angle, dihedral, and improper styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-MOLECULE: filenames -> commands
+* :doc:`molecular styles <Commands_bond>`
+
+----------
+
+.. _PKG-EXTRA-PAIR:
+
+EXTRA-PAIR package
+------------------
+
+**Contents:**
+
+Additional pair styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-PAIR: filenames -> commands
+* :doc:`pair_style <pair_style>`
+
 ----------
 
 .. _PKG-FEP:
@@ -933,6 +1031,24 @@ This package has :ref:`specific installation instructions <intel>` on the :doc:`
 
 ----------
 
+.. _PKG-INTERLAYER:
+
+INTERLAYER package
+------------------
+
+**Contents:**
+
+A collection of pair styles specifically to be used for modeling layered
+materials, most commonly graphene sheets (or equivalents).
+
+**Supporting info:**
+
+* src/INTERLAYER: filenames -> commands
+* :doc:`Pair style <Commands_pair>` page
+* examples/PACKAGES/interlayer
+
+----------
+
 .. _PKG-KIM:
 
 KIM package
@@ -1100,6 +1216,10 @@ can be used to model MD particles influenced by hydrodynamic forces.
 **Authors:** Frances Mackay and Colin Denniston (University of Western
 Ontario).
 
+**Install:**
+
+The LATBOLTZ package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
+
 **Supporting info:**
 
 * src/LATBOLTZ: filenames -> commands
@@ -1423,7 +1543,7 @@ MISC package
 
 **Contents:**
 
-A variety of compute, fix, pair, dump styles with specialized
+A variety of compute, fix, pair, bond styles with specialized
 capabilities that don't align with other packages.  Do a directory
 listing, "ls src/MISC", to see the list of commands.
 
@@ -1435,18 +1555,16 @@ listing, "ls src/MISC", to see the list of commands.
 **Supporting info:**
 
 * src/MISC: filenames -> commands
-* :doc:`compute ti <compute_ti>`
-* :doc:`fix evaporate <fix_evaporate>`
+* :doc:`bond_style special <bond_special>`
+* :doc:`compute viscosity/cos <compute_viscosity_cos>`
+* :doc:`fix accelerate/cos <fix_accelerate_cos>`
 * :doc:`fix imd <fix_imd>`
-* :doc:`fix oneway <fix_oneway>`
-* :doc:`fix orient/fcc <fix_orient>`
-* :doc:`fix ttm <fix_ttm>`
-* :doc:`fix thermal/conductivity <fix_thermal_conductivity>`
-* :doc:`fix viscosity <fix_viscosity>`
-* examples/KAPPA
-* examples/VISCOSITY
-* https://www.lammps.org/pictures.html#ttm
-* https://www.lammps.org/movies.html#evaporation
+* :doc:`fix ipi <fix_ipi>`
+* :doc:`pair_style agni <pair_agni>`
+* :doc:`pair_style list <pair_list>`
+* :doc:`pair_style srp <pair_srp>`
+* :doc:`pair_style tracker <pair_tracker>`
+* :doc:`fix pair/tracker <fix_pair_tracker>`
 
 ----------
 
@@ -1495,9 +1613,9 @@ A general interface for machine-learning interatomic potentials, including PyTor
 
 **Install:**
 
-To use this package, also the :ref:`ML-SNAP package <PKG-ML-SNAP>` package needs
+To use this package, also the :ref:`ML-SNAP <PKG-ML-SNAP>` package needs
 to be installed.  To make the *mliappy* model available, also the
-:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
+:ref:`PYTHON <PKG-PYTHON>` package needs to be installed, the version
 of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
 must be installed.
 
@@ -1762,6 +1880,10 @@ MPIIO library.  It adds :doc:`dump styles <dump>` with a "mpiio" in
 their style name.  Restart files with an ".mpiio" suffix are also
 written and read in parallel.
 
+**Install:**
+
+The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
+
 **Supporting info:**
 
 * src/MPIIO: filenames -> commands
@@ -1931,6 +2053,23 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
 * Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
 * `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
+.. _PKG-ORIENT:
+
+ORIENT package
+--------------
+
+**Contents:**
+
+A few fixes that apply orientation dependent forces for studying
+grain boundary migration.
+
+**Supporting info:**
+
+* src/ORIENT: filenames -> commands
+* :doc:`fix orient/bcc <fix_orient>`
+* :doc:`fix orient/fcc <fix_orient>`
+* :doc:`fix orient/eco <fix_orient_eco>`
+
 ----------
 
 .. _PKG-PERI:
@@ -1978,6 +2117,12 @@ And a :doc:`dynamical_matrix <dynamical_matrix>` as well as a
 :doc:`third_order <third_order>` command to compute the dynamical matrix
 and third order tensor from finite differences.
 
+**Install:**
+
+The PHONON package requires that also the `KSPACE <PKG-KSPACE>`_
+package is installed.
+
+
 **Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
 and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
 
@@ -2269,10 +2414,10 @@ for monitoring molecules as bonds are created and destroyed.
 
 * src/REAXFF: filenames -> commands
 * src/REAXFF/README
-* :doc:`pair_style reax/c <pair_reaxc>`
-* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
-* :doc:`fix reax/c/species <fix_reaxc_species>`
-* examples/reax
+* :doc:`pair_style reaxff <pair_reaxff>`
+* :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
+* :doc:`fix reaxff/species <fix_reaxff_species>`
+* examples/reaxff
 
 ----------
 
@@ -2300,10 +2445,13 @@ another set.
 * :doc:`prd <prd>`
 * :doc:`tad <tad>`
 * :doc:`temper <temper>`,
+* :doc:`temper/npt <temper_npt>`,
+* :doc:`temper/grem <temper_grem>`,
 * :doc:`run_style verlet/split <run_style>`
 * examples/neb
 * examples/prd
 * examples/tad
+* examples/PACKAGES/grem
 
 ----------
 
@@ -2358,6 +2506,7 @@ the Forschungszentrum Juelich.
 **Install:**
 
 This package has :ref:`specific installation instructions <scafacos>` on the :doc:`Build extras <Build_extras>` page.
+The SCAFACOS package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
 
 **Supporting info:**
 
@@ -2653,26 +2802,3 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/PACKAGES/yaff
-
-----------
-
-.. _PKG-USER-MISC:
-
-USER-MISC package
------------------
-
-**Contents:**
-
-A potpourri of (mostly) unrelated features contributed to LAMMPS by
-users.  Each feature is a single fix, compute, pair, bond, angle,
-dihedral, improper, or command style.
-
-**Authors:** The author for each style in the package is listed in the
-src/USER-MISC/README file.
-
-**Supporting info:**
-
-* src/USER-MISC: filenames -> commands
-* src/USER-MISC/README
-* one page per individual command listed in src/USER-MISC/README
-* examples/USER-MISC

doc/src/Packages_list.rst

@@ -143,6 +143,31 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair_style eff/cut <pair_eff>`
      - PACKAGES/eff
      - no
+   * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
+     - additional compute styles
+     - :doc:`compute <compute>`
+     - n/a
+     - no
+   * - :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
+     - additional dump styles
+     - :doc:`dump <dump>`
+     - n/a
+     - no
+   * - :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
+     - additional fix styles
+     - :doc:`fix <fix>`
+     - n/a
+     - no
+   * - :ref:`EXTRA-MOLECULE <PKG-EXTRA-MOLECULE>`
+     - additional molecular styles
+     - :doc:`molecular styles <Commands_bond>`
+     - n/a
+     - no
+   * - :ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>`
+     - additional pair styles
+     - :doc:`pair_style <pair_style>`
+     - n/a
+     - no
    * - :ref:`FEP <PKG-FEP>`
      - free energy perturbation
      - :doc:`compute fep <compute_fep>`
@@ -168,6 +193,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`Speed intel <Speed_intel>`
      - `Benchmarks <https://www.lammps.org/bench.html>`_
      - no
+   * - :ref:`INTERLAYER <PKG-INTERLAYER>`
+     - Inter-layer pair potentials
+     - :doc:`several pair styles <Commands_pair>`
+     - PACKAGES/interlayer
+     - no
    * - :ref:`KIM <PKG-KIM>`
      - OpenKIM wrapper
      - :doc:`pair_style kim <pair_kim>`
@@ -313,6 +343,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`Speed opt <Speed_opt>`
      - `Benchmarks <https://www.lammps.org/bench.html>`_
      - no
+   * - :ref:`ORIENT <PKG-ORIENT>`
+     - fixes for orientation depended forces
+     - :doc:`fix orient/* <fix_orient>`
+     - PACKAGES/orient_eco
+     - no
    * - :ref:`PERI <PKG-PERI>`
      - Peridynamics models
      - :doc:`pair_style peri <pair_peri>`
@@ -370,7 +405,7 @@ whether an extra library is needed to build and use the package:
      - no
    * - :ref:`REAXFF <PKG-REAXFF>`
      - ReaxFF potential (C/C++)
-     - :doc:`pair_style reaxc <pair_reaxc>`
+     - :doc:`pair_style reaxff <pair_reaxff>`
      - reax
      - no
    * - :ref:`REPLICA <PKG-REPLICA>`
@@ -423,11 +458,6 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix nvt/uef <fix_nh_uef>`
      - PACKAGES/uef
      - no
-   * - :ref:`USER-MISC <PKG-USER-MISC>`
-     - single-file contributions
-     - USER-MISC/README
-     - USER-MISC
-     - no
    * - :ref:`VORONOI <PKG-VORONOI>`
      - Voronoi tesselation
      - :doc:`compute voronoi/atom <compute_voronoi_atom>`

doc/src/Python_call.rst

@@ -43,7 +43,7 @@ complex loop with branching logic, than can be created using the
 simple looping and branching logic enabled by the :doc:`next <next>` and
 :doc:`if <if>` commands.
 
-See the :doc:`python <python>` doc page and the :doc:`variable <variable>`
+See the :doc:`python <python>` page and the :doc:`variable <variable>`
 doc page for its python-style variables for more info, including
 examples of Python code you can write for both pure Python operations
 and callbacks to LAMMPS.

doc/src/Python_examples.rst

@@ -35,9 +35,9 @@ visualization package you have installed.
 Note that for GL, you need to be able to run the Pizza.py GL tool,
 which is included in the pizza sub-directory.  See the Pizza.py doc pages for more info:
 
-* `https://pizza.sandia.gov <pizza_>`_
+* `https://lammps.github.io/pizza <pizza_>`_
 
-.. _pizza: https://pizza.sandia.gov
+.. _pizza: https://lammps.github.io/pizza
 
 Note that for AtomEye, you need version 3, and there is a line in the
 scripts that specifies the path and name of the executable.  See the

doc/src/Python_objects.rst

@@ -20,7 +20,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
       global vector or array, a single double value from the vector or array
       is returned, indexed by I (vector) or I and J (array).  I,J are
       zero-based indices.
-      See the :doc:`Howto output <Howto_output>` doc page for a discussion of
+      See the :doc:`Howto output <Howto_output>` page for a discussion of
       global, per-atom, and local data, and of scalar, vector, and array
       data types.  See the doc pages for individual :doc:`computes <compute>`
       and :doc:`fixes <fix>` for a description of what they calculate and

doc/src/Python_trouble.rst

@@ -41,4 +41,4 @@ first importing from the ``lammps`` module:
    >>> CDLL("liblammps.so")
 
 If an error occurs, carefully go through the steps in :ref:`python_install_guides` and on the
-:doc:`Build_basics <Build_basics>` doc page about building a shared library.
+:doc:`Build_basics <Build_basics>` page about building a shared library.

doc/src/Run_basics.rst

@@ -42,7 +42,7 @@ single processor.  In theory you should get identical answers on any
 number of processors and on any machine.  In practice, numerical
 round-off due to using floating-point math can cause slight differences
 and an eventual divergence of molecular dynamics trajectories.  See the
-:doc:`Errors common <Errors_common>` doc page for discussion of this.
+:doc:`Errors common <Errors_common>` page for discussion of this.
 
 LAMMPS can run as large a problem as will fit in the physical memory of
 one or more processors.  If you run out of memory, you must run on more

doc/src/Run_options.rst

@@ -365,7 +365,7 @@ to insure that a specific Kspace processor (in the second partition) is
 matched up with a specific set of processors in the first partition.
 See the :doc:`General tips <Speed_tips>` page for more details.
 
-If the keyword *nth* is used with a setting *N*\ , then it means every
+If the keyword *nth* is used with a setting *N*, then it means every
 Nth processor will be moved to the end of the ranking.  This is useful
 when using the :doc:`run_style verlet/split <run_style>` command with 2
 partitions via the -partition command-line switch.  The first set of
@@ -397,7 +397,7 @@ so that the processors in each partition will be
 See the "processors" command for how to insure processors from each
 partition could then be grouped optimally for quad-core nodes.
 
-If the keyword is *custom*\ , then a file that specifies a permutation
+If the keyword is *custom*, then a file that specifies a permutation
 of the processor ranks is also specified.  The format of the reorder
 file is as follows.  Any number of initial blank or comment lines
 (starting with a "#" character) can be present.  These should be
@@ -464,7 +464,7 @@ The syntax following restartfile (or remap), namely
    datafile keyword value ...
 
 is identical to the arguments of the :doc:`write_data <write_data>`
-command.  See its doc page for details.  This includes its
+command.  See its page for details.  This includes its
 optional keyword/value settings.
 
 ----------
@@ -505,11 +505,11 @@ The syntax following restartfile (or remap), namely
    group-ID dumpstyle dumpfile arg1 arg2 ...
 
 is identical to the arguments of the :doc:`write_dump <write_dump>`
-command.  See its doc page for details.  This includes what per-atom
+command.  See its 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
-:doc:`dump_modify <dump_modify>` doc page for details.
+:doc:`dump_modify <dump_modify>` page for details.
 
 ----------
 
@@ -537,7 +537,7 @@ partition screen files file.N.
 **-suffix style args**
 
 Use variants of various styles if they exist.  The specified style can
-be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ .  These
+be *gpu*, *intel*, *kk*, *omp*, *opt*, or *hybrid*\ .  These
 refer to optional packages that LAMMPS can be built with, as described
 in :doc:`Accelerate performance <Speed>`.  The "gpu" style corresponds to the
 GPU package, the "intel" style to the INTEL package, the "kk"

doc/src/Run_output.rst

@@ -152,7 +152,7 @@ information is provided about the line search and statistics on how
 many iterations and force-evaluations the minimizer required.
 Multiple force evaluations are typically done at each iteration to
 perform a 1d line minimization in the search direction.  See the
-:doc:`minimize <minimize>` doc page for more details.
+:doc:`minimize <minimize>` page for more details.
 
 ----------
 

doc/src/Speed_gpu.rst

@@ -71,7 +71,7 @@ by AMD.
 
 **Building LAMMPS with the GPU package:**
 
-See the :ref:`Build extras <gpu>` doc page for
+See the :ref:`Build extras <gpu>` page for
 instructions.
 
 **Run with the GPU package from the command line:**
@@ -118,7 +118,7 @@ automatic selection of the number of GPUs to use.
 Using the "-pk" switch explicitly allows for setting of the number of
 GPUs/node to use and additional options.  Its syntax is the same as
 the "package gpu" command.  See the :doc:`package <package>`
-command doc page for details, including the default values used for
+command page for details, including the default values used for
 all its options if it is not specified.
 
 Note that the default for the :doc:`package gpu <package>` command is to
@@ -182,7 +182,7 @@ deterministic results.
   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 :doc:`package <package>` command
-  doc page for details.
+  page for details.
 * As described by the :doc:`package gpu <package>` command, GPU
   accelerated pair styles can perform computations asynchronously with
   CPU computations. The "Pair" time reported by LAMMPS will be the

doc/src/Speed_intel.rst

@@ -103,7 +103,7 @@ Quick Start for Experienced Users
 """""""""""""""""""""""""""""""""
 
 LAMMPS should be built with the INTEL package installed.
-Simulations should be run with 1 MPI task per physical *core*\ ,
+Simulations should be run with 1 MPI task per physical *core*,
 not *hardware thread*\ .
 
 * Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary.
@@ -205,7 +205,7 @@ this information can normally be obtained with:
 Building LAMMPS with the INTEL package
 """""""""""""""""""""""""""""""""""""""""""
 
-See the :ref:`Build extras <intel>` doc page for
+See the :ref:`Build extras <intel>` page for
 instructions.  Some additional details are covered here.
 
 For building with make, several example Makefiles for building with

doc/src/Speed_kokkos.rst

@@ -67,7 +67,7 @@ produce an executable compatible with a specific hardware.
 Building LAMMPS with the KOKKOS package
 """""""""""""""""""""""""""""""""""""""
 
-See the :ref:`Build extras <kokkos>` doc page for instructions.
+See the :ref:`Build extras <kokkos>` page for instructions.
 
 Running LAMMPS with the KOKKOS package
 """"""""""""""""""""""""""""""""""""""
@@ -217,7 +217,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
    be best for many-body potentials. For simpler pair-wise potentials, it
    may be faster to use a "full" neighbor list with Newton flag to "off".
    Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
-   the default :doc:`package kokkos <package>` options. See its doc page for
+   the default :doc:`package kokkos <package>` options. See its page for
    details and default settings. Experimenting with its options can provide
    a speed-up for specific calculations. For example:
 
@@ -279,7 +279,7 @@ one or more nodes, each with two GPUs:
    setting the neighbor binsize equal to twice the CPU default value will
    give speedup, which is the default when running on GPUs. Use the "-pk
    kokkos" :doc:`command-line switch <Run_options>` to change the default
-   :doc:`package kokkos <package>` options. See its doc page for details and
+   :doc:`package kokkos <package>` options. See its page for details and
    default settings. Experimenting with its options can provide a speed-up
    for specific calculations. For example:
 

doc/src/Speed_omp.rst

@@ -18,7 +18,7 @@ launched by each MPI task on the local node (using shared memory).
 Building LAMMPS with the OPENMP package
 """""""""""""""""""""""""""""""""""""""""
 
-See the :ref:`Build extras <openmp>` doc page for
+See the :ref:`Build extras <openmp>` page for
 instructions.
 
 Run with the OPENMP package from the command line
@@ -50,7 +50,7 @@ threads per MPI task via the OMP_NUM_THREADS environment variable.
 
 You can also use the "-pk omp Nt" :doc:`command-line switch <Run_options>`, to explicitly set Nt = # of OpenMP threads
 per MPI task to use, as well as additional options.  Its syntax is the
-same as the :doc:`package omp <package>` command whose doc page gives
+same as the :doc:`package omp <package>` command whose page gives
 details, including the default values used if it is not specified.  It
 also gives more details on how to set the number of threads via the
 OMP_NUM_THREADS environment variable.
@@ -70,7 +70,7 @@ Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
 
 You must also use the :doc:`package omp <package>` command to enable the
 OPENMP package.  When you do this you also specify how many threads
-per MPI task to use.  The command doc page explains other options and
+per MPI task to use.  The command page explains other options and
 how to set the number of threads via the OMP_NUM_THREADS environment
 variable.
 

doc/src/Speed_opt.rst

@@ -15,7 +15,7 @@ Any hardware. Any compiler.
 Building LAMMPS with the OPT package
 """"""""""""""""""""""""""""""""""""
 
-See the :ref:`Build extras <opt>` doc page for instructions.
+See the :ref:`Build extras <opt>` page for instructions.
 
 Run with the OPT package from the command line
 """"""""""""""""""""""""""""""""""""""""""""""

doc/src/Tools.rst

@@ -15,7 +15,7 @@ Sandia which provides tools for doing setup, analysis, plotting, and
 visualization for LAMMPS simulations.
 
 .. _lws: https://www.lammps.org
-.. _pizza: https://pizza.sandia.gov
+.. _pizza: https://lammps.github.io/pizza
 .. _python: https://www.python.org
 
 Additional tools included in the LAMMPS distribution are described on
@@ -76,7 +76,6 @@ Post-processing tools
    * :ref:`phonon <phonon>`
    * :ref:`pymol_asphere <pymol>`
    * :ref:`python <pythontools>`
-   * :ref:`reax <reax_tool>`
    * :ref:`replica <replica>`
    * :ref:`smd <smd>`
    * :ref:`spin <spin>`
@@ -173,7 +172,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
 chain tool
 ----------------------
 
-The file chain.f creates a LAMMPS data file containing bead-spring
+The file chain.f90 creates a LAMMPS data file containing bead-spring
 polymer chains and/or monomer solvent atoms.  It uses a text file
 containing chain definition parameters as an input.  The created
 chains and solvent atoms can strongly overlap, so LAMMPS needs to run
@@ -364,7 +363,7 @@ michele.ceriotti at gmail.com, to interface to a variety of molecular
 dynamics codes.
 
 See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
-:doc:`fix ipi <fix_ipi>` doc page for further details on running PIMD
+:doc:`fix ipi <fix_ipi>` page for further details on running PIMD
 calculations with LAMMPS.
 
 ----------
@@ -947,20 +946,6 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
 
 ----------
 
-.. _reax_tool:
-
-reax tool
---------------------------
-
-The reax sub-directory contains stand-alone codes that can
-post-process the output of the :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
-command from a LAMMPS simulation using :doc:`ReaxFF <pair_reaxc>`.  See
-the README.txt file for more info.
-
-These tools were written by Aidan Thompson at Sandia.
-
-----------
-
 .. _smd:
 
 smd tool

doc/src/accel_styles.rst

@@ -1,4 +1,4 @@
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
@@ -7,11 +7,11 @@ produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, INTEL, KOKKOS,
 OPENMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
 :doc:`suffix <suffix>` command in your input script.
 
-See the :doc:`Speed packages <Speed_packages>` doc page for more
+See the :doc:`Speed packages <Speed_packages>` page for more
 instructions on how to use the accelerated styles effectively.

doc/src/angle_charmm.rst

@@ -56,7 +56,7 @@ radian\^2.
 
 ----------
 
-Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
@@ -65,13 +65,13 @@ produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, INTEL, KOKKOS,
 OPENMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
 :doc:`suffix <suffix>` command in your input script.
 
-See :doc:`Speed packages <Speed_packages>` doc page for more
+See :doc:`Speed packages <Speed_packages>` page for more
 instructions on how to use the accelerated styles effectively.
 
 ----------

doc/src/angle_cosine_delta.rst

@@ -54,7 +54,7 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
 for more info.
 
 Related commands

doc/src/angle_cosine_periodic.rst

@@ -58,7 +58,7 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
 for more info.
 
 Related commands

doc/src/angle_cosine_shift.rst

@@ -53,7 +53,8 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-USER-MISC package.
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
 
 Related commands
 """"""""""""""""