Merge branch 'stable' into maintenance

First Set of Collected Bug Fixes and Maintenance Updates for 29 August 2024 Stable Release

.github/CODEOWNERS

@@ -38,6 +38,7 @@ src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
 src/ML-POD/*          @exapde
+src/ML-UF3/*          @monk-04
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -49,6 +50,7 @@ src/PTM/*             @pmla
 src/QMMM/*            @akohlmey
 src/REACTION/*        @jrgissing
 src/REAXFF/*          @hasanmetin @stanmoore1
+src/RHEO/*            @jtclemm
 src/SCAFACOS/*        @rhalver
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
@@ -58,11 +60,15 @@ src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
-src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane @stanmoore1
+src/KOSSOS/pair_pod_kokkos.*        @exapde @stanmoore1
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
+src/EXTRA-COMMAND/geturl.*          @akohlmey
+src/EXTRA-COMMAND/group_ndx.*       @akohlmey
+src/EXTRA-COMMAND/ndx_group.*       @akohlmey
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
@@ -72,6 +78,8 @@ src/MC/fix_sgcmc.*                  @athomps
 src/REAXFF/compute_reaxff_atom.*    @rbberger
 src/KOKKOS/compute_reaxff_atom_kokkos.*    @rbberger
 src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
+src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
+src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -91,9 +99,10 @@ src/fix.*                 @sjplimp
 src/force.*               @sjplimp
 src/group.*               @sjplimp
 src/improper.*            @sjplimp
+src/info.*                @akohlmey
 src/kspace.*              @sjplimp
 src/lmptyp.h              @sjplimp
-src/library.*             @sjplimp
+src/library.*             @sjplimp @akohlmey
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
@@ -101,12 +110,12 @@ src/modify.*              @sjplimp @stanmoore1
 src/molecule.*            @sjplimp
 src/my_page.h             @sjplimp
 src/my_pool_chunk.h       @sjplimp
-src/npair*.*              @sjplimp
-src/ntopo*.*              @sjplimp
-src/nstencil*.*           @sjplimp
-src/neighbor.*            @sjplimp
-src/nbin*.*               @sjplimp
-src/neigh_*.*             @sjplimp
+src/npair*.*              @sjplimp @jtclemm
+src/ntopo*.*              @sjplimp @jtclemm
+src/nstencil*.*           @sjplimp @jtclemm
+src/neighbor.*            @sjplimp @jtclemm
+src/nbin*.*               @sjplimp @jtclemm
+src/neigh_*.*             @sjplimp @jtclemm
 src/output.*              @sjplimp
 src/pair.*                @sjplimp
 src/rcb.*                 @sjplimp

.github/workflows/unittest-macos.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-latest
+    runs-on: macos-13
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -43,6 +43,8 @@ jobs:
       working-directory: build
       run: |
         ccache -z
+        python3 -m venv macosenv
+        source macosenv/bin/activate
         python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \

.gitignore

@@ -43,12 +43,12 @@ Thumbs.db
 
 #cmake
 /build*
-/CMakeCache.txt
-/CMakeFiles/
-/Testing
+CMakeCache.txt
+CMakeFiles
 /Makefile
-/Testing
-/cmake_install.cmake
+Testing
+Temporary
+cmake_install.cmake
 /lmp
 out/Debug
 out/RelWithDebInfo
@@ -60,3 +60,4 @@ src/Makefile.package.settings-e
 /cmake/build/x64-Debug-Clang
 /install/x64-GUI-MSVC
 /install
+.Rhistory

cmake/CMakeLists.txt

@@ -12,6 +12,11 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
+# set policy to silence warnings about requiring execute permission for find_program
+# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
+if(POLICY CMP0109)
+  cmake_policy(SET CMP0109 OLD)
+endif()
 # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
@@ -23,6 +28,7 @@ project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -163,6 +169,22 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
+# warn about potentially problematic GCC compiler versions
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
+    endif()
+  endif()
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -197,18 +219,17 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 option(BUILD_SHARED_LIBS "Build shared library" OFF)
 option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
-option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
 # Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
 if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
 else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
-include(GNUInstallDirs)
+
 file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@@ -256,6 +277,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -281,10 +303,11 @@ set(STANDARD_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-POD
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -303,6 +326,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -407,6 +431,7 @@ pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
 pkg_depends(MESONT MOLECULE)
+pkg_depends(RHEO BPM)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -449,13 +474,13 @@ if(BUILD_OMP)
   if(CMAKE_VERSION VERSION_LESS 3.28)
     get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
     if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
     endif()
   else()
     if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
     endif()
   endif()
 endif()
@@ -490,6 +515,14 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
   endif()
 endif()
 
+find_package(CURL QUIET COMPONENTS HTTP HTTPS)
+option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
+if(WITH_CURL)
+  find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
+  target_link_libraries(lammps PRIVATE CURL::libcurl)
+endif()
+
 # tweak jpeg library names to avoid linker errors with MinGW cross-compilation
 set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
@@ -547,7 +580,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -689,7 +722,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -867,7 +900,7 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 8.0)
+find_package(ClangFormat 11.0)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src
@@ -937,6 +970,7 @@ message(STATUS "<<< Compilers and Flags: >>>
 -- C++ Compiler:     ${CMAKE_CXX_COMPILER}
       Type:          ${CMAKE_CXX_COMPILER_ID}
       Version:       ${CMAKE_CXX_COMPILER_VERSION}
+      C++ Standard:  ${CMAKE_CXX_STANDARD}
       C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
       Defines:       ${DEFINES}")
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)
@@ -1043,9 +1077,6 @@ endif()
 if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
-if(BUILD_LAMMPS_SHELL)
-  message(STATUS "<<< Building LAMMPS Shell >>>")
-endif()
 if(BUILD_LAMMPS_GUI)
   message(STATUS "<<< Building LAMMPS GUI >>>")
   if(LAMMPS_GUI_USE_PLUGIN)

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,8 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-20.0
+                                          clang-format-19.0
+                                          clang-format-18.0
                                           clang-format-17.0
                                           clang-format-16.0
                                           clang-format-15.0

cmake/Modules/LAMMPSUtils.cmake

@@ -32,7 +32,13 @@ function(check_omp_h_include)
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
     set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-    check_include_file_cxx(omp.h _have_omp_h)
+    # there are all kinds of problems with finding omp.h
+    # for Clang and derived compilers so we pretend it is there.
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+      set(_have_omp_h TRUE)
+    else()
+      check_include_file_cxx(omp.h _have_omp_h)
+    endif()
   else()
     set(_have_omp_h FALSE)
   endif()

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/Packages/COLVARS.cmake

@@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
+if(BUILD_OMP)
+  # Enable OpenMP for Colvars as well
+  target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
+  target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
+endif()
+
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

cmake/Modules/Packages/DPD-BASIC.cmake

@@ -0,0 +1,9 @@
+# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
+if(NOT PKG_KSPACE)
+  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
+  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
+  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -45,8 +45,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "889dcea2b5ced3debdc5b0820044bdc4" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.3.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.3.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,5 +1,11 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+# PACE library support for ML-PACE package
 
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -27,7 +27,7 @@ if(DOWNLOAD_QUIP)
   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 "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")

cmake/Modules/Packages/PLUMED.cmake

@@ -1,5 +1,14 @@
 # Plumed2 support for PLUMED package
 
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
+# for supporting multiple concurrent plumed2 installations for debugging and testing
+set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
+mark_as_advanced(PLUMED_SUFFIX)
+
 if(BUILD_MPI)
   set(PLUMED_CONFIG_MPI "--enable-mpi")
   set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
@@ -21,9 +30,11 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
@@ -75,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
     DEPENDS plumed_build
     COMMENT "Copying Plumed files"
   )
+  if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+    target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
+  endif()
 
 else()
 
@@ -149,21 +163,26 @@ else()
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
+    endif()
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed)
+    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
     add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
     if(PLUMED_MODE STREQUAL "STATIC")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
+    endif()
   endif()
 endif()
 
-target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/Modules/Packages/RHEO.cmake

@@ -0,0 +1,2 @@
+find_package(GSL 2.6 REQUIRED)
+target_link_libraries(lammps PRIVATE GSL::gsl)

cmake/Modules/Testing.cmake

@@ -102,9 +102,9 @@ endif()
 #######################################
 # select code sanitizer options
 #######################################
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
 mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
 set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
 validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
 string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)

cmake/Modules/Tools.cmake

@@ -37,37 +37,6 @@ if(BUILD_TOOLS)
   add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
-find_package(PkgConfig QUIET)
-if(BUILD_LAMMPS_SHELL)
-  if(NOT PkgConfig_FOUND)
-    message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
-  endif()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
-
-  # include resource compiler to embed icons into the executable on Windows
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    enable_language(RC)
-    set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
-  endif()
-
-  add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
-  target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
-  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
-
-  # workaround for broken readline pkg-config file on FreeBSD
-  if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
-    target_include_directories(lammps-shell PRIVATE /usr/local/include)
-  endif()
-  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
-    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
-    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
-  endif()
-  install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
-  install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
-endif()
-
 if(BUILD_LAMMPS_GUI)
   get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
   get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

cmake/packaging/build_linux_tgz.sh

@@ -2,9 +2,10 @@
 
 APP_NAME=lammps-gui
 DESTDIR=${PWD}/../LAMMPS_GUI
+VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
+rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
@@ -59,17 +60,19 @@ done
 
 echo "Set up wrapper script"
 MYDIR=$(dirname "$0")
+cp ${MYDIR}/xdg-open ${DESTDIR}/bin
 cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
 for s in ${DESTDIR}/bin/*
 do \
         EXE=$(basename $s)
         test ${EXE} = linux_wrapper.sh && continue
         test ${EXE} = qt.conf && continue
+        test ${EXE} = xdg-open && continue
         ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
 done
 
 pushd ..
-tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
+tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
 popd
 
 echo "Cleanup dir"

cmake/packaging/build_macos_dmg.sh

@@ -1,9 +1,10 @@
 #!/bin/bash
 
 APP_NAME=lammps-gui
+VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
+rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
 
 echo "Create initial dmg file with macdeployqt"
 macdeployqt  lammps-gui.app -dmg
@@ -96,12 +97,12 @@ sync
 
 echo "Unmount modified disk image and convert to compressed read-only image"
 hdiutil detach "${DEVICE}"
-hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
+hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
 
 echo "Attach icon to .dmg file"
 echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
-Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
-SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
+Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
+SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
 rm icon.rsrc
 
 echo "Delete temporary disk images"

cmake/packaging/build_windows_cross_zip.sh

@@ -3,9 +3,10 @@
 APP_NAME=lammps-gui
 DESTDIR=${PWD}/LAMMPS_GUI
 SYSROOT="$1"
+VERSION="$2"
 
 echo "Delete old files, if they exist"
-rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
@@ -60,5 +61,5 @@ cat > ${DESTDIR}/bin/qt.conf <<EOF
 [Paths]
 Plugins = ../qt5plugins
 EOF
-zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
+zip -9rvD LAMMPS-Win10-amd64-${VERSION}.zip LAMMPS_GUI
 

cmake/packaging/linux_wrapper.sh

@@ -4,15 +4,17 @@
 # reset locale to avoid problems with decimal numbers
 export LC_ALL=C
 
-BASEDIR=$(dirname "$0")
-EXENAME=$(basename "$0")
+BASEDIR="$(dirname "$0")"
+EXENAME="$(basename "$0")"
+
+PATH="${BASEDIR}/bin:${PATH}"
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
-LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
+LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
 
 # set some environment variables for LAMMPS etc.
-LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
-MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
+LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
+MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/presets/all_off.cmake

@@ -26,8 +26,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -60,6 +61,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -80,6 +82,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -28,8 +28,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -62,6 +63,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -82,6 +84,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/clang.cmake

@@ -1,10 +1,10 @@
 # preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
 
 # prefer flang over gfortran, if available
-find_program(CLANG_FORTRAN NAMES flang gfortran f95)
+find_program(CLANG_FORTRAN NAMES flang-new flang gfortran f95)
 set(ENV{OMPI_FC} ${CLANG_FORTRAN})
 get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
-if (_tmp_fc STREQUAL "flang")
+if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
   set(FC_STD_VERSION "-std=f2018")
   set(BUILD_MPI OFF)
 else()

cmake/presets/mingw-cross.cmake

@@ -22,8 +22,9 @@ set(WIN_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -32,7 +33,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON
@@ -50,6 +50,7 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/most.cmake

@@ -26,6 +26,7 @@ set(ALL_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -45,6 +46,7 @@ set(ALL_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   OPENMP

cmake/presets/windows.cmake

@@ -22,6 +22,7 @@ set(WIN_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -42,6 +43,7 @@ set(WIN_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -50,8 +52,8 @@ set(WIN_PACKAGES
   ORIENT
   PERI
   PHONON
-  POEMS
   PLUGIN
+  POEMS
   PTM
   QEQ
   QTB

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "17 April 2024" "2024-04-17"
+.TH LAMMPS "1" "29 August 2024" "2024-08-29"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 17 April 2024
+\- Molecular Dynamics Simulator.  Version 29 August 2024
 
 .SH SYNOPSIS
 .B lmp
@@ -226,6 +226,20 @@ arguments of the "dump" command. See the
 .B LAMMPS
 manual for details on either of the two commands.
 .TP
+\fB\-r2info <restart file> <keyword> ...\fR or
+\fB\-restart2info <restart file> <keyword> ...\fR
+Write information about the <restart file> previously written by
+.B LAMMPS
+to the screen and immediately exit.  Following <restart file>
+argument, additional keywords for the
+.B LAMMPS
+"info" command may be added to increase the amount of information
+written. By default "system" "group" "fix" "compute" are already
+set. See the
+.B LAMMPS
+manual for details on the "info" command.
+.TP
+.TP
 \fB\-sc <file name>\fR or \fB\-screen <file name>\fR
 Specify a file for
 .B LAMMPS

doc/src/Bibliography.rst

@@ -1,6 +1,12 @@
 Bibliography
 ************
 
+**(Abascal1)**
+   Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
+
+**(Abascal2)**
+   Abascal, J Chem Phys, 123, 234505 (2005)
+
 **(Ackland)**
    Ackland, Jones, Phys Rev B, 73, 054104 (2006).
 
@@ -22,21 +28,24 @@ Bibliography
 **(Agnolin and Roux 2007)**
    Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
 
+**(Ahrens-Iwers2022)**
+   Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
+
+**(Ahrens-Iwers)**
+   Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
+
 **(Aktulga)**
    Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
 
 **(Albe)**
    J.\  Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
 
-**(Albe)**
+**(Albe1)**
    K.\  Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
 
 **(Allen)**
    Allen and Germano, Mol Phys 104, 3225-3235 (2006).
 
-**(Allen)**
-   Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
-
 **(AllenTildesley)**
    Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
 
@@ -49,6 +58,9 @@ Bibliography
 **(Anderson)**
    Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
 
+**(Appshaw)**
+   Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
+
 **(Avendano)**
    C.\  Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
 
@@ -58,7 +70,7 @@ Bibliography
 **(Babadi)**
    Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
 
-**(Babadi)**
+**(Babadi2)**
    Babadi and Ejtehadi, EPL, 77 (2007) 23002.
 
 **(Baczewski)**
@@ -73,23 +85,23 @@ Bibliography
 **(Ballenegger)**
    Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
 
-**(Banna)**
-   Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
-
 **(Barrat)**
    Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
 
 **(Barrett)**
    Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
 
+**(Barros)**
+   Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
+
 **(Bartok)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
 **(Bartok2010)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
-**(Bartok_2010)**
-   AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).
+**(Bartok2013)**
+   Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
 
 **(Bartok_PhD)**
    A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
@@ -97,36 +109,51 @@ Bibliography
 **(Baskes)**
    Baskes, Phys Rev B, 46, 2727-2742 (1992).
 
+**(Baskes2)**
+   Baskes, Phys Rev B, 75, 094113 (2007).
+
 **(Beck)**
    Beck, Molecular Physics, 14, 311 (1968).
 
+**(Becton)**
+   Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
+
+**(Behler and Parrinello 2007)**
+   Behler, J.; Parrinello, M. Phys. Rev. Lett.  2007, 98 (14), 146401.
+
 **(Bennet)**
    Bennet, J Comput Phys, 22, 245 (1976)
 
 **(Berardi)**
    Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
 
-**(Berendsen)**
-   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
-
 **(Berendsen)**
    Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
 
+**(Berendsen2)**
+   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
+
 **(Bessarab)**
    Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
 
 **(Beutler)**
    Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
 
-**(Bialke)**
-   J.\  Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
-
 **(Bird)**
    G.\  A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
 
 **(Bitzek)**
    Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).
 
+**(Bolintineanu1)**
+   Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
+
+**(Bolintineanu2)**
+  Bolintineanu, Grest, Lechman, Pierce, Plimpton, Schunk, Comp Particle Mechanics, 1, 321-356 (2014).
+
+**(Bomont)**
+   Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006).
+
 **(Bond)**
    Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
 
@@ -134,7 +161,7 @@ Bibliography
    Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
 
 **(BoreschKarplus)**
-   Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
+   Boresch and Karplus, J Phys Chem A, 103, 103 (1999).
 
 **(Botu1)**
    V.\  Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
@@ -169,8 +196,11 @@ Bibliography
 **(Buck)**
    Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).
 
+**(Bulacu)**
+   Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
+
 **(Bussi)**
-   G.\  Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
+   G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
 
 **(Bussi1)**
    Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
@@ -178,20 +208,20 @@ Bibliography
 **(Bussi2)**
    Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
 
-**(COMB)**
+**(COMB_1)**
+   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+
+**(COMB_2)**
    T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
 
 **(COMB3)**
    T.\  Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
 
-**(COMB_1)**
-   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
-
 **(Calhoun)**
    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, Phys. Rev. B [74], 075420 (2006).
 
 **(Cao1)**
    J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@@ -215,6 +245,9 @@ Bibliography
    Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
 
 **(Ceriotti)**
+   M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
+
+**(Ceriotti1)**
    Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)
 
 **(Ceriotti2)**
@@ -232,6 +265,18 @@ Bibliography
 **(Clarke)**
    Clarke and Smith, J Chem Phys, 84, 2290 (1986).
 
+**(Clavier)**
+   G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
+
+**(Clemmer)**
+   Clemmer and Robbins, Phys. Rev. Lett. (2022).
+
+**(Clemmer1)**
+   Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
+
+**(Clemmer2)**
+   Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
+
 **(Coleman)**
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doc/src/Build_basics.rst

@@ -37,8 +37,9 @@ standard. A more detailed discussion of that is below.
 
       .. code-block:: bash
 
-         -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
-         -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
+         -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI
+         -D BUILD_OMP=value        # yes or no, default is yes if a compatible
+                                   # compiler is detected
          -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
                                    # no default value
 
@@ -54,9 +55,9 @@ standard. A more detailed discussion of that is below.
 
       .. code-block:: bash
 
-         make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
-         make serial             # serial build, produces lmp_serial using Makefile/serial
-         make mybox              # uses Makefile.mybox to produce lmp_mybox
+         make mpi      # parallel build, produces lmp_mpi using Makefile.mpi
+         make serial   # serial build, produces lmp_serial using Makefile/serial
+         make mybox    # uses Makefile.mybox to produce lmp_mybox
 
       Any ``make machine`` command will look up the make settings from a
       file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
@@ -74,15 +75,15 @@ standard. A more detailed discussion of that is below.
       this is ``-fopenmp``\ , which can be added to the ``CC`` and
       ``LINK`` makefile variables.
 
-      For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
+      For the serial build the following make variables are set (see ``src/MAKE/Makefile.serial``):
 
       .. code-block:: make
 
-         CC =            g++
-         LINK =          g++
-         MPI_INC =       -I../STUBS
-         MPI_PATH =      -L../STUBS
-         MPI_LIB =       -lmpi_stubs
+         CC =       g++
+         LINK =     g++
+         MPI_INC =  -I../STUBS
+         MPI_PATH = -L../STUBS
+         MPI_LIB =  -lmpi_stubs
 
       You also need to build the STUBS library for your platform before
       making LAMMPS itself.  A ``make serial`` build does this for you
@@ -231,24 +232,32 @@ LAMMPS.
       .. code-block:: bash
 
          # Building with GNU Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-         # Building with Intel Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ \
+               -DCMAKE_Fortran_COMPILER=gfortran ../cmake
+         # Building with Intel Classic Compilers:
+         cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc \
+               -DCMAKE_Fortran_COMPILER=ifort ../cmake
          # Building with Intel oneAPI Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
+         cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
+               -DCMAKE_Fortran_COMPILER=ifx ../cmake
          # Building with LLVM/Clang Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+         cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
+               -DCMAKE_Fortran_COMPILER=flang ../cmake
          # Building with PGI/Nvidia Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
+         cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ \
+               -DCMAKE_Fortran_COMPILER=pgfortran ../cmake
+         # Building with the NVHPC Compilers:
+         cmake -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ \
+               -DCMAKE_Fortran_COMPILER=nvfortran ../cmake
 
       For compiling with the Clang/LLVM compilers a CMake preset is
       provided that can be loaded with
-      `-C ../cmake/presets/clang.cmake`.  Similarly,
-      `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
+      ``-C ../cmake/presets/clang.cmake``.  Similarly,
+      ``-C ../cmake/presets/intel.cmake`` should switch the compiler
+      toolchain to the legacy Intel compilers, ``-C ../cmake/presets/oneapi.cmake``
       will switch to the LLVM based oneAPI Intel compilers,
-      and `-C ../cmake/presets/pgi.cmake`
-      will switch the compiler to the PGI compilers.
+      ``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
+      and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
 
       Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts.
@@ -259,7 +268,7 @@ LAMMPS.
          When the cmake command completes, it prints a summary to the
          screen which compilers it is using and what flags and settings
          will be used for the compilation.  Note that if the top-level
-         compiler is mpicxx, it is simply a wrapper on a real compiler.
+         compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
          The underlying compiler info is what CMake will try to
          determine and report.  You should check to confirm you are
          using the compiler and optimization flags you want.
@@ -278,19 +287,19 @@ LAMMPS.
 
       .. code-block:: make
 
-         CC =            mpicxx
-         CCFLAGS =       -g -O3
-         LINK =          mpicxx
-         LINKFLAGS =     -g -O
+         CC =        mpicxx
+         CCFLAGS =   -g -O3
+         LINK =      mpicxx
+         LINKFLAGS = -g -O
 
       Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
 
       .. code-block:: make
 
-         CC =            g++
-         CCFLAGS =       -g -O3
-         LINK =          g++
-         LINKFLAGS =     -g -O
+         CC =        g++
+         CCFLAGS =   -g -O3
+         LINK =      g++
+         LINKFLAGS = -g -O
 
       .. note::
 
@@ -316,10 +325,10 @@ LAMMPS.
          there may be specific compiler or linker flags that are either
          required or recommended to enable required features and to
          achieve optimal performance.  You need to include these in the
-         CCFLAGS and LINKFLAGS settings above.  For details, see the
+         ``CCFLAGS`` and ``LINKFLAGS`` settings above.  For details, see the
          documentation for the individual packages listed on the
          :doc:`Speed_packages` page.  Or examine these files in the
-         src/MAKE/OPTIONS directory.  They correspond to each of the 5
+         ``src/MAKE/OPTIONS`` directory.  They correspond to each of the 5
          accelerator packages and their hardware variants:
 
          .. code-block:: bash
@@ -388,7 +397,8 @@ running LAMMPS from Python via its library interface.
 
          make machine               # build LAMMPS executable lmp_machine
          make mode=static machine   # same as "make machine"
-         make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
+         make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so
+                                    # instead
 
       The "static" build will generate a static library called
       ``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
@@ -450,7 +460,7 @@ installation.
 Including or removing debug support
 -----------------------------------
 
-By default the compilation settings will include the *-g* flag which
+By default the compilation settings will include the ``-g`` flag which
 instructs the compiler to include debug information (e.g. which line of
 source code a particular instruction correspond to).  This can be
 extremely useful in case LAMMPS crashes and can help to provide crucial
@@ -463,7 +473,7 @@ If this is a concern, you can change the compilation settings or remove
 the debug information from the LAMMPS executable:
 
 - **Traditional make**: edit your ``Makefile.<machine>`` to remove the
-  *-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
+  ``-g`` flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
 - **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
   the applicable compiler flags (best done using the text mode or
   graphical user interface).
@@ -488,9 +498,10 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default). Build lammps-shell
-         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build lammps-gui
+         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt,
+                                      # chain.x, micelle2d.x, msi2lmp, phana,
+                                      # stl_bin2txt
+         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build LAMMPS-GUI
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -505,8 +516,9 @@ using CMake or Make.
          make chain            # build only chain tool
          make micelle2d        # build only micelle2d tool
 
-         cd lammps/tools/lammps-shell
-         make                  # build LAMMPS shell
+      .. note::
+
+         Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
 
 ----------
 

doc/src/Build_cmake.rst

@@ -131,20 +131,20 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
 configuration step.  The cache file contains all current CMake settings.
 
 To modify settings, enable or disable features, you need to set
-*variables* with either the *-D* command line flag (``-D
+*variables* with either the ``-D`` command line flag (``-D
 VARIABLE1_NAME=value``) or change them in the text mode of the graphical
-user interface.  The *-D* flag can be used several times in one command.
+user interface.  The ``-D`` flag can be used several times in one command.
 
 For your convenience, we provide :ref:`CMake presets <cmake_presets>`
 that combine multiple settings to enable optional LAMMPS packages or use
-a different compiler tool chain.  Those are loaded with the *-C* flag
+a different compiler tool chain.  Those are loaded with the ``-C`` flag
 (``-C ../cmake/presets/basic.cmake``).  This step would only be needed
 once, as the settings from the preset files are stored in the
 ``CMakeCache.txt`` file. It is also possible to customize the build
-by adding one or more *-D* flags to the CMake command line.
+by adding one or more ``-D`` flags to the CMake command line.
 
 Generating files for alternate build tools (e.g. Ninja) and project files
-for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
+for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
 command line flag.  A list of available generator settings for your
 specific CMake version is given when running ``cmake --help``.
 
@@ -171,7 +171,7 @@ files. E.g.  with:
 In that case the resulting binaries are not in the build folder directly
 but in subdirectories corresponding to the build type (i.e. Release in
 the example from above).  Similarly, for running unit tests the
-configuration is selected with the *-C* flag:
+configuration is selected with the ``-C`` flag:
 
 .. code-block:: bash
 

doc/src/Build_development.rst

@@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
-----------------------------------------------------------------------
+Address, Leak, 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
@@ -110,6 +110,7 @@ compilation and linking stages.  This is done through setting the
 
    -D ENABLE_SANITIZER=none       # no sanitizer active (default)
    -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=hwaddress  # enable hardware assisted address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
    -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
    -D ENABLE_SANITIZER=thread     # enable thread sanitizer
@@ -152,7 +153,12 @@ development headers to compile (if those are not found locally a recent
 version of that library will be downloaded and compiled along with
 LAMMPS and the test programs) and will download and compile a specific
 version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
-test framework that is used to implement the tests.
+test framework that is used to implement the tests.  Those unit tests
+may be combined with memory access and leak checking with valgrind
+(see below for how to enable it).  In that case, running so-called
+death tests will create a lot of false positives and thus they can be
+disabled by configuring compilation with the additional setting
+``-D SKIP_DEATH_TESTS=on``.
 
 .. admonition:: Software version and LAMMPS configuration requirements
    :class: note
@@ -175,24 +181,24 @@ The output of this command will be looking something like this:
     $ ctest
     Test project /home/akohlmey/compile/lammps/build-testing
          Start   1: RunLammps
-   1/563 Test   #1: RunLammps ..........................................   Passed    0.28 sec
+   1/563 Test   #1: RunLammps ..................................   Passed    0.28 sec
          Start   2: HelpMessage
-   2/563 Test   #2: HelpMessage ........................................   Passed    0.06 sec
+   2/563 Test   #2: HelpMessage ................................   Passed    0.06 sec
          Start   3: InvalidFlag
-   3/563 Test   #3: InvalidFlag ........................................   Passed    0.06 sec
+   3/563 Test   #3: InvalidFlag ................................   Passed    0.06 sec
          Start   4: Tokenizer
-   4/563 Test   #4: Tokenizer ..........................................   Passed    0.05 sec
+   4/563 Test   #4: Tokenizer ..................................   Passed    0.05 sec
          Start   5: MemPool
-   5/563 Test   #5: MemPool ............................................   Passed    0.05 sec
+   5/563 Test   #5: MemPool ....................................   Passed    0.05 sec
          Start   6: ArgUtils
-   6/563 Test   #6: ArgUtils ...........................................   Passed    0.05 sec
+   6/563 Test   #6: ArgUtils ...................................   Passed    0.05 sec
        [...]
          Start 561: ImproperStyle:zero
- 561/563 Test #561: ImproperStyle:zero .................................   Passed    0.07 sec
+ 561/563 Test #561: ImproperStyle:zero .........................   Passed    0.07 sec
          Start 562: TestMliapPyUnified
- 562/563 Test #562: TestMliapPyUnified .................................   Passed    0.16 sec
+ 562/563 Test #562: TestMliapPyUnified .........................   Passed    0.16 sec
          Start 563: TestPairList
- 563/563 Test #563: TestPairList .......................................   Passed    0.06 sec
+ 563/563 Test #563: TestPairList ...............................   Passed    0.06 sec
 
  100% tests passed, 0 tests failed out of 563
 
@@ -207,24 +213,25 @@ The output of this command will be looking something like this:
 The ``ctest`` command has many options, the most important ones are:
 
 .. list-table::
+   :widths: 20 80
 
    * - Option
      - Function
-   * - -V
+   * - ``-V``
      - verbose output: display output of individual test runs
-   * - -j <num>
+   * - ``-j <num>``
      - parallel run: run <num> tests in parallel
-   * - -R <regex>
+   * - ``-R <regex>``
      - run subset of tests matching the regular expression <regex>
-   * - -E <regex>
+   * - ``-E <regex>``
      - exclude subset of tests matching the regular expression <regex>
-   * - -L <regex>
+   * - ``-L <regex>``
      - run subset of tests with a label matching the regular expression <regex>
-   * - -LE <regex>
+   * - ``-LE <regex>``
      - exclude subset of tests with a label matching the regular expression <regex>
-   * - -N
+   * - ``-N``
      - dry-run: display list of tests without running them
-   * - -T memcheck
+   * - ``-T memcheck``
      - run tests with valgrind memory checker (if available)
 
 In its full implementation, the unit test framework will consist of multiple
@@ -330,16 +337,17 @@ paths in the individual source files.
 The force style test programs have a common set of options:
 
 .. list-table::
+   :widths: 25 75
 
    * - Option
      - Function
-   * - -g <newfile>
+   * - ``-g <newfile>``
      - regenerate reference data in new YAML file
-   * - -u
+   * - ``-u``
      - update reference data in the original YAML file
-   * - -s
+   * - ``-s``
      - print error statistics for each group of comparisons
-   * - -v
+   * - ``-v``
      - verbose output: also print the executed LAMMPS commands
 
 The ``ctest`` tool has no mechanism to directly pass flags to the individual
@@ -353,10 +361,10 @@ set in an environment variable ``TEST_ARGS``. Example:
 To add a test for a style that is not yet covered, it is usually best
 to copy a YAML file for a similar style to a new file, edit the details
 of the style (how to call it, how to set its coefficients) and then
-run test command with either the *-g* and the replace the initial
-test file with the regenerated one or the *-u* option.  The *-u* option
+run test command with either the ``-g`` and the replace the initial
+test file with the regenerated one or the ``-u`` option.  The ``-u`` option
 will destroy the original file, if the generation run does not complete,
-so using *-g* is recommended unless the YAML file is fully tested
+so using ``-g`` is recommended unless the YAML file is fully tested
 and working.
 
 Some of the force style tests are rather slow to run and some are very
@@ -506,27 +514,51 @@ After post-processing with ``gen_coverage_html`` the results are in
 a folder ``coverage_html`` and can be viewed with a web browser.
 The images below illustrate how the data is presented.
 
-.. list-table::
+.. only:: not latex
 
-      * - .. figure:: JPG/coverage-overview-top.png
-             :scale: 25%
+   .. list-table::
 
-          Top of the overview page
+         * - .. figure:: JPG/coverage-overview-top.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-overview-manybody.png
-             :scale: 25%
+             Top of the overview page
 
-          Styles with good coverage
+           - .. figure:: JPG/coverage-overview-manybody.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-file-top.png
-             :scale: 25%
+             Styles with good coverage
 
-          Top of individual source page
+           - .. figure:: JPG/coverage-file-top.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-file-branches.png
-             :scale: 25%
+             Top of individual source page
 
-          Source page with branches
+           - .. figure:: JPG/coverage-file-branches.png
+                :scale: 25%
+
+             Source page with branches
+
+.. only:: latex
+
+   .. figure:: JPG/coverage-overview-top.png
+      :width: 60%
+
+      Top of the overview page
+
+   .. figure:: JPG/coverage-overview-manybody.png
+      :width: 60%
+
+      Styles with good coverage
+
+   .. figure:: JPG/coverage-file-top.png
+      :width: 60%
+
+      Top of individual source page
+
+   .. figure:: JPG/coverage-file-branches.png
+      :width: 60%
+
+      Source page with branches
 
 Coding style utilities
 ----------------------

doc/src/Build_extras.rst

@@ -14,7 +14,7 @@ in addition to
 
           cmake -D PKG_NAME=yes
 
-     - .. code-block:: console
+     - .. code-block:: bash
 
           make yes-name
 
@@ -59,6 +59,7 @@ This is the list of packages that may require additional steps.
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -72,7 +73,7 @@ COMPRESS package
 
 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
+a ``/gz`` suffix.  There are also styles using the
 `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
 '/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.
@@ -94,7 +95,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile.
       <https://www.freedesktop.org/wiki/Software/pkg-config/>`_ tool to
       identify the necessary flags to compile with this library, so the
       corresponding ``libzstandard.pc`` file must be in a folder where
-      pkg-config can find it, which may require adding it to the
+      ``pkg-config`` can find it, which may require adding it to the
       ``PKG_CONFIG_PATH`` environment variable.
 
    .. tab:: Traditional make
@@ -126,46 +127,53 @@ CMake build
                                 # value = double or mixed (default) or single
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX (see below, default is sm_50)
-   -D GPU_DEBUG=value           # enable debug code in the GPU package library, mostly useful for developers
+   -D GPU_DEBUG=value           # enable debug code in the GPU package library,
+                                # mostly useful for developers
                                 # value = yes or no (default)
-   -D HIP_PATH=value            # value = path to HIP installation. Must be set if GPU_API=HIP
+   -D HIP_PATH=value            # value = path to HIP installation. Must be set if
+                                # GPU_API=HIP
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
+                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for
+                                # HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
-   -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
-                                # enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
+   -D CUDPP_OPT=value           # use GPU binning with CUDA (should be off for modern GPUs)
+                                # enables CUDA Performance Primitives, must be "no" for
+                                # CUDA_MPS_SUPPORT=yes
                                 # value = yes or no (default)
-   -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
+   -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active
+                                # nvidia-cuda-mps daemon
                                 # value = yes or no (default)
-   -D CUDA_BUILD_MULTIARCH=value  # enables building CUDA kernels for all supported GPU architectures
+   -D CUDA_BUILD_MULTIARCH=value  # enables building CUDA kernels for all supported GPU
+                                  # architectures
                                   # value = yes (default) or no
-   -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
+   -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library,
+                                      # no local OpenCL headers/libs needed
                                       # value = yes (default) or no
 
-:code:`GPU_ARCH` settings for different GPU hardware is as follows:
+``GPU_ARCH`` settings for different GPU hardware is as follows:
 
-* sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x)
-* sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x)
-* sm_50 or sm_52 for Maxwell (supported since CUDA 6)
-* sm_60 or sm_61 for Pascal (supported since CUDA 8)
-* sm_70 for Volta (supported since CUDA 9)
-* sm_75 for Turing (supported since CUDA 10)
-* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
-* sm_89 for Lovelace (supported since CUDA 11.8)
-* sm_90 for Hopper (supported since CUDA 12.0)
+* ``sm_30`` for Kepler (supported since CUDA 5 and until CUDA 10.x)
+* ``sm_35`` or ``sm_37`` for Kepler (supported since CUDA 5 and until CUDA 11.x)
+* ``sm_50`` or ``sm_52`` for Maxwell (supported since CUDA 6)
+* ``sm_60`` or ``sm_61`` for Pascal (supported since CUDA 8)
+* ``sm_70`` for Volta (supported since CUDA 9)
+* ``sm_75`` for Turing (supported since CUDA 10)
+* ``sm_80`` or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
+* ``sm_89`` for Lovelace (supported since CUDA 11.8)
+* ``sm_90`` for Hopper (supported since CUDA 12.0)
 
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
 
 CMake can detect which version of the CUDA toolkit is used and thus will
 try to include support for **all** major GPU architectures supported by
-this toolkit.  Thus the GPU_ARCH setting is merely an optimization, to
+this toolkit.  Thus the ``GPU_ARCH`` setting is merely an optimization, to
 have code for the preferred GPU architecture directly included rather
 than having to wait for the JIT compiler of the CUDA driver to translate
 it.  This behavior can be turned off (e.g. to speed up compilation) by
-setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
+setting ``CUDA_ENABLE_MULTIARCH`` to ``no``.
 
 When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
 CUDA toolkit is required and a GPU architecture of Kepler or later,
@@ -184,21 +192,21 @@ build, and link with a static OpenCL ICD loader library and standard
 OpenCL headers.  This way no local OpenCL development headers or library
 needs to be present and only OpenCL compatible drivers need to be
 installed to use OpenCL.  If this is not desired, you can set
-:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+``USE_STATIC_OPENCL_LOADER`` to ``no``.
 
 The GPU library has some multi-thread support using OpenMP.  If LAMMPS
 is built with ``-D BUILD_OMP=on`` this will also be enabled.
 
 If you are compiling with HIP, note that before running CMake you will
 have to set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
-necessary for :code:`hipcc` and the linker to work correctly.
+``HCC_AMDGPU_TARGET`` (for ROCm <= 4.0) or ``CUDA_PATH`` are
+necessary for ``hipcc`` and the linker to work correctly.
 
 .. versionadded:: 3Aug2022
 
 Using the CHIP-SPV implementation of HIP is supported. It allows one to
 run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
-CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
+CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
 command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
 the use of HIP for Intel GPUs is experimental. You should only use this
 option in preparations to run on Aurora system at Argonne.
@@ -256,28 +264,35 @@ script with the specified args:
 
 .. code-block:: bash
 
-  make lib-gpu               # print help message
-  make lib-gpu args="-b"     # build GPU library with default Makefile.linux
-  make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
-  make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  # print help message
+  make lib-gpu
+
+  # build GPU library with default Makefile.linux
+  make lib-gpu args="-b"
+
+  # create new Makefile.xk7.single, altered for single-precision
+  make lib-gpu args="-m xk7 -p single -o xk7.single"
+
+  # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  make lib-gpu args="-m mpi -a sm_60 -p mixed -b"
 
 Note that this procedure starts with a Makefile.machine in lib/gpu, as
-specified by the "-m" switch.  For your convenience, machine makefiles
+specified by the ``-m`` switch.  For your convenience, machine makefiles
 for "mpi" and "serial" are provided, which have the same settings as
 the corresponding machine makefiles in the main LAMMPS source
 folder. In addition you can alter 4 important settings in the
-Makefile.machine you start from via the corresponding -c, -a, -p, -e
+Makefile.machine you start from via the corresponding ``-c``, ``-a``, ``-p``, ``-e``
 switches (as in the examples above), and also save a copy of the new
 Makefile if desired:
 
 * ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system
-* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
+* ``CUDA_ARCH`` = ``sm_XX``, what GPU hardware you have, same as CMake ``GPU_ARCH`` above
 * ``CUDA_PRECISION`` = precision (double, mixed, single)
-* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
+* ``EXTRAMAKE`` = which ``Makefile.lammps.*`` file to copy to Makefile.lammps
 
-The file Makefile.cuda is set up to include support for multiple
+The file ``Makefile.cuda`` is set up to include support for multiple
 GPU architectures as supported by the CUDA toolkit in use. This is done
-through using the "--gencode " flag, which can be used multiple times and
+through using the ``--gencode`` flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
 To enable GPU binning via CUDA performance primitives set the Makefile variable
@@ -348,12 +363,16 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
-         -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
-         -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
-         -D KIM_EXTRA_UNITTESTS=value    # enables extra unit tests, value = no (default) or yes
+         -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build
+                                         # value = no (default) or yes
+         -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off
+                                         # value = off (default) or on
+         -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer
+                                         # value = no (default) or yes
+         -D KIM_EXTRA_UNITTESTS=value    # enables extra unit tests
+                                         # value = no (default) or yes
 
-      If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
+      If ``DOWNLOAD_KIM`` is set to ``yes`` (or ``on``), the KIM API library
       will be downloaded and built inside the CMake build directory.  If
       the KIM library is already installed on your system (in a location
       where CMake cannot find it), you may need to set the
@@ -361,7 +380,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
       found, or run the command ``source kim-api-activate``.
 
       Extra unit tests can only be available if they are explicitly requested
-      (``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
+      (``KIM_EXTRA_UNITTESTS`` is set to ``yes`` (or ``on``)) and the prerequisites
       are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
       more details on this.
 
@@ -375,15 +394,28 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         make lib-kim              # print help message
-         make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-         make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-         make lib-kim args="-b -a everything"     # install KIM API lib with all models
-         make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-         make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
-         make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+         # print help message
+         make lib-kim
 
-      When using the "-b " option, the KIM library is built using its native
+         # (re-)install KIM API lib with only example models
+         make lib-kim args="-b"
+
+         # ditto plus one model
+         make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"
+
+         # install KIM API lib with all models
+         make lib-kim args="-b -a everything"
+
+         # add one model or model driver
+         make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
+
+         # use an existing KIM API installation at the provided location
+         make lib-kim args="-p <prefix>"
+
+         # ditto but add one model or driver
+         make lib-kim args="-p <prefix> -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
+
+      When using the ``-b`` option, the KIM library is built using its native
       cmake build system.  The ``lib/kim/Install.py`` script supports a
       ``CMAKE`` environment variable if the cmake executable is named other
       than ``cmake`` on your system.  Additional environment variables may be
@@ -393,7 +425,9 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
+         # (re-)install KIM API lib using cmake3 and gnu v11 compilers
+         # with only example models
+         CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b"
 
       Settings for debugging OpenKIM web queries discussed below need to
       be applied by adding them to the ``LMP_INC`` variable through
@@ -433,7 +467,7 @@ KIM Extra unit tests (CMake only)
 During development, testing, or debugging, if
 :doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
 enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
-``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
+``KIM_EXTRA_UNITTESTS`` to ``yes`` (or ``on``).
 
 Enabling the extra unit tests have some requirements,
 
@@ -448,10 +482,12 @@ Enabling the extra unit tests have some requirements,
   *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
   Conda. More detailed information is available at:
   `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
-* It is also necessary to install
-  ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
-  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
-  ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
+* It is also necessary to install the following KIM models:
+
+  * ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``
+  * ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``
+  * ``LennardJones612_UniversalShifted__MO_959249795837_003``
+
   See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
   to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
@@ -638,6 +674,9 @@ They must be specified in uppercase.
    *  - AMD_GFX1100
       - GPU
       - AMD GPU RX7900XTX
+   *  - AMD_GFX1103
+      - GPU
+      - AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
    *  - INTEL_GEN
       - GPU
       - SPIR64-based devices, e.g. Intel GPUs, using JIT
@@ -725,7 +764,8 @@ This list was last updated for version 4.3.0 of the Kokkos library.
 
          mkdir build-kokkos-cuda
          cd build-kokkos-cuda
-         cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
+         cmake -C ../cmake/presets/basic.cmake \
+               -C ../cmake/presets/kokkos-cuda.cmake ../cmake
          cmake --build .
 
    .. tab:: Basic traditional make settings:
@@ -753,9 +793,10 @@ This list was last updated for version 4.3.0 of the Kokkos library.
       .. code-block:: make
 
          KOKKOS_DEVICES = Cuda
-         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is hosting the GPU
-         KOKKOS_CUDA_OPTIONS = "enable_lambda"
+         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is
+                                         #            hosting the GPU
                                          # GPUARCH = GPU from list above
+         KOKKOS_CUDA_OPTIONS = "enable_lambda"
          FFT_INC = -DFFT_CUFFT           # enable use of cuFFT (optional)
          FFT_LIB = -lcufft               # link to cuFFT library
 
@@ -783,10 +824,11 @@ This list was last updated for version 4.3.0 of the Kokkos library.
       .. code-block:: make
 
          KOKKOS_DEVICES = HIP
-         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is hosting the GPU
+         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is
+                                         #            hosting the GPU
                                          # GPUARCH = GPU from list above
-         FFT_INC = -DFFT_HIPFFT           # enable use of hipFFT (optional)
-         FFT_LIB = -lhipfft               # link to hipFFT library
+         FFT_INC = -DFFT_HIPFFT          # enable use of hipFFT (optional)
+         FFT_LIB = -lhipfft              # link to hipFFT library
 
 Advanced KOKKOS compilation settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -870,11 +912,16 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
       .. code-block:: bash
 
-         make lib-lepton                      # print help message
-         make lib-lepton args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         make lib-lepton args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         # print help message
+         make lib-lepton
 
-      The "machine" argument of the "-m" flag is used to find a
+         # build with GNU g++ compiler (settings as with "make serial")
+         make lib-lepton args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-lepton args="-m mpi"
+
+      The "machine" argument of the ``-m`` flag is used to find a
       Makefile.machine to use as build recipe.
 
       The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
@@ -896,7 +943,8 @@ Eigen3 is a template library, so you do not need to build it.
       .. code-block:: bash
 
          -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
-         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
+         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a
+                                       # custom location)
 
       If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
       downloaded and inside the CMake build directory.  If the Eigen3
@@ -914,9 +962,14 @@ Eigen3 is a template library, so you do not need to build it.
 
       .. code-block:: bash
 
-         make lib-machdyn                         # print help message
-         make lib-machdyn args="-b"               # download to lib/machdyn/eigen3
-         make lib-machdyn args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+         # print help message
+         make lib-machdyn
+
+         # download to lib/machdyn/eigen3
+         make lib-machdyn args="-b"
+
+         # use existing Eigen installation in /usr/include/eigen3
+         make lib-machdyn args="-p /usr/include/eigen3"
 
       Note that a symbolic (soft) link named ``includelink`` is created
       in ``lib/machdyn`` to point to the Eigen dir.  When LAMMPS builds it
@@ -990,7 +1043,7 @@ OPT package
 
       The compiler flag ``-restrict`` must be used to build LAMMPS with
       the OPT package when using Intel compilers.  It should be added to
-      the :code:`CCFLAGS` line of your ``Makefile.machine``.  See
+      the ``CCFLAGS`` line of your ``Makefile.machine``.  See
       ``src/MAKE/OPTIONS/Makefile.opt`` for an example.
 
 ----------
@@ -1017,10 +1070,17 @@ POEMS package
 
       .. code-block:: bash
 
-         make lib-poems                   # print help message
-         make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-         make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-poems args="-m icc"     # build with Intel icc compiler
+         # print help message
+         make lib-poems
+
+         # build with GNU g++ compiler (settings as with "make serial")
+         make lib-poems args="-m serial"
+
+         # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-poems args="-m mpi"
+
+         # build with Intel Classic compiler
+         make lib-poems args="-m icc"
 
       The build should produce two files: ``lib/poems/libpoems.a`` and
       ``lib/poems/Makefile.lammps``.  The latter is copied from an
@@ -1084,9 +1144,12 @@ binary package provided by your operating system.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
-         -D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location)
-         -D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location)
+         -D DOWNLOAD_VORO=value    # download Voro++ for build
+                                   # value = no (default) or yes
+         -D VORO_LIBRARY=path      # Voro++ library file
+                                   # (only needed if at custom location)
+         -D VORO_INCLUDE_DIR=path  # Voro++ include directory
+                                   # (only needed if at custom location)
 
       If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded
       and built inside the CMake build directory.  If the Voro++ library
@@ -1106,12 +1169,19 @@ binary package provided by your operating system.
 
       .. code-block:: bash
 
-         make lib-voronoi                          # print help message
-         make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-         make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-         make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+         # print help message
+         make lib-voronoi
 
-      Note that 2 symbolic (soft) links, ``includelink`` and
+         # download and build the default version in lib/voronoi/voro++-<version>
+         make lib-voronoi args="-b"
+
+         # use existing Voro++ installation in $HOME/voro++
+         make lib-voronoi args="-p $HOME/voro++"
+
+         # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+         make lib-voronoi args="-b -v voro++0.4.6"
+
+      Note that two symbolic (soft) links, ``includelink`` and
       ``liblink``, are created in lib/voronoi to point to the Voro++
       source dir.  When LAMMPS builds in ``src`` it will use these
       links.  You should not need to edit the
@@ -1185,10 +1255,17 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         make lib-atc                      # print help message
-         make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         make lib-atc args="-m icc"        # build with Intel icc compiler
+         # print help message
+         make lib-atc
+
+         # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-atc args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-atc args="-m mpi"
+
+         # build with Intel Classic compiler
+         make lib-atc args="-m icc"
 
       The build should produce two files: ``lib/atc/libatc.a`` and
       ``lib/atc/Makefile.lammps``.  The latter is copied from an
@@ -1207,10 +1284,17 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU Fortran compiler
+         # print help message
+         make lib-linalg
+
+         # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m serial"
+
+         # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m mpi"
+
+         # build with GNU Fortran compiler
+         make lib-linalg args="-m g++"
 
 ----------
 
@@ -1236,10 +1320,17 @@ AWPMD package
 
       .. code-block:: bash
 
-         make lib-awpmd                   # print help message
-         make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         make lib-awpmd args="-m icc"     # build with Intel icc compiler
+         # print help message
+         make lib-awpmd
+
+         # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-awpmd args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-awpmd args="-m mpi"
+
+         # build with Intel Classic compiler
+         make lib-awpmd args="-m icc"
 
       The build should produce two files: ``lib/awpmd/libawpmd.a`` and
       ``lib/awpmd/Makefile.lammps``.  The latter is copied from an
@@ -1258,10 +1349,17 @@ AWPMD package
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+         # print help message
+         make lib-linalg
+
+         # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m serial"
+
+         # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m mpi"
+
+         # build with GNU C++ compiler
+         make lib-linalg args="-m g++"
 
 ----------
 
@@ -1294,10 +1392,17 @@ module included in the LAMMPS source distribution.
 
       .. code-block:: bash
 
-         make lib-colvars                      # print help message
-         make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+         # print help message
+         make lib-colvars
+
+         # build with GNU g++ compiler (settings as with "make serial")
+         make lib-colvars args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-colvars args="-m mpi"
+
+         # build with GNU g++ compiler and colvars debugging enabled
+         make lib-colvars args="-m g++-debug"
 
       The "machine" argument of the "-m" flag is used to find a
       ``Makefile.machine`` file to use as build recipe.  If such recipe does
@@ -1316,8 +1421,11 @@ module included in the LAMMPS source distribution.
 
       .. code-block:: bash
 
-         COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
-         COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+         # Build with debug code (much slower)
+         COLVARS_DEBUG=yes make lib-colvars args="-m machine"
+
+         # Build without Lepton (included otherwise)
+         COLVARS_LEPTON=no make lib-colvars args="-m machine"
 
       The build should produce two files: the library
       ``lib/colvars/libcolvars.a`` and the specification file
@@ -1364,9 +1472,14 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         make lib-electrode                   # print help message
-         make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         # print help message
+         make lib-electrode
+
+         # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-electrode args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-electrode args="-m mpi"
 
 
       Note that the ``Makefile.lammps`` file has settings for the BLAS
@@ -1377,10 +1490,17 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+         # print help message
+         make lib-linalg
+
+         # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m serial"
+
+         # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m mpi"
+
+         # build with GNU C++ compiler
+         make lib-linalg args="-m g++"
 
       The package itself is activated with ``make yes-KSPACE`` and
       ``make yes-ELECTRODE``
@@ -1397,6 +1517,11 @@ in lib/pace or somewhere else, which must be done before building
 LAMMPS with this package. The code for the library can be found
 at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
 
+Instead of including the ML-PACE package directly into LAMMPS, it
+is also possible to skip this step and build the ML-PACE package as
+a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
+folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
+
 .. tabs::
 
    .. tab:: CMake build
@@ -1420,8 +1545,11 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
       .. code-block:: bash
 
-         make lib-pace                          # print help message
-         make lib-pace args="-b"                # download and build the default version in lib/pace
+         # print help message
+         make lib-pace
+
+         # download and build the default version in lib/pace
+         make lib-pace args="-b"
 
       You should not need to edit the ``lib/pace/Makefile.lammps`` file.
 
@@ -1448,10 +1576,17 @@ ML-POD package
 
       .. code-block:: bash
 
-         make lib-mlpod                   # print help message
-         make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
+         # print help message
+         make lib-mlpod
+
+         # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-mlpod args="-m serial"
+
+         # build with default MPI compiler (settings as with "make mpi")
+         make lib-mlpod args="-m mpi"
+
+         # same as above but use the bundled linalg lib
+         make lib-mlpod args="-m mpi -e linalg"
 
       Note that the ``Makefile.lammps`` file has settings to use the BLAS
       and LAPACK linear algebra libraries.  These can either exist on
@@ -1461,10 +1596,17 @@ ML-POD package
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+         # print help message
+         make lib-linalg
+
+         # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m serial"
+
+         # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m mpi"
+
+         # build with GNU C++ compiler
+         make lib-linalg args="-m g++"
 
       The package itself is activated with ``make yes-ML-POD``.
 
@@ -1487,10 +1629,13 @@ within CMake will download the non-commercial use version.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
-         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build
+                                      # value = no (default) or yes
+         -D QUIP_LIBRARY=path         # path to libquip.a
+                                      # (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library
+                                      # instead of LAPACK
+                                      # value = no (default) or yes
 
       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
@@ -1561,29 +1706,38 @@ try a different one, switch to a different build system, consider a
 global PLUMED installation or consider downloading PLUMED during the
 LAMMPS build.
 
+Instead of including the PLUMED package directly into LAMMPS, it
+is also possible to skip this step and build the PLUMED package as
+a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
+folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
+
 .. tabs::
 
    .. tab:: CMake build
 
       When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
-      command you must ensure that GSL is installed in locations that
-      are specified in your environment.  There are then two additional
-      variables that control the manner in which PLUMED is obtained and
-      linked into LAMMPS.
+      command you must ensure that `the GNU Scientific Library (GSL)
+      <https://www.gnu.org/software/gsl/>` is installed in locations
+      that are accessible in your environment.  There are then two
+      additional variables that control the manner in which PLUMED is
+      obtained and linked into LAMMPS.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
-         -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime
+         -D DOWNLOAD_PLUMED=value   # download PLUMED for build
+                                    # value = no (default) or yes
+         -D PLUMED_MODE=value       # Linkage mode for PLUMED
+                                    # value = static (default), shared,
+                                    #         or runtime
 
-      If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
+      If ``DOWNLOAD_PLUMED`` is set to ``yes``, the PLUMED library will be
       downloaded (the version of PLUMED that will be downloaded is
       hard-coded to a vetted version of PLUMED, usually a recent stable
       release version) and built inside the CMake build directory.  If
       ``DOWNLOAD_PLUMED`` is set to "no" (the default), CMake will try
       to detect and link to an installed version of PLUMED.  For this to
       work, the PLUMED library has to be installed into a location where
-      the ``pkg-config`` tool can find it or the PKG_CONFIG_PATH
+      the ``pkg-config`` tool can find it or the ``PKG_CONFIG_PATH``
       environment variable has to be set up accordingly.  PLUMED should
       be installed in such a location if you compile it using the
       default make; make install commands.
@@ -1612,14 +1766,21 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         make lib-plumed                         # print help message
-         make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
-         make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
-         make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
-                                                           # /usr/local and use shared linkage mode
+         # print help message
+         make lib-plumed
 
-      Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
-      are created in lib/plumed that point to the location of the PLUMED
+         # download and build PLUMED in lib/plumed/plumed2
+         make lib-plumed args="-b"
+
+         # use existing PLUMED installation in $HOME/.local
+         make lib-plumed args="-p $HOME/.local"
+
+         # use existing PLUMED installation in /usr/local and
+         # use shared linkage mode
+         make lib-plumed args="-p /usr/local -m shared"
+
+      Note that two symbolic (soft) links, ``includelink`` and ``liblink``
+      are created in ``lib/plumed`` that point to the location of the PLUMED
       build to use. A new file ``lib/plumed/Makefile.lammps`` is also
       created with settings suitable for LAMMPS to compile and link
       PLUMED using the desired linkage mode. After this step is
@@ -1634,17 +1795,17 @@ LAMMPS build.
       Once this compilation completes you should be able to run LAMMPS
       in the usual way.  For shared linkage mode, libplumed.so must be
       found by the LAMMPS executable, which on many operating systems
-      means, you have to set the LD_LIBRARY_PATH environment variable
+      means, you have to set the ``LD_LIBRARY_PATH`` environment variable
       accordingly.
 
       Support for the different linkage modes in LAMMPS varies for
       different operating systems, using the static linkage is expected
       to be the most portable, and thus set to be the default.
 
-      If you want to change the linkage mode, you have to re-run "make
-      lib-plumed" with the desired settings **and** do a re-install if
-      the PLUMED package with "make yes-plumed" to update the
-      required makefile settings with the changes in the lib/plumed
+      If you want to change the linkage mode, you have to re-run ``make
+      lib-plumed`` with the desired settings **and** do a re-install if
+      the PLUMED package with ``make yes-plumed`` to update the
+      required makefile settings with the changes in the ``lib/plumed``
       folder.
 
 ----------
@@ -1718,8 +1879,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
       .. code-block:: bash
 
-         -D DOWNLOAD_N2P2=value    # download n2p2 for build, value = no (default) or yes
-         -D N2P2_DIR=path          # n2p2 base directory (only needed if a custom location)
+         -D DOWNLOAD_N2P2=value    # download n2p2 for build
+                                   # value = no (default) or yes
+         -D N2P2_DIR=path          # n2p2 base directory
+                                   # (only needed if a custom location)
 
       If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
       built inside the CMake build directory.  If the *n2p2* library is already
@@ -1736,12 +1899,19 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
       .. code-block:: bash
 
-         make lib-hdnnp             # print help message
-         make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
-         make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
-         make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+         # print help message
+         make lib-hdnnp
 
-      Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
+         # download and build in lib/hdnnp/n2p2-...
+         make lib-hdnnp args="-b"
+
+         # download and build specific version
+         make lib-hdnnp args="-b -v 2.1.4"
+
+         # use the existing n2p2 installation in /usr/local/n2p2
+         make lib-hdnnp args="-p /usr/local/n2p2"
+
+      Note that three symbolic (soft) links, ``includelink``, ``liblink`` and
       ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
       ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
       respectively. When LAMMPS is built in ``src`` it will use these links.
@@ -1788,19 +1958,19 @@ code when using features from the INTEL package.
 
       .. code-block:: make
 
-         OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
-         CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-         LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
-         LIB =           -ltbbmalloc
+         OPTFLAGS =  -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
+         CCFLAGS =   -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+         LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+         LIB =       -ltbbmalloc
 
       For KNLs:
 
       .. code-block:: make
 
-         OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-         CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-         LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
-         LIB =           -ltbbmalloc
+         OPTFLAGS =  -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+         CCFLAGS =   -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+         LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+         LIB =       -ltbbmalloc
 
 In Long-range thread mode (LRT) a modified verlet style is used, that
 operates the Kspace calculation in a separate thread concurrently to
@@ -1829,7 +1999,8 @@ MDI package
 
       .. code-block:: bash
 
-         -D DOWNLOAD_MDI=value    # download MDI Library for build, value = no (default) or yes
+         -D DOWNLOAD_MDI=value    # download MDI Library for build
+                                  # value = no (default) or yes
 
    .. tab:: Traditional make
 
@@ -1858,7 +2029,8 @@ MOLFILE package
 
       .. code-block:: bash
 
-         -D MOLFILE_INCLUDE_DIR=path   # (optional) path where VMD molfile plugin headers are installed
+         -D MOLFILE_INCLUDE_DIR=path   # (optional) path where VMD molfile
+                                       # plugin headers are installed
          -D PKG_MOLFILE=yes
 
       Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
@@ -2017,10 +2189,17 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
       .. code-block:: bash
 
-         make lib-qmmm                      # print help message
-         make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
-         make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
-         make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+         # print help message
+         make lib-qmmm
+
+         # build with GNU Fortran compiler (settings as in "make serial")
+         make lib-qmmm args="-m serial"
+
+         # build with default MPI compiler (settings as in "make mpi")
+         make lib-qmmm args="-m mpi"
+
+         # build with GNU Fortran compiler
+         make lib-qmmm args="-m gfortran"
 
       The build should produce two files: ``lib/qmmm/libqmmm.a`` and
       ``lib/qmmm/Makefile.lammps``.  The latter is copied from an
@@ -2033,10 +2212,40 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
       You can then install QMMM package and build LAMMPS in the usual
       manner.  After completing the LAMMPS build and compiling Quantum
-      ESPRESSO with external library support (via "make couple"), go
+      ESPRESSO with external library support (via ``make couple``), go
       back to the ``lib/qmmm`` folder and follow the instructions in the
       README file to build the combined LAMMPS/QE QM/MM executable
-      (pwqmmm.x) in the lib/qmmm folder.
+      (``pwqmmm.x``) in the ``lib/qmmm`` folder.
+
+----------
+
+.. _rheo:
+
+RHEO package
+------------
+
+To build with this package you must have the `GNU Scientific Library
+(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
+are accessible in your environment.  The GSL library should be at least
+version 2.7.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      If CMake cannot find the GSL library or include files, you can set:
+
+      .. code-block:: bash
+
+         -D GSL_ROOT_DIR=path    # path to root of GSL installation
+
+   .. tab:: Traditional make
+
+      LAMMPS will try to auto-detect the GSL compiler and linker flags
+      from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
+      you can edit the file ``lib/rheo/Makefile.lammps``
+      to specify the paths and library names where indicated by comments.
+      This must be done **before** the package is installed.
 
 ----------
 
@@ -2076,11 +2285,16 @@ To build with this package, you must download and build the
 
       .. code-block:: bash
 
-         make lib-scafacos                         # print help message
-         make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>
-         make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos
+         # print help message
+         make lib-scafacos
 
-      Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
+         # download and build in lib/scafacos/scafacos-<version>
+         make lib-scafacos args="-b"
+
+         # use existing ScaFaCoS installation in $HOME/scafacos
+         make lib-scafacos args="-p $HOME/scafacos
+
+      Note that two symbolic (soft) links, ``includelink`` and ``liblink``, are
       created in ``lib/scafacos`` to point to the ScaFaCoS src dir.  When LAMMPS
       builds in src it will use these links.  You should not need to edit
       the ``lib/scafacos/Makefile.lammps`` file.

doc/src/Build_link.rst

@@ -37,7 +37,7 @@ executable code from the library is copied into the calling executable.
    .. tab:: CMake build
 
       This assumes that LAMMPS has been configured without setting a
-      ``LAMMPS_MACHINE`` name, installed with "make install", and the
+      ``LAMMPS_MACHINE`` name, installed with ``make install``, and the
       ``PKG_CONFIG_PATH`` environment variable has been updated to
       include the ``liblammps.pc`` file installed into the configured
       destination folder.  The commands to compile and link a coupled
@@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
-         mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 
@@ -59,10 +59,10 @@ executable code from the library is copied into the calling executable.
          mpicc -c -O -I${HOME}/lammps/src caller.c
          mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
 
-      The *-I* argument is the path to the location of the ``library.h``
+      The ``-I`` argument is the path to the location of the ``library.h``
       header file containing the interface to the LAMMPS C-style library
-      interface.  The *-L* argument is the path to where the
-      ``liblammps_mpi.a`` file is located.  The *-llammps_mpi* argument
+      interface.  The ``-L`` argument is the path to where the
+      ``liblammps_mpi.a`` file is located.  The ``-llammps_mpi`` argument
       is shorthand for telling the compiler to link the file
       ``liblammps_mpi.a``.  If LAMMPS has been built as a shared
       library, then the linker will use ``liblammps_mpi.so`` instead.
@@ -142,7 +142,7 @@ When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
 in the shared library or registered as a dependent library in the shared
 library file.  Thus, those libraries need not be specified when linking
-the calling executable.  Only the *-I* flags are needed.  So the example
+the calling executable.  Only the ``-I`` flags are needed.  So the example
 case from above of the serial version static LAMMPS library with the
 POEMS package installed becomes:
 
@@ -155,8 +155,8 @@ POEMS package installed becomes:
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
-         mpicxx -o caller caller.o -$(pkgconf --libs)
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 

doc/src/Build_make.rst

@@ -25,7 +25,7 @@ additional tools to be available and functioning.
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
   * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
   * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * Python (optional, required for ``make lib-<pkg>`` in the src
+  * Python (optional, required for ``make lib-<pkg>`` in the ``src``
     folder).  Python scripts are currently tested with python 2.7 and
     3.6 to 3.11. The procedure for :doc:`building the documentation
     <Build_manual>` *requires* Python 3.5 or later.

doc/src/Build_package.rst

@@ -62,6 +62,7 @@ packages:
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -99,10 +100,10 @@ versus make.
       .. code-block:: bash
 
          cd lammps/src
-         make ps                    # check which packages are currently installed
-         make yes-name              # install a package with name
-         make no-name               # uninstall a package with name
-         make mpi                   # build LAMMPS with whatever packages are now installed
+         make ps        # check which packages are currently installed
+         make yes-name  # install a package with name
+         make no-name   # uninstall a package with name
+         make mpi       # build LAMMPS with whatever packages are now installed
 
       Examples:
 
@@ -171,18 +172,41 @@ make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake  # enable just a few core packages
-    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
-    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
-    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
-    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
-    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake  # change settings to use the GNU compilers by default
-    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
-    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
-    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
-    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
-    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
+    # enable just a few core packages
+    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake
+
+    # enable most packages
+    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake
+
+    # enable packages which download sources or potential files
+    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
+
+    # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the GNU compilers by default
+    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake
+
+    # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the PGI compilers by default
+    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake
+
+    # enable all packages
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake
+
+    # disable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake
+
+    #  compile with MinGW cross-compilers
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
+
+    # compile serial multi-arch binaries on macOS
+    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@@ -208,7 +232,8 @@ Example
    # GPU package and configure it for using CUDA. You can run.
    mkdir build
    cd build
-   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
+         -D PKG_GPU=on -D GPU_API=cuda ../cmake
 
    # to add another package, say BODY to the previous configuration you can run:
    cmake -D PKG_BODY=on .

doc/src/Build_settings.rst

@@ -1,3 +1,7 @@
+.. raw:: latex
+
+    \clearpage
+
 Optional build settings
 =======================
 
@@ -8,7 +12,8 @@ explains how to do this for building both with CMake and make.
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
 * `Size of LAMMPS integer types and size limits`_
 * `Read or write compressed files`_
-* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
+* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
+* `Support for downloading files`_
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
@@ -19,7 +24,7 @@ explains how to do this for building both with CMake and make.
 .. _cxx11:
 
 C++11 standard compliance
-------------------------------------------
+-------------------------
 
 A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
 LAMMPS version 3 March 2020 is the last version compatible with the previous
@@ -31,12 +36,16 @@ flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
 
    CCFLAGS = -g -O3 -std=c++11
 
+Individual packages may require compliance with a later C++ standard
+like C++14 or C++17.  These requirements will be documented with the
+:doc:`individual packages <Packages_details>`.
+
 ----------
 
 .. _fft:
 
 FFT library
----------------------
+-----------
 
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@@ -58,8 +67,10 @@ libraries and better pipelining for packing and communication.
 
       .. code-block:: bash
 
-         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
+         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found,
+                                   # else KISS
+         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT,
+                                   # default is KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
          -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
@@ -67,11 +78,11 @@ libraries and better pipelining for packing and communication.
       .. note::
 
          When the Kokkos variant of a package is compiled and selected at run time,
-         the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
+         the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
          the FFT library selected by the FFT variable applies.
-         The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
+         The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
          Kokkos back end - for example, when using the CUDA back end of Kokkos,
-         you must use either CUFFT or KISS.
+         you must use either ``CUFFT`` or ``KISS``.
 
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
@@ -89,7 +100,8 @@ libraries and better pipelining for packing and communication.
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
-         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
+         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
+                                     # heFFTe back end
          -D Heffte_ROOT=path         # path to an existing heFFTe installation
 
       .. note::
@@ -108,30 +120,50 @@ libraries and better pipelining for packing and communication.
 
       .. code-block:: make
 
-         FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
-                                       # default is KISS if not specified
-         FFT_INC = -DFFT_KOKKOS_CUFFT  # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
-                                       # default is KISS if not specified
-         FFT_INC = -DFFT_SINGLE        # do not specify for double precision
-         FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
-         FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
-         FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
-                                       # default is FFT_PACK_ARRAY if not specified
+         FFT_INC = -DFFT_<NAME>        # where <NAME> is KISS (default), FFTW3,
+                                       # FFTW (same as FFTW3), or MKL
+         FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
+                                       # FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
+         FFT_INC = -DFFT_SINGLE       # do not specify for double precision
+         FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
+         FFT_INC = -DFFT_MKL_THREADS  # enable using threaded FFTs with MKL libraries
+         FFT_INC = -DFFT_PACK_ARRAY   # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+                                      # default is FFT_PACK_ARRAY if not specified
 
       .. code-block:: make
 
-         FFT_INC =       -I/usr/local/include
-         FFT_PATH =      -L/usr/local/lib
-         FFT_LIB =       -lhipfft            # hipFFT either precision
-         FFT_LIB =       -lcufft             # cuFFT either precision
-         FFT_LIB =       -lfftw3             # FFTW3 double precision
-         FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
-         FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-         FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
-         FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
-         FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
-         FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
-         FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
+         FFT_INC =  -I/usr/local/include
+         FFT_PATH = -L/usr/local/lib
+
+         # hipFFT either precision
+         FFT_LIB =  -lhipfft
+
+         # cuFFT either precision
+         FFT_LIB =  -lcufft
+
+         # FFTW3 double precision
+         FFT_LIB =  -lfftw3
+
+         # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
+         FFT_LIB =  -lfftw3 -lfftw3_omp
+
+         # FFTW3 single precision
+         FFT_LIB =  -lfftw3 -lfftw3f
+
+         # serial MKL with Intel compiler
+         FFT_LIB =  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
+
+         # serial MKL with GNU compiler
+         FFT_LIB =  -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
+
+         # threaded MKL with Intel compiler
+         FFT_LIB =  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
+
+         # threaded MKL with GNU compiler
+         FFT_LIB =  -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
+
+         # MKL with automatic runtime selection of interface libs
+         FFT_LIB =  -lmkl_rt
 
       As with CMake, you do not need to set paths in ``FFT_INC`` or
       ``FFT_PATH``, if the compiler can find the FFT header and library
@@ -147,11 +179,11 @@ libraries and better pipelining for packing and communication.
          FFT_PATH =
          FFT_LIB = $(heffte_link) $(heffte_libs)
 
-      The heFFTe install path will contain `HeffteMakefile.in`.
-      which will define the `heffte_` include variables needed to link to heFFTe from
+      The heFFTe install path will contain ``HeffteMakefile.in``.
+      which will define the ``heffte_`` include variables needed to link to heFFTe from
       an external project using traditional make.
-      The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
-      selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
+      The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
+      selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
       omitting the variable will default to the `stock` back end.
       The heFFTe `stock` back end is intended to be used for testing and debugging,
       but is not performance optimized for large scale production runs.
@@ -179,7 +211,7 @@ it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
-the "--prefix" option of configure.  Type ``./configure --help`` to see
+the ``--prefix`` option of configure.  Type ``./configure --help`` to see
 various options.
 
 The Intel MKL math library is part of the Intel compiler suite.  It
@@ -215,7 +247,7 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 Performing 3d FFTs requires communication to transpose the 3d FFT
 grid.  The data packing/unpacking for this can be done in one of 3
-modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
+modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
 Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
@@ -232,6 +264,10 @@ and those variables will be passed into the heFFTe build.
 
 ----------
 
+.. raw:: latex
+
+    \clearpage
+
 .. _size:
 
 Size of LAMMPS integer types and size limits
@@ -272,7 +308,7 @@ LAMMPS system size restrictions
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 18 27 28 27
    :align: center
 
    * -
@@ -341,8 +377,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
 
 .. _graphics:
 
-Output of JPG, PNG, and movie files
---------------------------------------------------
+Output of JPEG, PNG, and movie files
+------------------------------------
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
 PNG image files.  Likewise, the :doc:`dump movie <dump_image>` command
@@ -355,12 +391,13 @@ requires the following settings:
 
       .. code-block:: bash
 
-         -D WITH_JPEG=value      # yes or no
-                                 # default = yes if CMake finds JPEG files, else no
-         -D WITH_PNG=value       # yes or no
-                                 # default = yes if CMake finds PNG and ZLIB files, else no
-         -D WITH_FFMPEG=value    # yes or no
-                                 # default = yes if CMake can find ffmpeg, else no
+         -D WITH_JPEG=value    # yes or no
+                               # default = yes if CMake finds JPEG development files, else no
+         -D WITH_PNG=value     # yes or no
+                               # default = yes if CMake finds PNG and ZLIB development files,
+                               # else no
+         -D WITH_FFMPEG=value  # yes or no
+                               # default = yes if CMake can find ffmpeg, else no
 
       Usually these settings are all that is needed.  If CMake cannot
       find the graphics header, library, executable files, you can set
@@ -382,8 +419,10 @@ requires the following settings:
 
          LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG  <other LMP_INC settings>
 
-         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
-         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h headers
+                                          # if make cannot find them
+         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so)
+                                          # files if make cannot find them
          JPG_LIB = -ljpeg -lpng -lz       # library names
 
       As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@@ -414,8 +453,8 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Supported compression tools are currently
-``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
+:doc:`dump <dump>`.  Supported compression tools and algorithms are currently
+``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
 
 .. tabs::
 
@@ -423,8 +462,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
 
       .. code-block:: bash
 
-         -D WITH_GZIP=value       # yes or no
-                                  # default is yes if CMake can find the gzip program, else no
+         -D WITH_GZIP=value  # yes or no
+                             # default is yes if CMake can find the gzip program
 
    .. tab:: Traditional make
 
@@ -446,18 +485,64 @@ during a run.
    available using a compression library instead, which is what the
    :ref:`COMPRESS package <PKG-COMPRESS>` enables.
 
+--------------------------------------------------
+
+.. _libcurl:
+
+Support for downloading files
+-----------------------------
+
+.. versionadded:: 29Aug2024
+
+The :doc:`geturl command <geturl>` command uses the `the libcurl library
+<https://curl.se/libcurl/>`_ to download files.  This requires that
+LAMMPS is compiled accordingly which needs the following settings:
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D WITH_CURL=value      # yes or no
+                                 # default = yes if CMake finds CURL development files, else no
+
+      Usually these settings are all that is needed.  If CMake cannot
+      find the graphics header, library, executable files, you can set
+      these variables:
+
+      .. code-block:: bash
+
+         -D CURL_INCLUDE_DIR=path    # path to folder which contains curl.h header file
+         -D CURL_LIBRARY=path        # path to libcurls.a (.so) file
+
+   .. tab:: Traditional make
+
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_CURL  <other LMP_INC settings>
+
+         CURL_INC = -I/usr/local/include   # path to curl folder with curl.h
+         CURL_PATH = -L/usr/lib            # paths to libcurl.a(.so) if make cannot find it
+         CURL_LIB = -lcurl                 # library names
+
+      As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
+      if make can find the libcurl header and library files in their
+      default system locations.  You must specify ``CURL_LIB`` with a
+      paths or linker flags to link to libcurl.
+
 ----------
 
 .. _align:
 
 Memory allocation alignment
----------------------------------------
+---------------------------
 
-This setting enables the use of the "posix_memalign()" call instead of
-"malloc()" when LAMMPS allocates large chunks of memory.  Vector
+This setting enables the use of the ``posix_memalign()`` call instead of
+``malloc()`` when LAMMPS allocates large chunks of memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
-current operating systems, the "malloc()" implementation returns
+current operating systems, the ``malloc()`` implementation returns
 pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being aligned
 on 64-byte boundaries.
@@ -471,9 +556,9 @@ on 64-byte boundaries.
          -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
       Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
-      "posix_memalign()" and revert to using the "malloc()" C-library
+      ``posix_memalign()`` and revert to using the ``malloc()`` C-library
       function instead.  When compiling LAMMPS for Windows systems,
-      "malloc()" will always be used and this setting is ignored.
+      ``malloc()`` will always be used and this setting is ignored.
 
    .. tab:: Traditional make
 
@@ -482,7 +567,7 @@ on 64-byte boundaries.
          LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
 
       Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
-      allocated with the "malloc()" function call
+      allocated with the ``malloc()`` function call
       instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
       Windows different function calls with different semantics for
       allocating aligned memory, that are not compatible with how LAMMPS

doc/src/Commands_all.rst

@@ -1,26 +1,30 @@
-.. table_from_list::
-   :columns: 3
+.. only:: html
 
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
+   .. table_from_list::
+      :columns: 5
+
+      * :doc:`General commands <Commands_all>`
+      * :doc:`Fix styles <Commands_fix>`
+      * :doc:`Compute styles <Commands_compute>`
+      * :doc:`Pair styles <Commands_pair>`
+      * :ref:`Bond styles <bond>`
+      * :ref:`Angle styles <angle>`
+      * :ref:`Dihedral styles <dihedral>`
+      * :ref:`Improper styles <improper>`
+      * :doc:`KSpace styles <Commands_kspace>`
+      * :doc:`Dump styles <Commands_dump>`
+
+.. raw:: latex
+
+   \clearpage
 
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.  Note that style
-commands with many variants, can be more easily accessed via the small
-table above.
+An alphabetic list of general LAMMPS commands.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 6
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
@@ -54,6 +58,7 @@ table above.
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
    * :doc:`fix_modify <fix_modify>`
+   * :doc:`geturl <geturl>`
    * :doc:`group <group>`
    * :doc:`if <if>`
    * :doc:`improper_coeff <improper_coeff>`
@@ -121,7 +126,7 @@ commands have accelerated versions.  This is indicated by an
 additional letter in parenthesis: k = KOKKOS.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 6
 
    * :doc:`dynamical_matrix (k) <dynamical_matrix>`
    * :doc:`group2ndx <group2ndx>`

doc/src/Commands_bond.rst

@@ -1,21 +1,7 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
 .. _bond:
 
-Bond_style potentials
-=====================
+Bond styles
+===========
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -23,11 +9,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <bond_none>`
    * :doc:`zero <bond_zero>`
-   * :doc:`hybrid <bond_hybrid>`
+   * :doc:`hybrid (k) <bond_hybrid>`
+   *
+   *
    *
    *
    *
@@ -54,13 +42,14 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`rheo/shell <bond_rheo_shell>`
    * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 
 .. _angle:
 
-Angle_style potentials
-======================
+Angle styles
+============
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -68,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <angle_none>`
    * :doc:`zero <angle_zero>`
-   * :doc:`hybrid <angle_hybrid>`
+   * :doc:`hybrid (k) <angle_hybrid>`
+   *
+   *
    *
    *
    *
@@ -100,13 +91,13 @@ OPT.
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`spica (o) <angle_spica>`
+   * :doc:`spica (ko) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
 
-Dihedral_style potentials
-=========================
+Dihedral styles
+===============
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -114,11 +105,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <dihedral_none>`
    * :doc:`zero <dihedral_zero>`
-   * :doc:`hybrid <dihedral_hybrid>`
+   * :doc:`hybrid (k) <dihedral_hybrid>`
+   *
+   *
    *
    *
    *
@@ -143,8 +136,8 @@ OPT.
 
 .. _improper:
 
-Improper_style potentials
-=========================
+Improper styles
+===============
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -152,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <improper_none>`
    * :doc:`zero <improper_zero>`
-   * :doc:`hybrid <improper_hybrid>`
+   * :doc:`hybrid (k) <improper_hybrid>`
+   *
+   *
    *
    *
    *

doc/src/Commands_category.rst

@@ -1,3 +1,7 @@
+.. raw:: latex
+
+   \clearpage
+
 Commands by category
 ====================
 
@@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category.  The
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 
-Initialization:
-------------------------------
+Initialization
+--------------
 
 .. table_from_list::
    :columns: 5
@@ -18,8 +22,8 @@ Initialization:
    * :doc:`suffix <suffix>`
    * :doc:`units <units>`
 
-Setup simulation box:
-------------------------------
+Setup simulation box
+--------------------
 
 .. table_from_list::
    :columns: 4
@@ -31,8 +35,8 @@ Setup simulation box:
    * :doc:`lattice <lattice>`
    * :doc:`region <region>`
 
-Setup atoms:
-------------------------------
+Setup atoms
+-----------
 
 .. table_from_list::
    :columns: 4
@@ -55,8 +59,8 @@ Setup atoms:
    * :doc:`set <set>`
    * :doc:`velocity <velocity>`
 
-Force fields:
-------------------------------
+Force fields
+------------
 
 .. table_from_list::
    :columns: 4
@@ -79,8 +83,8 @@ Force fields:
    * :doc:`pair_write <pair_write>`
    * :doc:`special_bonds <special_bonds>`
 
-Settings:
-------------------------------
+Settings
+--------
 
 .. table_from_list::
    :columns: 4
@@ -98,8 +102,8 @@ Settings:
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
 
-Operations within timestepping (fixes) and diagnostics (computes):
-------------------------------------------------------------------------------------------
+Operations within timestepping (fixes) and diagnostics (computes)
+-----------------------------------------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes):
    * :doc:`uncompute <uncompute>`
    * :doc:`unfix <unfix>`
 
-Output:
-------------------------------
+Output
+------
 
 .. table_from_list::
    :columns: 4
@@ -131,8 +135,8 @@ Output:
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
 
-Actions:
-------------------------------
+Actions
+-------
 
 .. table_from_list::
    :columns: 6
@@ -146,8 +150,8 @@ Actions:
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
 
-Input script control:
-------------------------------
+Input script control
+--------------------
 
 .. table_from_list::
    :columns: 7

doc/src/Commands_compute.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Compute commands
-================
+Compute styles
+==============
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
@@ -21,7 +7,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
 KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`ackland/atom <compute_ackland_atom>`
    * :doc:`adf <compute_adf>`
@@ -108,6 +94,10 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/mol/tally <compute_tally>`
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pod/atom <compute_pod_atom>`
+   * :doc:`podd/atom <compute_pod_atom>`
+   * :doc:`pod/local <compute_pod_atom>`
+   * :doc:`pod/global <compute_pod_atom>`
    * :doc:`pressure <compute_pressure>`
    * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
@@ -122,6 +112,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rheo/property/atom <compute_rheo_property_atom>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
    * :doc:`slcsa/atom <compute_slcsa_atom>`

doc/src/Commands_dump.rst

@@ -1,24 +1,10 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Dump commands
-=============
+Dump styles
+===========
 
 An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 6
 
    * :doc:`atom <dump>`
    * :doc:`atom/adios <dump_adios>`

doc/src/Commands_fix.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Fix commands
-============
+Fix styles
+==========
 
 An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -21,13 +7,14 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
    * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
+   * :doc:`add/heat <fix_add_heat>`
    * :doc:`addtorque <fix_addtorque>`
    * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@@ -204,6 +191,11 @@ OPT.
    * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
+   * :doc:`rheo <fix_rheo>`
+   * :doc:`rheo/oxidation <fix_rheo_oxidation>`
+   * :doc:`rheo/pressure <fix_rheo_pressure>`
+   * :doc:`rheo/thermal <fix_rheo_thermal>`
+   * :doc:`rheo/viscosity <fix_rheo_viscosity>`
    * :doc:`rhok <fix_rhok>`
    * :doc:`rigid (o) <fix_rigid>`
    * :doc:`rigid/meso <fix_rigid_meso>`

doc/src/Commands_input.rst

@@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
 internal variable, read in a file, or run a simulation.  These actions
 can be grouped into three categories:
 
-a) commands that change a global setting (examples: timestep, newton,
-   echo, log, thermo, restart),
+a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
+   :doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
 b) commands that add, modify, remove, or replace "styles" that are
-   executed during a "run" (examples: pair_style, fix, compute, dump,
-   thermo_style, pair_modify), and
+   executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
+   :doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
 c) commands that execute a "run" or perform some other computation or
-   operation (examples: print, run, minimize, temper, write_dump, rerun,
-   read_data, read_restart)
+   operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
+   :doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
 
 Commands in category a) have default settings, which means you only
 need to use the command if you wish to change the defaults.
@@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
     <read_data>` command initializes the system by setting up the
     simulation box and assigning atoms to processors.  If default values
     are not desired, the :doc:`processors <processors>` and
-    :doc:`boundary <boundary>` commands need to be used before read_data
+    :doc:`boundary <boundary>` commands need to be used before ``read_data``
     to tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
@@ -70,6 +70,6 @@ more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
 
 You can use the :ref:`-skiprun <skiprun>` command line flag
-to have LAMMPS skip the execution of any "run", "minimize", or similar
+to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
 commands to check the entire input for correct syntax to avoid crashes
 on typos or syntax errors in long runs.

doc/src/Commands_kspace.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-KSpace solvers
-==============
+KSpace styles
+=============
 
 All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`

doc/src/Commands_pair.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Pair_style potentials
-======================
+Pair styles
+===========
 
 All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -21,20 +7,20 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 3
 
    * :doc:`none <pair_none>`
    * :doc:`zero <pair_zero>`
-   * :doc:`hybrid (k) <pair_hybrid>`
-   * :doc:`hybrid/overlay (k) <pair_hybrid>`
-   * :doc:`hybrid/scaled <pair_hybrid>`
+   * :doc:`hybrid (ko) <pair_hybrid>`
+   * :doc:`hybrid/molecular (o) <pair_hybrid>`
+   * :doc:`hybrid/overlay (ko) <pair_hybrid>`
+   * :doc:`hybrid/scaled (o) <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    * :doc:`tracker <pair_tracker>`
    *
    *
    *
-   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@@ -94,9 +80,10 @@ OPT.
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
-   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
    * :doc:`dpd/ext (ko) <pair_dpd_ext>`
    * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -190,7 +177,7 @@ OPT.
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/spica (gko) <pair_spica>`
-   * :doc:`lj/spica/coul/long (go) <pair_spica>`
+   * :doc:`lj/spica/coul/long (gko) <pair_spica>`
    * :doc:`lj/spica/coul/msm (o) <pair_spica>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (go) <pair_lj_smooth>`
@@ -246,7 +233,7 @@ OPT.
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
    * :doc:`pedone (o) <pair_pedone>`
-   * :doc:`pod <pair_pod>`
+   * :doc:`pod (k) <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -259,6 +246,8 @@ OPT.
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`rebomos (o) <pair_rebomos>`
    * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`rheo <pair_rheo>`
+   * :doc:`rheo/solid <pair_rheo_solid>`
    * :doc:`saip/metal (t) <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smatb <pair_smatb>`
@@ -269,7 +258,7 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (ik) <pair_snap>`
-   * :doc:`soft (go) <pair_soft>`
+   * :doc:`soft (gko) <pair_soft>`
    * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
    * :doc:`sph/lj (g) <pair_sph_lj>`
@@ -303,6 +292,7 @@ OPT.
    * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`tri/lj <pair_tri_lj>`
    * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`uf3 (k) <pair_uf3>`
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`

doc/src/Commands_parse.rst

@@ -42,8 +42,8 @@ LAMMPS:
    If the $ is followed by text in curly brackets '{}', then the
    variable name is the text inside the curly brackets.  If no curly
    brackets follow the $, then the variable name is the single character
-   immediately following the $.  Thus ${myTemp} and $x refer to variables
-   named "myTemp" and "x", while "$xx" will be interpreted as a variable
+   immediately following the $.  Thus ``${myTemp}`` and ``$x`` refer to variables
+   named "myTemp" and "x", while ``$xx`` will be interpreted as a variable
    named "x" followed by an "x" character.
 
    How the variable is converted to a text string depends on what style
@@ -79,10 +79,10 @@ LAMMPS:
 
    Additionally, the entire "immediate" variable expression may be
    followed by a colon, followed by a C-style format string,
-   e.g. ":%f" or ":%.10g".  The format string must be appropriate for
+   e.g. ``:%f`` or ``:%.10g``.  The format string must be appropriate for
    a double-precision floating-point value.  The format string is used
    to output the result of the variable expression evaluation.  If a
-   format string is not specified, a high-precision "%.20g" is used as
+   format string is not specified, a high-precision ``%.20g`` is used as
    the default format.
 
    This can be useful for formatting print output to a desired precision:
@@ -101,8 +101,8 @@ LAMMPS:
       variable        b2 equal 4
       print           "B2 = ${b$a}"
 
-   Nor can you specify an expression like "$($x-1.0)" for an immediate
-   variable, but you could use $(v_x-1.0), since the latter is valid
+   Nor can you specify an expression like ``$($x-1.0)`` for an immediate
+   variable, but you could use ``$(v_x-1.0)``, since the latter is valid
    syntax for an :doc:`equal-style variable <variable>`.
 
    See the :doc:`variable <variable>` command for more details of how

doc/src/Commands_removed.rst

@@ -8,6 +8,18 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
+restart2data tool
+-----------------
+
+.. versionchanged:: 23Nov2013
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For
+added convenience this conversion can also be triggered by
+:doc:`command line flags <Run_options>`
+
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
@@ -148,12 +160,19 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
-restart2data tool
------------------
+i-PI tool
+---------
+
+.. versionchanged:: 27Jun2024
+
+The i-PI tool has been removed from the LAMMPS distribution.  Instead,
+instructions to install i-PI from PyPI via pip are provided.
+
+LAMMPS shell
+------------
+
+.. versionchanged:: 29Aug2024
+
+The LAMMPS shell has been removed from the LAMMPS distribution. Users
+are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
 
-The functionality of the restart2data tool has been folded into the
-LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For
-added convenience this conversion can also be triggered by
-:doc:`command line flags <Run_options>`

doc/src/Commands_structure.rst

@@ -8,10 +8,10 @@ page.
 
 A LAMMPS input script typically has 4 parts:
 
-1. :ref:`Initialization <init>`
-2. :ref:`System definition <system>`
-3. :ref:`Simulation settings <settings>`
-4. :ref:`Run a simulation <run>`
+#. :ref:`Initialization <init>`
+#. :ref:`System definition <system>`
+#. :ref:`Simulation settings <settings>`
+#. :ref:`Run a simulation <run>`
 
 The last 2 parts can be repeated as many times as desired.  I.e. run a
 simulation, change some settings, run some more, etc.  Each of the 4

doc/src/Developer_atom.rst

@@ -2,7 +2,7 @@ Accessing per-atom data
 -----------------------
 
 This page discusses how per-atom data is managed in LAMMPS, how it can
-be accessed, what communication patters apply, and some of the utility
+be accessed, what communication patterns apply, and some of the utility
 functions that exist for a variety of purposes.
 
 
@@ -14,11 +14,11 @@ As described on the :doc:`parallel partitioning algorithms
 simulation domain, either in a *brick* or *tiled* manner.  Each MPI
 process *owns* exactly one subdomain and the atoms within it. To compute
 forces for tuples of atoms that are spread across sub-domain boundaries,
-also a "halo" of *ghost* atoms are maintained within a the communication
+also a "halo" of *ghost* atoms are maintained within the communication
 cutoff distance of its subdomain.
 
 The total number of atoms is stored in `Atom::natoms` (within any
-typical class this can be referred to at `atom->natoms`. The number of
+typical class this can be referred to at `atom->natoms`). The number of
 *owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
 *ghost* atoms is stored in `Atom::nghost`.  The sum of `Atom::nlocal`
 over all MPI processes should be `Atom::natoms`. This is by default
@@ -27,8 +27,8 @@ LAMMPS stops with a "lost atoms" error.  For convenience also the
 property `Atom::nmax` is available, this is the maximum of
 `Atom::nlocal + Atom::nghost` across all MPI processes.
 
-Per-atom properties are either managed by the atom style, or individual
-classes.  or as custom arrays by the individual classes. If only access
+Per-atom properties are either managed by the atom style, individual
+classes,  or as custom arrays by the individual classes. If only access
 to *owned* atoms is needed, they are usually allocated to be of size
 `Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
 per-atom properties are available or updated on *ghost* atoms. For
@@ -61,7 +61,7 @@ can be found via the `Atom::sametag` array. It points to the next atom
 index with the same tag or -1 if there are no more atoms with the same
 tag.  The list will be exhaustive when starting with an index of an
 *owned* atom, since the atom IDs are unique, so there can only be one
-such atom.  Example code to count atoms with same atom ID in subdomain:
+such atom.  Example code to count atoms with same atom ID in a subdomain:
 
 .. code-block:: c++
 

doc/src/Developer_code_design.rst

@@ -69,7 +69,7 @@ The basic LAMMPS class hierarchy which is created by the LAMMPS class
 constructor is shown in :ref:`class-topology`.  When input commands
 are processed, additional class instances are created, or deleted, or
 replaced.  Likewise, specific member functions of specific classes are
-called to trigger actions such creating atoms, computing forces,
+called to trigger actions such as creating atoms, computing forces,
 computing properties, time-propagating the system, or writing output.
 
 Compositing and Inheritance
@@ -110,9 +110,10 @@ As mentioned above, there can be multiple instances of classes derived
 from the ``Fix`` or ``Compute`` base classes.  They represent a
 different facet of LAMMPS' flexibility, as they provide methods which
 can be called at different points within a timestep, as explained in
-`Developer_flow`.  This allows the input script to tailor how a specific
-simulation is run, what diagnostic computations are performed, and how
-the output of those computations is further processed or output.
+the :doc:`How a timestep works <Developer_flow>` doc page.  This allows
+the input script to tailor how a specific simulation is run, what
+diagnostic computations are performed, and how the output of those
+computations is further processed or output.
 
 Additional code sharing is possible by creating derived classes from the
 derived classes (e.g., to implement an accelerated version of a pair

doc/src/Developer_flow.rst

@@ -128,7 +128,7 @@ reflect particles off box boundaries in the :doc:`FixWallReflect class
 The ``decide()`` method in the Neighbor class determines whether
 neighbor lists need to be rebuilt on the current timestep (conditions
 can be changed using the :doc:`neigh_modify every/delay/check
-<neigh_modify>` command.  If not, coordinates of ghost atoms are
+<neigh_modify>` command).  If not, coordinates of ghost atoms are
 acquired by each processor via the ``forward_comm()`` method of the Comm
 class.  If neighbor lists need to be built, several operations within
 the inner if clause of the pseudocode are first invoked.  The

doc/src/Developer_grid.rst

@@ -433,7 +433,7 @@ from owned to ghost cells, or ghost to owned cells, respectively, as
 described above.  The *caller* argument should be one of these values
 -- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
 depending on the style of the caller class.  The *ptr* argument is the
-"this" pointer to the caller class.  These 2 arguments are used to
+"this" pointer to the caller class.  These two arguments are used to
 call back to pack()/unpack() functions in the caller class, as
 explained below.
 

doc/src/Developer_notes.rst

@@ -20,7 +20,7 @@ Available topics are:
 Reading and parsing of text and text files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-It is frequently required for a class in LAMMPS to read in additional
+Classes in LAMMPS frequently need to read in additional
 data from a file, e.g. potential parameters from a potential file for
 manybody potentials.  LAMMPS provides several custom classes and
 convenience functions to simplify the process.  They offer the
@@ -128,9 +128,8 @@ that determines the kind of neighbor list requested.  The default value
 used here asks for a perpetual "half" neighbor list.
 
 Non-default values of the second argument need to be used to adjust a
-neighbor list request to the specific needs of a style an additional
-request flag is needed.  The :doc:`tersoff <pair_tersoff>` pair style,
-for example, needs a "full" neighbor list:
+neighbor list request to the specific needs of a style.  The :doc:`tersoff
+<pair_tersoff>` pair style, for example, needs a "full" neighbor list:
 
 .. code-block:: c++
 
@@ -141,8 +140,8 @@ for example, needs a "full" neighbor list:
    }
 
 When a pair style supports r-RESPA time integration with different cutoff regions,
-the request flag may depend on the corresponding r-RESPA settings. Here an example
-from pair style lj/cut:
+the request flag may depend on the corresponding r-RESPA settings. Here is an
+example from pair style lj/cut:
 
 .. code-block:: c++
 
@@ -160,7 +159,7 @@ from pair style lj/cut:
    }
 
 Granular pair styles need neighbor lists based on particle sizes and not cutoff
-and also may require to have the list of previous neighbors available ("history").
+and also may need to store data across timesteps ("history").
 For example with:
 
 .. code-block:: c++
@@ -169,7 +168,7 @@ For example with:
    else neighbor->add_request(this, NeighConst::REQ_SIZE);
 
 In case a class would need to make multiple neighbor list requests with different
-settings each request can set an id which is then used in the corresponding
+settings, each request can set an id which is then used in the corresponding
 ``init_list()`` function to assign it to the suitable pointer variable. This is
 done for example by the :doc:`pair style meam <pair_meam>`:
 
@@ -279,8 +278,8 @@ And here is how the code operates:
 * The :doc:`thermo_style custom <thermo_style>` command defines
   *ecouple* and *econserve* keywords.
 * These keywords sum the energy contributions from all the
-  *ecouple_flag* = 1 fixes by invoking the energy_couple() method in
-  the Modify class, which calls the compute_scalar() method of each
+  *ecouple_flag* = 1 fixes by invoking the *energy_couple()* method in
+  the Modify class, which calls the *compute_scalar()* method of each
   fix in the list.
 
 ------------------
@@ -320,19 +319,19 @@ The fix must also do the following:
 
    The ev_init() and ev_tally() methods also account for global and
    peratom virial contributions.  Thus you do not need to invoke the
-   v_init() and v_tally() methods, if the fix also calculates peratom
+   v_init() and v_tally() methods if the fix also calculates peratom
    energies.
 
 The fix must also specify whether (by default) to include or exclude
 these contributions to the global/peratom energy/virial of the system.
-For the fix to include the contributions, set either of both of these
+For the fix to include the contributions, set either or both of these
 variables in the constructor:
 
 * *thermo_energy* = 1, for global and peratom energy
 * *thermo_virial* = 1, for global and peratom virial
 
 Note that these variables are zeroed in fix.cpp.  Thus if you don't
-set the variables, the contributions will be excluded (by default)
+set the variables, the contributions will be excluded (by default).
 
 However, the user has ultimate control over whether to include or
 exclude the contributions of the fix via the :doc:`fix modify
@@ -406,9 +405,11 @@ processor owns, within the global grid:
 
 .. parsed-literal::
 
-   nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
-   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
-   nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
+   nFOO_in = 3d decomposition brick
+   nFOO_fft = FFT decomposition brick
+   nFOO_out = 3d decomposition brick + ghost cells
+
+where ``FOO`` corresponds to ``xlo, xhi, ylo, yhi, zlo,`` or ``zhi``.
 
 The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
 dimension, where N is the grid size.

doc/src/Developer_par_comm.rst

@@ -4,8 +4,7 @@ Communication
 Following the selected partitioning scheme, all per-atom data is
 distributed across the MPI processes, which allows LAMMPS to handle very
 large systems provided it uses a correspondingly large number of MPI
-processes.  Since The per-atom data (atom IDs, positions, velocities,
-types, etc.)  To be able to compute the short-range interactions, MPI
+processes.  To be able to compute the short-range interactions, MPI
 processes need not only access to the data of atoms they "own" but also
 information about atoms from neighboring subdomains, in LAMMPS referred
 to as "ghost" atoms.  These are copies of atoms storing required
@@ -37,7 +36,7 @@ be larger than half the simulation domain.
 
 Efficient communication patterns are needed to update the "ghost" atom
 data, since that needs to be done at every MD time step or minimization
-step.  The diagrams of the `ghost-atom-comm` figure illustrate how ghost
+step.  The diagrams of the :ref:`ghost-atom-comm` figure illustrate how ghost
 atom communication is performed in two stages for a 2d simulation (three
 in 3d) for both a regular and irregular partitioning of the simulation
 box.  For the regular case (left) atoms are exchanged first in the

doc/src/Developer_par_long.rst

@@ -93,7 +93,7 @@ processors, since each tile in the initial tiling overlaps with a
 handful of tiles in the final tiling.
 
 The transformations could also be done using collective communication
-across all $P$ processors with a single call to ``MPI_Alltoall()``, but
+across all :math:`P` processors with a single call to ``MPI_Alltoall()``, but
 this is typically much slower.  However, for the specialized brick and
 pencil tiling illustrated in :ref:`fft-parallel` figure, collective
 communication across the entire MPI communicator is not required.  In
@@ -138,7 +138,7 @@ grid/particle operations that LAMMPS supports:
   :math:`O(P^{\frac{1}{2}})`.
 
 - For efficiency in performing 1d FFTs, the grid transpose
-  operations illustrated in Figure \ref{fig:fft} also involve
+  operations illustrated in Figure :ref:`fft-parallel` also involve
   reordering the 3d data so that a different dimension is contiguous
   in memory.  This reordering can be done during the packing or
   unpacking of buffers for MPI communication.

doc/src/Developer_par_neigh.rst

@@ -149,7 +149,7 @@ supports:
 
 - Dependent on the "pair" setting of the :doc:`newton <newton>` command,
   the "half" neighbor lists may contain **all** pairs of atoms where
-  atom *j* is a ghost atom (i.e. when the newton pair setting is *off*)
+  atom *j* is a ghost atom (i.e. when the newton pair setting is *off*).
   For the newton pair *on* setting the atom *j* is only added to the
   list if its *z* coordinate is larger, or if equal the *y* coordinate
   is larger, and that is equal, too, the *x* coordinate is larger.  For

doc/src/Developer_par_openmp.rst

@@ -1,13 +1,13 @@
 OpenMP Parallelism
 ^^^^^^^^^^^^^^^^^^
 
-The styles in the INTEL, KOKKOS, and OPENMP package offer to use OpenMP
+The styles in the INTEL, KOKKOS, and OPENMP packages offer to use OpenMP
 thread parallelism to predominantly distribute loops over local data
 and thus follow an orthogonal parallelization strategy to the
 decomposition into spatial domains used by the :doc:`MPI partitioning
 <Developer_par_part>`.  For clarity, this section discusses only the
 implementation in the OPENMP package, as it is the simplest. The INTEL
-and KOKKOS package offer additional options and are more complex since
+and KOKKOS packages offer additional options and are more complex since
 they support more features and different hardware like co-processors
 or GPUs.
 
@@ -16,7 +16,7 @@ keep the changes to the source code small, so that it would be easier to
 maintain the code and keep it in sync with the non-threaded standard
 implementation.  This is achieved by a) making the OPENMP version a
 derived class from the regular version (e.g. ``PairLJCutOMP`` from
-``PairLJCut``) and overriding only methods that are multi-threaded or
+``PairLJCut``) and only overriding methods that are multi-threaded or
 need to be modified to support multi-threading (similar to what was done
 in the OPT package), b) keeping the structure in the modified code very
 similar so that side-by-side comparisons are still useful, and c)

doc/src/Developer_plugins.rst

@@ -53,7 +53,7 @@ Members of ``lammpsplugin_t``
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 15 85
 
    * - Member
      - Description
@@ -135,7 +135,7 @@ unique inside the entire LAMMPS executable.
 Fix style example
 ^^^^^^^^^^^^^^^^^
 
-If the factory function would be for a fix or compute, which take three
+If the factory function is for a fix or compute, which take three
 arguments (a pointer to the LAMMPS class, the number of arguments and the
 list of argument strings), then the pointer type is ``lammpsplugin_factory2``
 and it must be assigned to the *creator.v2* member of the plugin struct.
@@ -271,7 +271,7 @@ Plugins need to be compiled with the same compilers and libraries
 as the LAMMPS executable and library.  Otherwise the plugin will likely
 not load due to mismatches in the function signatures (LAMMPS is C++ so
 scope, type, and number of arguments are encoded into the symbol names
-and thus differences in them will lead to failed plugin load commands.
+and thus differences in them will lead to failed plugin load commands).
 Compilation of the plugin can be managed via both, CMake or traditional
 GNU makefiles.  Some examples that can be used as a template are in the
 ``examples/plugins`` folder.  The CMake script code has some small
@@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder.  No changes to the sources of the
 KIM package themselves are needed; only the plugin interface and loader
 code needs to be added.  This example only supports building with CMake,
 but is probably a more typical example. To compile you need to run CMake
-with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
+with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``.  Other
 configuration setting are identical to those for compiling LAMMPS.
 
 A second example for a plugin from a package is in the

doc/src/Developer_unittest.rst

@@ -44,7 +44,7 @@ available:
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 32 18 50
    :align: left
 
    * - File name:
@@ -227,12 +227,12 @@ Tests for the C-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Tests for validating the LAMMPS C-style library interface are in the
-``unittest/c-library`` folder.  They are implemented in either way used
-for utility functions and for LAMMPS commands, but use the functions
+``unittest/c-library`` folder.  They are implemented either to be used
+for utility functions or for LAMMPS commands, but use the functions
 implemented in the ``src/library.cpp`` file as much as possible.  There
 may be some overlap with other tests, but only in as much as is required
 to test the C-style library API.  The tests are distributed over
-multiple test programs which tries to match the grouping of the
+multiple test programs which try to match the grouping of the
 functions in the source code and :ref:`in the manual <lammps_c_api>`.
 
 This group of tests also includes tests invoking LAMMPS in parallel
@@ -258,7 +258,7 @@ Tests for the Python module and package
 
 The ``unittest/python`` folder contains primarily tests for classes and
 functions in the LAMMPS python module but also for commands in the
-PYTHON package.  These tests are only enabled, if the necessary
+PYTHON package.  These tests are only enabled if the necessary
 prerequisites are detected or enabled during configuration and
 compilation of LAMMPS (shared library build enabled, Python interpreter
 found, Python development files found).
@@ -272,7 +272,7 @@ Tests for the Fortran interface
 
 Tests for using the Fortran module are in the ``unittest/fortran``
 folder.  Since they are also using the GoogleTest library, they require
-to also implement test wrappers in C++ that will call fortran functions
+implementing test wrappers in C++ that will call fortran functions
 which provide a C function interface through ISO_C_BINDINGS that will in
 turn call the functions in the LAMMPS Fortran module.
 
@@ -293,7 +293,7 @@ The ``unittest/formats`` folder contains test programs for reading and
 writing files like data files, restart files, potential files or dump files.
 This covers simple things like the file i/o convenience functions in the
 ``utils::`` namespace to complex tests of atom styles where creating and
-deleting of atoms with different properties is tested in different ways
+deleting atoms with different properties is tested in different ways
 and through script commands or reading and writing of data or restart files.
 
 Tests for styles computing or modifying forces
@@ -411,7 +411,7 @@ With this scheme a large fraction of the code of any tested pair style
 will be executed and consistent results are required for different
 settings and between different accelerated pair style variants and the
 base class, as well as for computing individual pairs through the
-``Pair::single()`` where supported.
+``Pair::single()`` method where supported.
 
 The ``test_pair_style`` tester is used with 4 categories of test inputs:
 
@@ -443,7 +443,7 @@ file for a style that is similar to one to be tested.  The file name should
 follow the naming conventions described above and after copying the file,
 the first step is to replace the style names where needed.  The coefficient
 values do not have to be meaningful, just in a reasonable range for the
-given system.  It does not matter if some forces are large, for as long as
+given system.  It does not matter if some forces are large, as long as
 they do not diverge.
 
 The template input files define a large number of index variables at the top
@@ -535,7 +535,7 @@ The are by default no unit tests for newly added features (e.g. pair, fix,
 or compute styles) unless your pull request also includes tests for the
 added features.  If you are modifying some features, you may see failures
 for existing tests, if your modifications have some unexpected side effects
-or your changes render the existing text invalid.  If you are adding an
+or your changes render the existing test invalid.  If you are adding an
 accelerated version of an existing style, then only tests for INTEL,
 KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
 Tests for the GPU package are time consuming and thus are only run
@@ -543,7 +543,7 @@ Tests for the GPU package are time consuming and thus are only run
 to the pull request.  After the test has started, it is often best to
 remove the label since every PR activity will re-trigger the test (that
 is a limitation of triggering a test with a label).  Support for unit
-tests with using KOKKOS with GPU acceleration is currently not supported.
+tests when using KOKKOS with GPU acceleration is currently not supported.
 
 When you see a failed build on GitHub, click on ``Details`` to be taken
 to the corresponding LAMMPS Jenkins CI web page.  Click on the "Exit"
@@ -589,11 +589,10 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
 point operation is at about 2.2e-16, the achievable precision for the
 tests is lower due to most numbers being sums over intermediate results
 and the non-associativity of floating point math leading to larger
-errors.  In some cases specific properties of the tested style.  As a
-rule of thumb, the test epsilon can often be in the range 5.0e-14 to
-1.0e-13.  But for "noisy" force kernels, e.g. those a larger amount of
-arithmetic operations involving `exp()`, `log()` or `sin()` functions,
-and also due to the effect of compiler optimization or differences
+errors.  As a rule of thumb, the test epsilon can often be in the range
+5.0e-14 to 1.0e-13.  But for "noisy" force kernels, e.g. those a larger
+amount of arithmetic operations involving `exp()`, `log()` or `sin()`
+functions, and also due to the effect of compiler optimization or differences
 between compilers or platforms, epsilon may need to be further relaxed,
 sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
 tables are used, epsilon may need to be set to 1.0e-10 or even higher.

doc/src/Developer_updating.rst

@@ -52,10 +52,9 @@ Rename of pack/unpack_comm() to pack/unpack_forward_comm()
 
 .. versionchanged:: 8Aug2014
 
-In this change set the functions to pack data into communication buffers
-and to unpack data from communication buffers for :doc:`forward
-communications <Developer_comm_ops>` were renamed from ``pack_comm()``
-and ``unpack_comm()`` to ``pack_forward_comm()`` and
+In this change set, the functions to pack/unpack data into communication buffers
+for :doc:`forward communications <Developer_comm_ops>` were renamed from
+``pack_comm()`` and ``unpack_comm()`` to ``pack_forward_comm()`` and
 ``unpack_forward_comm()``, respectively.  Also the meaning of the return
 value of these functions was changed: rather than returning the number
 of items per atom stored in the buffer, now the total number of items
@@ -109,7 +108,7 @@ Use ev_init() to initialize variables derived from eflag and vflag
 There are several variables that need to be initialized based on
 the values of the "eflag" and "vflag" variables and since sometimes
 there are new bits added and new variables need to be set to 1 or 0.
-To make this consistent, across all styles, there is now an inline
+To make this consistent across all styles, there is now an inline
 function ``ev_init(eflag, vflag)`` that makes those settings
 consistently and calls either ``ev_setup()`` or ``ev_unset()``.
 Example from a pair style:
@@ -211,14 +210,14 @@ The :cpp:func:`utils::open_potential()
 calls to ``force->open_potential()`` and should be used to replace
 ``fopen()`` for opening potential files for reading.  The custom
 function does three additional steps compared to ``fopen()``: 1) it will
-try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
+try to parse the ``UNITS:`` and ``DATE:`` metadata and will stop with an
 error on a units mismatch and will print the date info, if present, in
 the log file; 2) for pair styles that support it, it will set up
 possible automatic unit conversions based on the embedded unit
 information and LAMMPS' current units setting; 3) it will not only try
 to open a potential file at the given path, but will also search in the
 folders listed in the ``LAMMPS_POTENTIALS`` environment variable.  This
-allows to keep potential files in a common location instead of having to
+allows potential files to reside in a common location instead of having to
 copy them around for simulations.
 
 Old:
@@ -246,36 +245,38 @@ to use scoped enumerators instead.
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 23 10 23 10 23 10
 
    * - Symbolic Constant
      - Value
      - Symbolic Constant
      - Value
+     - Symbolic Constant
+     - Value
    * - Atom::GROW
+     - 0
+     - Atom::ATOMIC
      - 0
      - Atom::MAP_NONE
      - 0
    * - Atom::RESTART
+     - 1
+     - Atom::MOLECULAR
      - 1
      - Atom::MAP_ARRAY
      - 1
    * - Atom::BORDER
+     - 2
+     - Atom::TEMPLATE
      - 2
      - Atom::MAP_HASH
      - 2
-   * - Atom::ATOMIC
+   * - AtomVec::PER_ATOM
      - 0
-     - Atom::MAP_YES
-     - 3
-   * - Atom::MOLECULAR
-     - 1
-     - AtomVec::PER_ATOM
-     - 0
-   * - Atom::TEMPLATE
-     - 2
      - AtomVec::PER_TYPE
      - 1
+     - Atom::MAP_YES
+     - 3
 
 Old:
 
@@ -306,7 +307,7 @@ Simplify customized error messages
 
 Aided by features of the bundled {fmt} library, error messages now
 can have a variable number of arguments and the string will be interpreted
-as a {fmt} style format string so that custom error messages can be
+as a {fmt} style format string so that error messages can be
 easily customized without having to use temporary buffers and ``sprintf()``.
 Example:
 
@@ -332,7 +333,7 @@ Use of "override" instead of "virtual"
 
 .. versionchanged:: 17Feb2022
 
-Since LAMMPS requires C++11 we switched to use the "override" keyword
+Since LAMMPS requires C++11, we switched to use the "override" keyword
 instead of "virtual" to indicate polymorphism in derived classes.  This
 allows the C++ compiler to better detect inconsistencies when an
 override is intended or not.  Please note that "override" has to be
@@ -370,7 +371,7 @@ Simplified function names for forward and reverse communication
 
 .. versionchanged:: 24Mar2022
 
-Rather then using the function name to distinguish between the different
+Rather than using the function name to distinguish between the different
 forward and reverse communication functions for styles, LAMMPS now uses
 the type of the "this" pointer argument.
 

doc/src/Developer_utils.rst

@@ -211,6 +211,9 @@ Argument processing
 .. doxygenfunction:: bounds
    :project: progguide
 
+.. doxygenfunction:: bounds_typelabel
+   :project: progguide
+
 .. doxygenfunction:: expand_args
    :project: progguide
 
@@ -619,7 +622,7 @@ classes:
    of a dense, symmetric, real matrix.
 
 #. The "PEigenDense" class only calculates the principal eigenvalue
-   (ie. the largest or smallest eigenvalue), and its corresponding
+   (i.e. the largest or smallest eigenvalue), and its corresponding
    eigenvector.  However it is much more efficient than "Jacobi" when
    applied to large matrices (larger than 13x13).  PEigenDense also can
    understand complex-valued Hermitian matrices.

doc/src/Developer_write_fix.rst

@@ -74,8 +74,7 @@ The next method we need to implement is ``setmask()``:
 
 Here the we specify which methods of the fix should be called during
 :doc:`execution of a timestep <Developer_flow>`.  The constant
-``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
-important available methods that are called during a timestep.
+``END_OF_STEP`` corresponds to the ``end_of_step()`` method.
 
 .. code-block:: c++
 
@@ -127,7 +126,7 @@ there is no need to inherit from it directly.
 The code above computes average velocity for all particles in the
 simulation.  Yet you have one unused parameter in fix call from the
 script: ``group_name``.  This parameter specifies the group of atoms
-used in the fix. So we should compute average for all particles in the
+used in the fix. So we should compute the average for all particles in the
 simulation only if ``group_name == "all"``, but it can be any group.
 The group membership information of an atom is contained in the *mask*
 property of an atom and the bit corresponding to a given group is
@@ -142,7 +141,7 @@ stored in the groupbit variable which is defined in Fix base class:
    }
 
 Class Atom encapsulates atoms positions, velocities, forces, etc. Users
-can access them using particle index. Note, that particle indexes are
+can access them using the particle index. Note, that particle indexes are
 usually changed every few timesteps because of neighbor list rebuilds
 and spatial sorting (to improve cache efficiency).
 
@@ -154,8 +153,8 @@ this situation there are several methods which should be implemented:
 - ``double memory_usage()``: return how much memory the fix uses (optional)
 - ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
 - ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
-  information to j-th. Used when atom sorting is performed. if delflag is set
-  and atom j owns a body, move the body information to atom i.
+  information to j-th particle position. Used when atom sorting is performed.
+  if delflag is set and atom j owns a body, move the body information to atom i.
 - ``void set_arrays(int i)``: sets i-th particle related information to zero
 
 Note, that if your class implements these methods, it must add calls of
@@ -230,11 +229,11 @@ is just a bunch of template functions for allocating 1D and 2D
 arrays. So you need to add include ``memory.h`` to have access to them.
 
 Finally, if you need to write/read some global information used in
-your fix to the restart file, you might do it by setting flag
-``restart_global = 1`` in the constructor and implementing methods void
-``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
+your fix to the restart file, you might do it by setting the flag
+``restart_global = 1`` in the constructor and implementing methods
+``void write_restart(FILE *fp)`` and ``void restart(char *buf)``.
 If, in addition, you want to write the per-atom property to restart
-files additional settings and functions are needed:
+files then these additional settings and functions are needed:
 
 - a fix flag indicating this needs to be set ``restart_peratom = 1;``
 - ``atom->add_callback()`` and ``atom->delete_callback()`` must be called

doc/src/Developer_write_pair.rst

@@ -50,6 +50,30 @@ We are looking at the following cases:
 - `Case 3: a potential requiring communication`_
 - `Case 4: potentials without a compute() function`_
 
+Package and build system considerations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In general, new pair styles should be added to the :ref:`EXTRA-PAIR
+package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
+then they should be added to the corresponding accelerator package
+(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
+<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`).  If
+you feel that your contribution should be added to a different package,
+please consult with the LAMMPS developers first.
+
+The contributed code needs to support the :doc:`traditional GNU make
+build process <Build_make>` **and** the :doc:`CMake build process
+<Build_cmake>`.  For the GNU make process and if the package has an
+``Install.sh`` file, most likely that file needs to be updated to
+correctly copy the sources when installing the package and properly
+delete them when uninstalling.  This is particularly important when
+added a new pair style that is a derived class from an existing pair
+style in a package, so that its installation depends on the the
+installation status of the package of the derived class.  For the CMake
+process, it is sometimes necessary to make changes to the package
+specific CMake scripting in ``cmake/Modules/Packages``.
+
+
 ----
 
 Case 1: a pairwise additive model
@@ -347,9 +371,9 @@ but moving this to a separate function allows users to change global
 settings like the default cutoff without having to reissue all
 pair_coeff commands or re-read the ``Pair Coeffs`` sections from the
 data file.  In the ``settings()`` function, also the arrays for storing
-parameters, to define cutoffs, track with pairs of parameters have been
-explicitly set are allocated and, if needed, initialized.  In this case,
-the memory allocation and initialization is moved to a function
+parameters, to define cutoffs, track which pairs of parameters have been
+explicitly set and allocated and, if needed, initialized.  In this case,
+the memory allocation and initialization are moved to a function
 ``allocate()``.
 
 .. code-block:: c++
@@ -564,17 +588,20 @@ loop atoms are also initialized.
        jnum = numneigh[i];
 
 The inner loop (index *j*) processes the neighbor lists.  The neighbor
-list code encodes in the upper 2 bits whether a pair is a regular pair
-of neighbor (= 0) or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3)
-:doc:`"special" neighbor <special_bonds>`.  The ``sbmask()`` inline
-function extracts those bits and converts them into a number.  This
-number is used to look up the corresponding scaling factor for the
-non-bonded interaction from the ``force->special_lj`` array and stores
-it in the `factor_lj` variable.  Due to the additional bits, the value
-of *j* would be out of range when accessing data from per-atom arrays,
-so we apply the NEIGHMASK constant with a bit-wise and operation to mask
-them out.  This step *must* be done, even if a pair style does not use
-special bond scaling of forces and energies to avoid segmentation faults.
+list code encodes extra information using the upper 3 bits. The 2
+highest bits encode whether a pair is a regular pair of neighbor (= 0)
+or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3) :doc:`"special" neighbor
+<special_bonds>`.  The next highest bit encodes whether the pair stores
+data in a ``fix neigh/history`` instance (an undocumented internal fix
+style).  The ``sbmask()`` inline function extracts those bits and
+converts them into a number.  This number is used to look up the
+corresponding scaling factor for the non-bonded interaction from the
+``force->special_lj`` array and stores it in the `factor_lj` variable.
+Due to the additional bits, the value of *j* would be out of range when
+accessing data from per-atom arrays, so we apply the NEIGHMASK constant
+with a bit-wise and operation to mask them out.  This step *must* be
+done, even if a pair style does not use special bond scaling of forces
+and energies to avoid segmentation faults.
 
 With the corrected *j* index, it is now possible to compute the distance
 of the pair.  For efficiency reasons, the square root is only taken
@@ -867,7 +894,7 @@ through *multiple* :doc:`pair_coeff commands <pair_coeff>`.  Pair styles
 that require a single "pair_coeff \* \*" command line are not compatible
 with reading their parameters from data files.  For pair styles like
 *born/gauss* that do support writing to data files, the potential
-parameters will be read from the data file, if present and
+parameters will be read from the data file, if present, and
 :doc:`pair_coeff commands <pair_coeff>` may not be needed.
 
 The member variable ``writedata`` should be set to 1 in the constructor,

doc/src/Errors_common.rst

@@ -39,7 +39,8 @@ figure out your physics or numerical mistakes, like choosing too big a
 timestep, specifying erroneous force field coefficients, or putting 2
 atoms on top of each other!  If you run into errors that LAMMPS
 does not catch that you think it should flag, please send an email to
-the `developers <https://www.lammps.org/authors.html>`_.
+the `developers <https://www.lammps.org/authors.html>`_ or create an new
+topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by

doc/src/Errors_messages.rst

@@ -96,13 +96,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    are too far apart to make a valid angle.
 
 *Angle atoms %d %d %d missing on proc %d at step %ld*
-   One or more of 3 atoms needed to compute a particular angle are
+   One or more of three atoms needed to compute a particular angle are
    missing on this processor.  Typically this is because the pairwise
    cutoff is set too short or the angle has blown apart and an atom is
    too far away.
 
 *Angle atoms missing on proc %d at step %ld*
-   One or more of 3 atoms needed to compute a particular angle are
+   One or more of three atoms needed to compute a particular angle are
    missing on this processor.  Typically this is because the pairwise
    cutoff is set too short or the angle has blown apart and an atom is
    too far away.
@@ -1932,7 +1932,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Compute chunk/atom fix array is accessed out-of-range*
-   the index for the array is out of bounds.
+   The index for the array is out of bounds.
 
 *Compute chunk/atom fix does not calculate a per-atom array*
    Self-explanatory.
@@ -6073,9 +6073,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *New atom IDs exceed maximum allowed ID*
    See the setting for tagint in the src/lmptype.h file.
 
-*New bond exceeded bonds per atom in create_bonds*
-See the read_data command for info on using the "extra/bond/per/atom"
-keyword to allow for additional bonds to be formed
+*New bond exceeded bonds per atom in create\_bonds*
+   See the read_data command for info on using the "extra/bond/per/atom"
+   keyword to allow for additional bonds to be formed
 
 *New bond exceeded bonds per atom in fix bond/create*
    See the read_data command for info on using the "extra/bond/per/atom"
@@ -7310,12 +7310,12 @@ keyword to allow for additional bonds to be formed
    atom has moved too far.
 
 *Restrain atoms %d %d %d missing on proc %d at step %ld*
-   The 3 atoms in a restrain angle specified by the fix restrain
+   The three atoms in a restrain angle specified by the fix restrain
    command are not all accessible to a processor.  This probably means an
    atom has moved too far.
 
 *Restrain atoms %d %d missing on proc %d at step %ld*
-   The 2 atoms in a restrain bond specified by the fix restrain
+   The two atoms in a restrain bond specified by the fix restrain
    command are not all accessible to a processor.  This probably means an
    atom has moved too far.
 
@@ -7406,7 +7406,7 @@ keyword to allow for additional bonds to be formed
 *Shake angles have different bond types*
    All 3-atom angle-constrained SHAKE clusters specified by the fix shake
    command that are the same angle type, must also have the same bond
-   types for the 2 bonds in the angle.
+   types for the two bonds in the angle.
 
 *Shake atoms %d %d %d %d missing on proc %d at step %ld*
    The 4 atoms in a single shake cluster specified by the fix shake
@@ -7414,12 +7414,12 @@ keyword to allow for additional bonds to be formed
    an atom has moved too far.
 
 *Shake atoms %d %d %d missing on proc %d at step %ld*
-   The 3 atoms in a single shake cluster specified by the fix shake
+   The three atoms in a single shake cluster specified by the fix shake
    command are not all accessible to a processor.  This probably means
    an atom has moved too far.
 
 *Shake atoms %d %d missing on proc %d at step %ld*
-   The 2 atoms in a single shake cluster specified by the fix shake
+   The two atoms in a single shake cluster specified by the fix shake
    command are not all accessible to a processor.  This probably means
    an atom has moved too far.
 

doc/src/Errors_warnings.rst

@@ -23,7 +23,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    adjusted to match the user-specified accuracy.
 
 *Angle atoms missing at step %ld*
-   One or more of 3 atoms needed to compute a particular angle are
+   One or more of three atoms needed to compute a particular angle are
    missing on this processor.  Typically this is because the pairwise
    cutoff is set too short or the angle has blown apart and an atom is
    too far away.
@@ -233,7 +233,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    style.
 
 *Fix langevin gjf using random gaussians is not implemented with kokkos*
-This will most likely cause errors in kinetic fluctuations.
+   This will most likely cause errors in kinetic fluctuations.
 
 *Fix property/atom mol or charge w/out ghost communication*
    A model typically needs these properties defined for ghost atoms.
@@ -324,7 +324,7 @@ This will most likely cause errors in kinetic fluctuations.
    Specifically they are further apart than half a periodic box length.
    Or they are more than a box length apart in a non-periodic dimension.
    This is usually due to the initial data file not having correct image
-   flags for the 2 atoms in a bond that straddles a periodic boundary.
+   flags for the two atoms in a bond that straddles a periodic boundary.
    They should be different by 1 in that case.  This is a warning because
    inconsistent image flags will not cause problems for dynamics or most
    LAMMPS simulations.  However they can cause problems when such atoms

doc/src/Examples.rst

@@ -134,6 +134,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | rerun       | use of rerun and read_dump commands                              |
 +-------------+------------------------------------------------------------------+
+| rheo        | RHEO simulations of fluid flows and phase transitions            |
++-------------+------------------------------------------------------------------+
 | rigid       | rigid bodies modeled as independent or coupled                   |
 +-------------+------------------------------------------------------------------+
 | shear       | sideways shear applied to 2d solid, with and without a void      |

doc/src/Fortran.rst

@@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype extract_setting: function
    :f extract_global: :f:func:`extract_global`
    :ftype extract_global: function
+   :f map_atom: :f:func:`map_atom`
+   :ftype map_atom: function
    :f extract_atom: :f:func:`extract_atom`
    :ftype extract_atom: function
    :f extract_compute: :f:func:`extract_compute`
@@ -1075,7 +1077,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. list-table::
       :header-rows: 1
-      :widths: auto
+      :widths: 21 20 40 19
 
       * - Style
         - Type
@@ -1165,7 +1167,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. list-table::
       :header-rows: 1
-      :widths: auto
+      :widths: 20 19 11 11 21 18
 
       * - Style
         - Type
@@ -2325,7 +2327,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    retrieved via :f:func:`get_last_error_message`.  This allows to
    restart a calculation or delete and recreate the LAMMPS instance when
    a C++ exception occurs.  One application of using exceptions this way
-   is the :ref:`lammps_shell`.
+   is the :ref:`lammps_gui`.
 
    :to: :cpp:func:`lammps_config_has_exceptions`
    :r has_exceptions:

doc/src/Howto.rst

@@ -89,6 +89,7 @@ Packages howto
    Howto_drude2
    Howto_peri
    Howto_manifold
+   Howto_rheo
    Howto_spins
 
 Tutorials howto

doc/src/Howto_bioFF.rst

@@ -1,6 +1,10 @@
 CHARMM, AMBER, COMPASS, and DREIDING force fields
 =================================================
 
+A compact summary of the concepts, definitions, and properties of
+force fields with explicit bonded interactions (like the ones discussed
+in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
+
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly used
@@ -11,12 +15,42 @@ commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
 <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
 additional tools that can use CHARMM, AMBER, or Materials Studio
 generated files to assign force field coefficients and convert their
-output into LAMMPS input.
+output into LAMMPS input. LAMMPS input scripts can also be generated by
+`charmm-gui.org <https://charmm-gui.org/>`_.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
-force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
-the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
-of the COMPASS force field.
+CHARMM and AMBER
+----------------
+
+The `CHARMM force field
+<https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref:`(MacKerell)
+<howto-MacKerell>` and `AMBER force field
+<https://ambermd.org/AmberModels.php>`_ :ref:`(Cornell) <howto-Cornell>`
+have potential energy function of the form
+
+.. math::
+
+  V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
+         \text{charmm} \\
+        \text{charmmfsw}
+      }} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
+      & \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
+         \text{lj/charmm/coul/charmm} \\
+        \text{lj/charmm/coul/charmm/implicit} \\
+        \text{lj/charmm/coul/long} \\
+        \text{lj/charmm/coul/msm} \\
+         \text{lj/charmmfsw/coul/charmmfsh} \\
+        \text{lj/charmmfsw/coul/long}
+      }} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
+
+
+The terms are computed by bond styles (relationship between two atoms),
+angle styles (between 3 atoms) , dihedral/improper styles (between 4
+atoms), pair styles (non-covalently bonded pair interactions) and
+special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for
+details) corrects for pairs of dihedral angles ("Correction MAP") to
+significantly improve the structural and dynamic properties of proteins
+in crystalline and solution environments :ref:`(Brooks)
+<howto-Brooks>`. The AMBER force field does not include the CMAP term.
 
 The interaction styles listed below compute force field formulas that
 are consistent with common options in CHARMM or AMBER.  See each
@@ -31,10 +65,81 @@ command's documentation for the formula it computes.
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
-
 * :doc:`special_bonds <special_bonds>` charmm
 * :doc:`special_bonds <special_bonds>` amber
 
+The pair styles compute Lennard Jones (LJ) and Coulombic interactions
+with additional switching or shifting functions that ramp the energy
+and/or force smoothly to zero between an inner :math:`(a)` and outer
+:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
+*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
+with an energy switching function (esw) :math:`S(r)` which ramps the energy
+smoothly to zero between the inner and outer cutoff. This can cause
+irregularities in pairwise forces (due to the discontinuous second
+derivative of energy at the boundaries of the switching region), which
+in some cases can result in complications in energy minimization and
+detectable artifacts in MD simulations.
+
+.. grid:: 1 1 2 2
+
+   .. grid-item::
+
+      .. math::
+
+         LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+                  \left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
+         C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
+         S(r) &=  \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)}
+                 { \left(b^2 - a^2\right)^3 }\\[.6em]
+         E_{LJ}(r) &=  \begin{cases}
+           LJ(r), & r \leq a \\
+           LJ(r) S(r), & a < r \leq b \\
+           0, &r > b
+         \end{cases} \\[.6em]
+         E_{coul}(r) &=  \begin{cases}
+           C(r), & r \leq a \\
+           C(r) S(r), & a < r \leq b \\
+           0, & r > b
+         \end{cases}
+
+   .. grid-item::
+
+      .. image:: img/howto_charmm_ELJ.png
+         :align: center
+
+The newer styles with *charmmfsw* or *charmmfsh* in their name replace
+energy switching with force switching (fsw) for LJ interactions and
+force shifting (fsh) functions for Coulombic interactions
+:ref:`(Steinbach) <howto-Steinbach>`
+
+.. grid:: 1 1 2 2
+
+   .. grid-item::
+
+      .. math::
+
+           E_{LJ}(r) = & \begin{cases}
+       4  \epsilon \sigma^6  \left(\frac{\displaystyle\sigma
+         ^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
+         b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
+       \frac{\displaystyle 4 \epsilon \sigma^6   \left(\sigma ^6
+         \left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
+         \left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
+         \left(b^6-a^6\right)} & a<r \leq b\\
+         0, & r>b
+        \end{cases}\\[.6em]
+         E_{coul}(r) & =  \begin{cases}
+              C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, &  r \leq b \\
+              0, & r > b
+            \end{cases}
+
+   .. grid-item::
+      .. image:: img/howto_charmmfsw_ELJ.png
+         :align: center
+
+These styles are used by LAMMPS input scripts generated by
+https://charmm-gui.org/ :ref:`(Brooks) <howto-Brooks>`.
+
 .. note::
 
    For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
@@ -43,17 +148,33 @@ command's documentation for the formula it computes.
    <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
    pages.
 
+.. note::
+
+  The TIP3P water model is strongly recommended for use with the CHARMM
+  force field. In fact, `"using the SPC model with CHARMM parameters is
+  a bad idea"
+  <https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to
+  enable TIP4P style water in CHARMM, you would have to write a new pair
+  style"
+  <https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_
+  . LAMMPS input scripts generated by Solution Builder on https://charmm-gui.org
+  use TIP3P molecules for solvation.  Any other water model can and
+  probably will lead to false conclusions.
+
+COMPASS
+-------
+
 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>` 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
-provided force field files, especially additions during the last decade.
-You should watch the output carefully and compare results, where
-possible.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
-field.
+developed using ab initio and empirical parameterization techniques
+:ref:`(Sun) <howto-Sun>`.  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 provided force field files, especially additions
+during the last decade.  You should watch the output carefully and
+compare results, where possible.  See :ref:`(Sun) <howto-Sun>` for a
+description of the COMPASS force field.
 
 These interaction styles listed below compute force field formulas that
 are consistent with the COMPASS force field.  See each command's
@@ -70,14 +191,21 @@ documentation for the formula it computes.
 
 * :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
 
-DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
-predicting structures and dynamics of organic, biological and main-group
-inorganic molecules. The philosophy in DREIDING is to use general force
-constants and geometry parameters based on simple hybridization
-considerations, rather than individual force constants and geometric
-parameters that depend on the particular combinations of atoms involved
-in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
-hydrogen atom on very electronegative atoms (N, O, F).
+DREIDING
+--------
+
+DREIDING is a generic force field developed by the `Goddard group
+<http://www.wag.caltech.edu>`_ at Caltech and is useful for predicting
+structures and dynamics of organic, biological and main-group inorganic
+molecules.  The philosophy in DREIDING is to use general force constants
+and geometry parameters based on simple hybridization considerations,
+rather than individual force constants and geometric parameters that
+depend on the particular combinations of atoms involved in the bond,
+angle, or torsion terms.  DREIDING has an :doc:`explicit hydrogen bond
+term <pair_hbond_dreiding>` to describe interactions involving a
+hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM
+or AMBER, the DREIDING force field has not been parameterized for
+considering solvents (like water).
 
 See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
 
@@ -110,21 +238,31 @@ documentation for the formula it computes.
 
 ----------
 
+.. _Typelabel2:
+
+**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
+
 .. _howto-MacKerell:
 
-**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
-Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998).  J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f
 
 .. _howto-Cornell:
 
-**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
-Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995).  JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002
+
+.. _howto-Steinbach:
+
+**(Steinbach)** Steinbach, Brooks (1994). J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702
+
+.. _howto-Brooks:
+
+**(Brooks)** Brooks, et al (2009). J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287
 
 .. _howto-Sun:
 
-**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
+**(Sun)** Sun (1998). J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v
 
 .. _howto-Mayo:
 
-**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).
+**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
+

doc/src/Howto_bpm.rst

@@ -15,7 +15,10 @@ orientation for rotational models. This produces a stress-free initial
 state. Furthermore, bonds are allowed to break under large strains,
 producing fracture. The examples/bpm directory has sample input scripts
 for simulations of the fragmentation of an impacted plate and the
-pouring of extended, elastic bodies.
+pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
+for more general information on the approach and the LAMMPS implementation.
+Example movies illustrating some of these capabilities are found at
+https://www.lammps.org/movies.html#bpmpackage.
 
 ----------
 
@@ -150,3 +153,9 @@ the following are currently compatible with BPM bond styles:
    interactions, one will need to switch between different *special_bonds*
    settings in the input script. An example is found in
    ``examples/bpm/impact``.
+
+----------
+
+.. _howto-Clemmer:
+
+**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

doc/src/Howto_chunk.rst

@@ -1,7 +1,7 @@
 Use chunks to calculate system properties
 =========================================
 
-In LAMMS, "chunks" are collections of atoms, as defined by the
+In LAMMPS, "chunks" are collections of atoms, as defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
 each atom to a chunk ID (or to no chunk at all).  The number of chunks
 and the assignment of chunk IDs to atoms can be static or change over
@@ -148,14 +148,14 @@ Example calculations with chunks
 Here are examples using chunk commands to calculate various
 properties:
 
-(1) Average velocity in each of 1000 2d spatial bins:
+1. Average velocity in each of 1000 2d spatial bins:
 
 .. code-block:: LAMMPS
 
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
    fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
 
-(2) Temperature in each spatial bin, after subtracting a flow
+2. Temperature in each spatial bin, after subtracting a flow
 velocity:
 
 .. code-block:: LAMMPS
@@ -164,7 +164,7 @@ velocity:
    compute vbias all temp/profile 1 0 0 y 10
    fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
 
-(3) Center of mass of each molecule:
+3. Center of mass of each molecule:
 
 .. code-block:: LAMMPS
 
@@ -172,7 +172,7 @@ velocity:
    compute myChunk all com/chunk cc1
    fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
 
-(4) Total force on each molecule and ave/max across all molecules:
+4. Total force on each molecule and ave/max across all molecules:
 
 .. code-block:: LAMMPS
 
@@ -183,7 +183,7 @@ velocity:
    thermo 1000
    thermo_style custom step temp v_xave v_xmax
 
-(5) Histogram of cluster sizes:
+5. Histogram of cluster sizes:
 
 .. code-block:: LAMMPS
 
@@ -192,16 +192,16 @@ velocity:
    compute size all property/chunk cc1 count
    fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
 
-(6) An example for using a per-chunk value to apply per-atom forces to
+6. An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
 
-(7) An example for using one set of per-chunk values for molecule
+7. An example for using one set of per-chunk values for molecule
 chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the
 :doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
 
-(8) An example for using one set of per-chunk values (dipole moment
+8. An example for using one set of per-chunk values (dipole moment
 vectors) for molecule chunks, spreading the values to each atom in
 each chunk, then defining a second set of chunks as spatial bins, and
 using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

doc/src/Howto_cmake.rst

@@ -339,8 +339,6 @@ Some common LAMMPS specific variables
      - build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
    * - ``BUILD_TOOLS``
      - compile some additional executables from the ``tools`` folder (default: ``off``)
-   * - ``BUILD_LAMMPS_SHELL``
-     - compile the LAMMPS shell from the ``tools/lammps-shell`` folder (default: ``off``)
    * - ``BUILD_DOC``
      - include building the HTML format documentation for packaging/installing (default: ``off``)
    * - ``CMAKE_TUNE_FLAGS``

doc/src/Howto_coreshell.rst

@@ -178,7 +178,7 @@ the pairs.  This can be done by using the *bias* keyword of the
 To maintain the correct polarizability of the core/shell pairs, the
 kinetic energy of the internal motion shall remain nearly constant.
 Therefore the choice of spring force and mass ratio need to ensure
-much faster relative motion of the 2 atoms within the core/shell pair
+much faster relative motion of the two atoms within the core/shell pair
 than their center-of-mass velocity. This allows the shells to
 effectively react instantaneously to the electrostatic environment and
 limits energy transfer to or from the core/shell oscillators.

doc/src/Howto_couple.rst

@@ -36,7 +36,7 @@ the context of your application.
    steps, invoke the command, etc.
 
    In this scenario, the other code can be called as a library, as in
-   1., or it could be a stand-alone code, invoked by a system() call
+   1., or it could be a stand-alone code, invoked by a ``system()`` call
    made by the command (assuming your parallel machine allows one or
    more processors to start up another program).  In the latter case the
    stand-alone code could communicate with LAMMPS through files that the

doc/src/Howto_diffusion.rst

@@ -1,8 +1,8 @@
 Calculate diffusion coefficients
 ================================
 
-The diffusion coefficient D of a material can be measured in at least
-2 ways using various options in LAMMPS.  See the examples/DIFFUSE
+The diffusion coefficient :math:`D` of a material can be measured in at least
+2 ways using various options in LAMMPS.  See the ``examples/DIFFUSE``
 directory for scripts that implement the 2 methods discussed here for
 a simple Lennard-Jones fluid model.
 
@@ -12,7 +12,7 @@ of the MSD versus time is proportional to the diffusion coefficient.
 The instantaneous MSD values can be accumulated in a vector via the
 :doc:`fix vector <fix_vector>` command, and a line fit to the vector to
 compute its slope via the :doc:`variable slope <variable>` function, and
-thus extract D.
+thus extract :math:`D`.
 
 The second method is to measure the velocity auto-correlation function
 (VACF) of the system, via the :doc:`compute vacf <compute_vacf>`
@@ -20,4 +20,4 @@ command.  The time-integral of the VACF is proportional to the
 diffusion coefficient.  The instantaneous VACF values can be
 accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
 and time integrated via the :doc:`variable trap <variable>` function,
-and thus extract D.
+and thus extract :math:`D`.

doc/src/Howto_elastic.rst

@@ -4,21 +4,27 @@ Calculate elastic constants
 Elastic constants characterize the stiffness of a material. The formal
 definition is provided by the linear relation that holds between the
 stress and strain tensors in the limit of infinitesimal deformation.
-In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where
-the repeated indices imply summation. s_ij are the elements of the
-symmetric stress tensor. e_kl are the elements of the symmetric strain
-tensor. C_ijkl are the elements of the fourth rank tensor of elastic
-constants. In three dimensions, this tensor has 3\^4=81 elements. Using
-Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
-is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
-derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
-most 7\*6/2 = 21 distinct elements.
+In tensor notation, this is expressed as
+
+.. math::
+
+   s_{ij} = C_{ijkl} e_{kl}
+
+where
+the repeated indices imply summation. :math:`s_{ij}` are the elements of the
+symmetric stress tensor. :math:`e_{kl}` are the elements of the symmetric strain
+tensor. :math:`C_{ijkl}` are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has :math:`3^4=81` elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where :math:`C_{ij}`
+is now the derivative of :math:`s_i` w.r.t. :math:`e_j`. Because :math:`s_i` is itself a
+derivative w.r.t. :math:`e_i`, it follows that :math:`C_{ij}` is also symmetric, with at
+most :math:`\frac{7 \times 6}{2}` = 21 distinct elements.
 
 At zero temperature, it is easy to estimate these derivatives by
 deforming the simulation box in one of the six directions using the
 :doc:`change_box <change_box>` command and measuring the change in the
 stress tensor. A general-purpose script that does this is given in the
-examples/ELASTIC directory described on the :doc:`Examples <Examples>`
+``examples/ELASTIC`` directory described on the :doc:`Examples <Examples>`
 doc page.
 
 Calculating elastic constants at finite temperature is more
@@ -33,7 +39,7 @@ the :doc:`compute born/matrix <compute_born_matrix>` command,
 which works for any bonded or non-bonded potential in LAMMPS.
 The most expensive part of the calculation is the sampling of
 the stress fluctuations. Several examples of this method are
-provided in the examples/ELASTIC_T/BORN_MATRIX directory
+provided in the ``examples/ELASTIC_T/BORN_MATRIX`` directory
 described on the :doc:`Examples <Examples>` doc page.
 
 A second way is to measure
@@ -43,7 +49,7 @@ the systematic and statistical errors in this method, the magnitude of
 the deformation must be chosen judiciously, and care must be taken to
 fully equilibrate the deformed cell before sampling the stress
 tensor. An example of this method is provided in the
-examples/ELASTIC_T/DEFORMATION directory
+``examples/ELASTIC_T/DEFORMATION`` directory
 described on the :doc:`Examples <Examples>` doc page.
 
 Another approach is to sample the triclinic cell fluctuations

doc/src/Howto_kappa.rst

@@ -1,20 +1,22 @@
 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
+The thermal conductivity :math:`\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>` page for an analogous discussion
 for viscosity.
 
-The thermal conductivity tensor kappa is a measure of the propensity
+The thermal conductivity tensor :math:`\mathbf{\kappa}` is a measure of the propensity
 of a material to transmit heat energy in a diffusive manner as given
 by Fourier's law
 
-J = -kappa grad(T)
+.. math::
 
-where J is the heat flux in units of energy per area per time and
-grad(T) is the spatial gradient of temperature.  The thermal
+   J = -\kappa \cdot \text{grad}(T)
+
+where :math:`J` is the heat flux in units of energy per area per time and
+:math:`\text{grad}(T)` is the spatial gradient of temperature.  The thermal
 conductivity thus has units of energy per distance per time per degree
 K and is often approximated as an isotropic quantity, i.e. as a
 scalar.
@@ -49,7 +51,7 @@ details.
 
 The fourth method is based on the Green-Kubo (GK) formula which
 relates the ensemble average of the auto-correlation of the heat flux
-to kappa.  The heat flux can be calculated from the fluctuations of
+to :math:`\kappa`.  The heat flux can be calculated from the fluctuations of
 per-atom potential and kinetic energies and per-atom stress tensor in
 a steady-state equilibrated simulation.  This is in contrast to the
 two preceding non-equilibrium methods, where energy flows continuously

doc/src/Howto_moltemplate.rst

@@ -367,5 +367,4 @@ And execute the simulation with the following:
 
 .. _OPLSAA96:
 
-**(OPLS-AA)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
-118(45), 11225-11236 (1996).
+**(OPLS-AA)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).

doc/src/Howto_multiple.rst

@@ -44,7 +44,7 @@ For large numbers of independent simulations, you can use
 :doc:`variables <variable>` and the :doc:`next <next>` and
 :doc:`jump <jump>` commands to loop over the same input script
 multiple times with different settings.  For example, this
-script, named in.polymer
+script, named ``in.polymer``
 
 .. code-block:: LAMMPS
 
@@ -57,7 +57,7 @@ script, named in.polymer
    next d
    jump in.polymer
 
-would run 8 simulations in different directories, using a data.polymer
+would run 8 simulations in different directories, using a ``data.polymer``
 file in each directory.  The same concept could be used to run the
 same system at 8 different temperatures, using a temperature variable
 and storing the output in different log and dump files, for example
@@ -83,10 +83,10 @@ partition of processors.  LAMMPS can be run on multiple partitions via
 the :doc:`-partition command-line switch <Run_options>`.
 
 In the last 2 examples, if LAMMPS were run on 3 partitions, the same
-scripts could be used if the "index" and "loop" variables were
+scripts could be used if the ``index`` and ``loop`` variables were
 replaced with *universe*\ -style variables, as described in the
-:doc:`variable <variable>` command.  Also, the "next t" and "next a"
-commands would need to be replaced with a single "next a t" command.
+:doc:`variable <variable>` command.  Also, the :lammps:`next t` and :lammps:`next a`
+commands would need to be replaced with a single :lammps:`next a t` command.
 With these modifications, the 8 simulations of each script would run
 on the 3 partitions one after the other until all were finished.
 Initially, 3 simulations would be started simultaneously, one on each

doc/src/Howto_pylammps.rst

@@ -6,19 +6,22 @@ PyLammps Tutorial
 Overview
 --------
 
-``PyLammps`` is a Python wrapper class for LAMMPS which can be created
-on its own or use an existing lammps Python object.  It creates a simpler,
+:py:class:`PyLammps <lammps.PyLammps>` is a Python wrapper class for
+LAMMPS which can be created on its own or use an existing
+:py:class:`lammps Python <lammps.lammps>` object.  It creates a simpler,
 more "pythonic" interface to common LAMMPS functionality, in contrast to
-the ``lammps`` wrapper for the C-style LAMMPS library interface which
-is written using `Python ctypes <ctypes_>`_.  The ``lammps`` wrapper
-is discussed on the :doc:`Python_head` doc page.
+the :py:class:`lammps <lammps.lammps>` wrapper for the LAMMPS :ref:`C
+language library interface API <lammps_c_api>` which is written using
+`Python ctypes <ctypes_>`_.  The :py:class:`lammps <lammps.lammps>`
+wrapper is discussed on the :doc:`Python_head` doc page.
 
-Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable
-API.  It no longer requires knowledge of the underlying C++ code
-implementation.  Finally, the ``IPyLammps`` wrapper builds on top of
-``PyLammps`` and adds some additional features for
-`IPython integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_,
-e.g. for embedded visualization output from :doc:`dump style image <dump_image>`.
+Unlike the flat `ctypes <ctypes_>`_ interface, PyLammps exposes a
+discoverable API.  It no longer requires knowledge of the underlying C++
+code implementation.  Finally, the :py:class:`IPyLammps
+<lammps.IPyLammps>` wrapper builds on top of :py:class:`PyLammps
+<lammps.PyLammps>` and adds some additional features for `IPython
+integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for
+embedded visualization output from :doc:`dump style image <dump_image>`.
 
 .. _ctypes: https://docs.python.org/3/library/ctypes.html
 .. _ipython: https://ipython.org/
@@ -30,19 +33,22 @@ Comparison of lammps and PyLammps interfaces
 lammps.lammps
 """""""""""""
 
-* uses ``ctypes``
-* direct memory access to native C++ data
+* uses `ctypes <ctypes_>`_
+* direct memory access to native C++ data with optional support for NumPy arrays
 * provides functions to send and receive data to LAMMPS
+* interface modeled after the LAMMPS :ref:`C language library interface API <lammps_c_api>`
 * requires knowledge of how LAMMPS internally works (C pointers, etc)
+* full support for running Python with MPI using `mpi4py <https://mpi4py.readthedocs.io>`_
 
 lammps.PyLammps
 """""""""""""""
 
-* higher-level abstraction built on top of original ctypes interface
+* higher-level abstraction built on *top* of original :py:class:`ctypes based interface <lammps.lammps>`
 * manipulation of Python objects
 * communication with LAMMPS is hidden from API user
 * shorter, more concise Python
 * better IPython integration, designed for quick prototyping
+* designed for serial execution
 
 Quick Start
 -----------
@@ -506,14 +512,26 @@ inside of the IPython notebook.
 Using PyLammps and mpi4py (Experimental)
 ----------------------------------------
 
-PyLammps can be run in parallel using mpi4py. This python package can be installed using
+PyLammps can be run in parallel using `mpi4py
+<https://mpi4py.readthedocs.io>`_. This python package can be installed
+using
 
 .. code-block:: bash
 
    pip install mpi4py
 
-The following is a short example which reads in an existing LAMMPS input file and
-executes it in parallel.  You can find in.melt in the examples/melt folder.
+.. warning::
+
+   Usually, any :py:class:`PyLammps <lammps.PyLammps>` command must be
+   executed by *all* MPI processes. However, evaluations and querying
+   the system state is only available on MPI rank 0.  Using these
+   functions from other MPI ranks will raise an exception.
+
+The following is a short example which reads in an existing LAMMPS input
+file and executes it in parallel.  You can find in.melt in the
+examples/melt folder.  Please take note that the
+:py:meth:`PyLammps.eval() <lammps.PyLammps.eval>` is called only from
+MPI rank 0.
 
 .. code-block:: python
 
@@ -535,10 +553,6 @@ following mpirun command:
 
    mpirun -np 4 python melt.py
 
-.. warning::
-
-   Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
-
 Feedback and Contributing
 -------------------------
 

doc/src/Howto_restart.rst

@@ -26,8 +26,8 @@ scripts are based on.  If that script had the line
 
    restart         50 tmp.restart
 
-added to it, it would produce 2 binary restart files (tmp.restart.50
-and tmp.restart.100) as it ran.
+added to it, it would produce two binary restart files (``tmp.restart.50``
+and ``tmp.restart.100``) as it ran.
 
 This script could be used to read the first restart file and re-run the
 last 50 timesteps:
@@ -47,21 +47,21 @@ last 50 timesteps:
    run             50
 
 Note that the following commands do not need to be repeated because
-their settings are included in the restart file: *units, atom_style,
-special_bonds, pair_style, bond_style*.  However, these commands do
+their settings are included in the restart file: :lammps:`units`, :lammps:`atom_style`,
+:lammps:`special_bonds`, :lammps:`pair_style`, :lammps:`bond_style`.  However, these commands do
 need to be used, since their settings are not in the restart file:
-*neighbor, fix, timestep*\ .
+:lammps:`neighbor`, :lammps:`fix`, :lammps:`timestep`.
 
 If you actually use this script to perform a restarted run, you will
 notice that the thermodynamic data match at step 50 (if you also put a
-"thermo 50" command in the original script), but do not match at step
+:lammps:`thermo 50` command in the original script), but do not match at step
 100.  This is because the :doc:`fix langevin <fix_langevin>` command
 uses random numbers in a way that does not allow for perfect restarts.
 
 As an alternate approach, the restart file could be converted to a data
 file as follows:
 
-.. code-block:: LAMMPS
+.. code-block:: bash
 
    lmp_g++ -r tmp.restart.50 tmp.restart.data
 
@@ -89,8 +89,8 @@ Then, this script could be used to re-run the last 50 steps:
    reset_timestep  50
    run             50
 
-Note that nearly all the settings specified in the original *in.chain*
-script must be repeated, except the *pair_coeff* and *bond_coeff*
+Note that nearly all the settings specified in the original ``in.chain``
+script must be repeated, except the :lammps:`pair_coeff` and :lammps:`bond_coeff`
 commands, since the new data file lists the force field coefficients.
 Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
 LAMMPS the current timestep.  This value is stored in restart files, but

doc/src/Howto_rheo.rst

@@ -0,0 +1,112 @@
+Reproducing hydrodynamics and elastic objects (RHEO)
+====================================================
+
+The RHEO package is a hybrid implementation of smoothed particle
+hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
+<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
+mesh-free modeling of multi-phase material systems. Its SPH solver supports
+many advanced options including reproducing kernels, particle shifting, free
+surface identification, and solid surface reconstruction. To model fluid-solid
+systems, the status of particles can dynamically change between a fluid and
+solid state, e.g. during melting/solidification, which determines how they
+interact and their physical behavior. The package is designed with modularity
+in mind, so one can easily turn various features on/off, adjust physical
+details of the system, or develop new capabilities. For instance, the numerics
+associated with calculating gradients, reproducing kernels, etc. are separated
+into distinct classes to simplify the development of new integration schemes
+which can call these calculations. Additional numerical details can be found in
+:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
+capabilities are found at https://www.lammps.org/movies.html#rheopackage.
+
+Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
+<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
+features and therefore benefits from improved performance. The :ref:`MACHDYN
+<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
+
+----------
+
+At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
+particle trajectories and controls many optional features (e.g. the use
+of reproducing kernels). In conjunction to fix rheo, one must specify an
+instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
+of state and viscosity model, respectively. Optionally, one can model
+a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
+allows the user to specify equations for a particle's thermal conductivity,
+specific heat, latent heat, and melting temperature. The ordering of these
+fixes in an an input script matters. Fix rheo must be defined prior to all
+other RHEO fixes.
+
+Typically, RHEO requires atom style rheo. In addition to typical atom
+properties like positions and forces, particles store a local density,
+viscosity, pressure, and status. If thermal evolution is modeled, one must
+use atom style rheo/thermal which also includes a local energy, temperature, and
+conductivity. Note that the temperature is always derived from the energy.
+This implies the *temperature* attribute of :doc:`the set command <set>` does not
+affect particles. Instead, one should use the *sph/e* attribute.
+
+The status variable uses bit-masking to track various properties of a particle
+such as its current state of matter (fluid or solid) and its location relative
+to a surface. Some of these properties (and others) can be accessed using
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
+attribute in :doc:`the set command <set>` only allows control over the first bit
+which sets the state of matter, 0 is fluid and 1 is solid.
+
+Fluid interactions, including pressure forces, viscous forces, and heat exchange,
+are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
+pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
+it determines whether to calculate forces based on the status of particles: e.g.,
+hydrodynamic forces are only calculated if a fluid particle is involved.
+
+----------
+
+To model elastic objects, there are currently two mechanisms in RHEO, one designed
+for bulk solid bodies and the other for thin shells. Both mechanisms rely on
+introducing bonded forces between particles and therefore require a hybrid of atom
+style bond and rheo (or rheo/thermal).
+
+To create an elastic solid body, one has to (a) change the status of constituent
+particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
+bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
+more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
+apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
+pair rheo/solid considers a particles fluid/solid phase to determine whether to
+apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
+settings such that contact forces do not have to be calculated between two bonded
+solid particles in the same elastic body.
+
+In systems with thermal evolution, fix rheo/thermal can optionally set a
+melting/solidification temperature allowing particles to dynamically swap their
+state between fluid and solid when the temperature exceeds or drops below the
+critical temperature, respectively. Using the *react* option, one can specify a maximum
+bond length and a bond type. Then, when solidifying, particles will search their
+local neighbors and automatically create bonds with any neighboring solid particles
+in range. For BPM bond styles, bonds will then use the immediate position of the two
+particles to calculate a reference state. When melting, particles will delete any
+bonds of the specified type when reverting to a fluid state. Special bonds are updated
+as bonds are created/broken.
+
+The other option for elastic objects is an elastic shell that is nominally much
+thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
+on the surface of a fluid. Currently, this is implemented using
+:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
+:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
+bonds of a specified type between surface fluid particles within a specified distance.
+a newly created rheo/shell bond will then start a timer. While the timer is counting
+down, the bond will delete itself if particles move too far apart or move away from the
+surface. However, if the timer reaches a user-defined threshold, then the bond will
+activate and apply additional forces to the fluid particles. Bond style rheo/shell
+then operates very similarly to a BPM bond style, storing a reference length and
+breaking if stretched too far. Unlike the above method, this option does not remove
+the underlying fluid interactions (although particle shifting is turned off) and does
+not modify special bond settings of particles.
+
+While these two options are not expected to be appropriate for every system,
+either framework can be modified to create more suitable models (e.g. by changing the
+criteria for creating/deleting a bond or altering force calculations).
+
+----------
+
+.. _howto_rheo_clemmer:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/Howto_spc.rst

@@ -2,7 +2,7 @@ SPC water model
 ===============
 
 The SPC water model specifies a 3-site rigid water molecule with
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+charges and Lennard-Jones parameters assigned to each of the three atoms.
 In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
 *harmonic* and an angle style of *harmonic* or *charmm* should also be
@@ -33,7 +33,7 @@ the partial charge assignments change:
 | O charge = -0.8476
 | H charge = 0.4238
 
-See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
+See the :ref:`(Berendsen2) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
 Below is the code for a LAMMPS input file and a molecule file
@@ -149,4 +149,4 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
 
 .. _howto-Berendsen:
 
-**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
+**(Berendsen2)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).

doc/src/Howto_structured_data.rst

@@ -341,7 +341,12 @@ data files and obtain a list of dictionaries.
 
 .. 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}]
+   [{'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)
 -----------------------------
@@ -352,7 +357,8 @@ 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
+   fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" &
+       title "" file output.json screen no
 
 .. code-block:: json
    :caption: output.json

doc/src/Howto_tip3p.rst

@@ -3,7 +3,7 @@ TIP3P water model
 
 The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
 <howto-tip3p>` specifies a 3-site rigid water molecule with charges and
-Lennard-Jones parameters assigned to each of the 3 atoms.
+Lennard-Jones parameters assigned to each of the three atoms.
 
 A suitable pair style with cutoff Coulomb would be:
 
@@ -32,9 +32,9 @@ optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
 model (without fix shake) is desired, for rigid bonds/angles they are
 ignored.
 
-   .. list-table::
+.. list-table::
       :header-rows: 1
-      :widths: auto
+      :widths: 38 22 20 20
 
       * - Parameter
         - TIP3P-CHARMM

doc/src/Howto_tip4p.rst

@@ -25,7 +25,7 @@ There are two ways to implement TIP4P water in LAMMPS:
 
    This can be done with the following pair styles for Coulomb with a cutoff:
 
-   * :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
+   * :doc:`pair_style tip4p/cut <pair_coul>`
    * :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
    or these commands for a long-range Coulomb treatment:
@@ -70,9 +70,9 @@ parameters adjusted for use with a long-range Coulombic solver
 OM distance is specified in the :doc:`pair_style <pair_style>` command,
 not as part of the pair coefficients.
 
-   .. list-table::
+.. list-table::
       :header-rows: 1
-      :widths: auto
+      :widths: 36 19 13 15 17
 
       * - Parameter
         - TIP4P (original)

doc/src/Howto_tip5p.rst

@@ -32,9 +32,9 @@ The table below lists the force field parameters (in real :doc:`units
 <Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
 long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
 
-   .. list-table::
+.. list-table::
       :header-rows: 1
-      :widths: auto
+      :widths: 50 25 25
 
       * - Parameter
         - TIP5P

doc/src/Howto_viscosity.rst

@@ -1,22 +1,24 @@
 Calculate viscosity
 ===================
 
-The shear viscosity eta of a fluid can be measured in at least 6 ways
-using various options in LAMMPS.  See the examples/VISCOSITY directory
+The shear viscosity :math:`\eta` of a fluid can be measured in at least 6 ways
+using various options in LAMMPS.  See the ``examples/VISCOSITY`` directory
 for scripts that implement the 5 methods discussed here for a simple
 Lennard-Jones fluid model and 1 method for SPC/E water model.
 Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>`
 for an analogous discussion for thermal conductivity.
 
-Eta is a measure of the propensity of a fluid to transmit momentum in
+:math:`\eta` is a measure of the propensity of a fluid to transmit momentum in
 a direction perpendicular to the direction of velocity or momentum
 flow.  Alternatively it is the resistance the fluid has to being
 sheared.  It is given by
 
-J = -eta grad(Vstream)
+.. math::
 
-where J is the momentum flux in units of momentum per area per time.
-and grad(Vstream) is the spatial gradient of the velocity of the fluid
+   J = -\eta \cdot \text{grad}(V_{\text{stream}})
+
+where :math:`J` is the momentum flux in units of momentum per area per time.
+and :math:`\text{grad}(V_{\text{stream}})` is the spatial gradient of the velocity of the fluid
 moving in another direction, normal to the area through which the
 momentum flows.  Viscosity thus has units of pressure-time.
 
@@ -38,11 +40,11 @@ velocity to prevent the fluid from heating up.
 
 In both cases, the velocity profile setup in the fluid by this
 procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>`
-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
+command, which determines :math:`\text{grad}(V_{\text{stream}})` in the equation above.
+E.g. the derivative in the y-direction of the :math:`V_x` component of fluid
+motion or :math:`\text{grad}(V_{\text{stream}}) = \frac{\text{d} V_x}{\text{d} y}`.  The :math:`P_{xy}` 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>` page for details on NEMD simulations.
+is the :math:`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
@@ -55,7 +57,7 @@ See the :doc:`fix viscosity <fix_viscosity>` command for details.
 
 The fourth method is based on the Green-Kubo (GK) formula which
 relates the ensemble average of the auto-correlation of the
-stress/pressure tensor to eta.  This can be done in a fully
+stress/pressure tensor to :math:`\eta`.  This can be done in a fully
 equilibrated simulation which is in contrast to the two preceding
 non-equilibrium methods, where momentum flows continuously through the
 simulation box.

doc/src/Howto_viz.rst

@@ -6,7 +6,7 @@ analyzed in a variety of ways.
 
 LAMMPS snapshots are created by the :doc:`dump <dump>` command, which
 can create files in several formats. The native LAMMPS dump format is a
-text file (see "dump atom" or "dump custom") which can be visualized by
+text file (see :lammps:`dump atom` or :lammps:`dump custom`) which can be visualized by
 `several visualization tools <https://www.lammps.org/viz.html>`_ for MD
 simulation trajectories.  `OVITO <https://www.ovito.org>`_ and `VMD
 <https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular
@@ -14,7 +14,13 @@ choices among them.
 
 The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
 styles can output internally rendered images or convert them to a movie
-during the MD run.
+during the MD run.  It is also possible to create visualizations from
+LAMMPS inputs or restart file with the :doc:`LAMMPS-GUI
+<Howto_lammps_gui>`, which uses the :doc:`dump image <dump_image>`
+command internally.  The ``Snapshot Image Viewer`` can be used to
+adjust the visualization of the system interactively and then export
+the corresponding LAMMPS commands to the clipboard to be inserted
+into input files.
 
 Programs included with LAMMPS as auxiliary tools can convert
 between LAMMPS format files and other formats.  See the :doc:`Tools

doc/src/Install.rst

@@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code.
 
 These are the files and subdirectories in the LAMMPS distribution:
 
-+------------+---------------------------------------------+
-| README     | Short description of the LAMMPS package     |
-+------------+---------------------------------------------+
-| LICENSE    | GNU General Public License (GPL)            |
-+------------+---------------------------------------------+
-| SECURITY.md| Security policy for the LAMMPS package      |
-+------------+---------------------------------------------+
-| bench      | benchmark inputs                            |
-+------------+---------------------------------------------+
-| cmake      | CMake build files                           |
-+------------+---------------------------------------------+
-| doc        | documentation and tools to build the manual |
-+------------+---------------------------------------------+
-| examples   | example input files                         |
-+------------+---------------------------------------------+
-| fortran    | Fortran module for LAMMPS library interface |
-+------------+---------------------------------------------+
-| lib        | additional provided or external libraries   |
-+------------+---------------------------------------------+
-| potentials | selected interatomic potential files        |
-+------------+---------------------------------------------+
-| python     | Python module for LAMMPS library interface  |
-+------------+---------------------------------------------+
-| src        | LAMMPS source files                         |
-+------------+---------------------------------------------+
-| tools      | pre- and post-processing tools              |
-+------------+---------------------------------------------+
-| unittest   | source code and inputs for testing LAMMPS   |
-+------------+---------------------------------------------+
++-----------------+---------------------------------------------+
+| ``README``      | Short description of the LAMMPS package     |
++-----------------+---------------------------------------------+
+| ``LICENSE``     | GNU General Public License (GPL)            |
++-----------------+---------------------------------------------+
+| ``SECURITY.md`` | Security policy for the LAMMPS package      |
++-----------------+---------------------------------------------+
+| ``bench``       | benchmark inputs                            |
++-----------------+---------------------------------------------+
+| ``cmake``       | CMake build files                           |
++-----------------+---------------------------------------------+
+| ``doc``         | documentation and tools to build the manual |
++-----------------+---------------------------------------------+
+| ``examples``    | example input files                         |
++-----------------+---------------------------------------------+
+| ``fortran``     | Fortran module for LAMMPS library interface |
++-----------------+---------------------------------------------+
+| ``lib``         | additional provided or external libraries   |
++-----------------+---------------------------------------------+
+| ``potentials``  | selected interatomic potential files        |
++-----------------+---------------------------------------------+
+| ``python``      | Python module for LAMMPS library interface  |
++-----------------+---------------------------------------------+
+| ``src``         | LAMMPS source files                         |
++-----------------+---------------------------------------------+
+| ``tools``       | pre- and post-processing tools              |
++-----------------+---------------------------------------------+
+| ``unittest``    | source code and inputs for testing LAMMPS   |
++-----------------+---------------------------------------------+
 
 You will have all of these if you downloaded the LAMMPS source code.
 You will have only some of them if you downloaded executables, as

doc/src/Install_git.rst

@@ -60,7 +60,7 @@ between them at any time using "git checkout <branch name>".)
    files (mostly by accident).  If you do not need access to the entire
    commit history (most people don't), you can speed up the "cloning"
    process and reduce local disk space requirements by using the
-   *--depth* git command line flag.  That will create a "shallow clone"
+   ``--depth`` git command line flag.  That will create a "shallow clone"
    of the repository, which contains only a subset of the git history.
    Using a depth of 1000 is usually sufficient to include the head
    commits of the *develop*, the *release*, and the *maintenance*
@@ -122,7 +122,7 @@ changed.  How to do this depends on the build system you are using.
 
       .. code-block:: bash
 
-         cmake . --build
+         cmake --build .
 
       CMake should auto-detect whether it needs to re-run the CMake
       configuration step and otherwise redo the build for all files

doc/src/Install_linux.rst

@@ -35,11 +35,11 @@ packages listed below), they do not depend on any installed software and
 thus should run on *any* 64-bit x86 machine with *any* Linux version.
 
 These executable include most of the available packages and multi-thread
-parallelization (via INTEL, KOKKOS, or OPENMP package).  They are **not**
-compatible with MPI.  Several of the LAMMPS tools executables (e.g. ``msi2lmp``)
-and the ``lammps-shell`` program are included as well.  Because of the
-static linkage, there is no ``liblammps.so`` library file and thus also the
-LAMMPS python module, which depends on it, is not included.
+parallelization (via INTEL, KOKKOS, or OPENMP package).  They are
+**not** compatible with MPI.  Several of the LAMMPS tools executables
+(e.g. ``msi2lmp``) are included as well.  Because of the static linkage,
+there is no ``liblammps.so`` library file and thus also the LAMMPS
+python module, which depends on it, is not included.
 
 The compressed tar archives available for download have names following
 the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack

doc/src/Install_tarball.rst

@@ -31,7 +31,7 @@ command:
    tar -xzvf lammps*.tar.gz
 
 This will create a LAMMPS directory with the version date in its name,
-e.g. lammps-28Mar23.
+e.g. ``lammps-28Mar23``.
 
 ----------
 

doc/src/Install_windows.rst

@@ -34,7 +34,7 @@ When you download the installer package, you run it on your Windows
 machine.  It will then prompt you with a dialog, where you can choose
 the installation directory, unpack and copy several executables,
 potential files, documentation PDFs, selected example files, etc.  It
-will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
+will then update a few system settings (e.g. ``PATH``, ``LAMMPS_POTENTIALS``)
 and add an entry into the Start Menu (with references to the
 documentation, LAMMPS homepage and more).  From that menu, there is
 also a link to an uninstaller that removes the files and undoes the

doc/src/Intro_authors.rst

@@ -1,19 +1,88 @@
 Authors of LAMMPS
 -----------------
 
-The primary LAMMPS developers are at Sandia National Labs and Temple
-University:
+The current core LAMMPS developers are listed here (grouped by seniority
+and sorted alphabetically by last name). You can email an individual
+developer with code related questions for their area of expertise, or
+send an email to all of them at this address: "developers at
+lammps.org".  General questions about LAMMPS should be posted in the
+`LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
 
-* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
-* Aidan Thompson, athomps at sandia.gov
-* Stan Moore, stamoor at sandia.gov
-* `Axel Kohlmeyer <https://sites.google.com/site/akohlmey/>`_, akohlmey at gmail.com
-* Richard Berger, richard.berger at outlook.com
+.. raw:: latex
 
+   \small
+
+.. list-table::
+   :widths: 17 15 25 43
+   :header-rows: 1
+
+   * - Name
+     - Affiliation
+     - Email
+     - Areas of expertise
+   * - `Axel Kohlmeyer <ak_>`_
+     - Temple U
+     - akohlmey at gmail.com
+     - OpenMP, library interfaces, LAMMPS-GUI, GitHub, MatSci forum, code maintenance, testing, releases
+   * - `Steve Plimpton <sjp_>`_
+     - SNL (retired)
+     - sjplimp at gmail.com
+     - MD kernels, parallel algorithms & scalability, code structure and design
+   * - `Aidan Thompson <at_>`_
+     - SNL
+     - athomps at sandia.gov
+     - manybody potentials, machine learned potentials, materials science, statistical mechanics
+   * -
+     -
+     -
+     -
+   * - `Richard Berger <rb_>`_
+     - LANL
+     - richard.berger at outlook.com
+     - Python, HPC, DevOps
+   * - `Germain Clavier <gc_>`_
+     - U Caen
+     - germain.clavier at unicaen.fr
+     - organic molecules, polymers, mechanical properties, surfaces, integrators, coarse-graining
+   * - Joel Clemmer
+     - SNL
+     - jtclemm at sandia.gov
+     -  granular systems fluid/solid mechanics
+   * - `Jacob R. Gissinger <jg_>`_
+     - Stevens Institute of Technology
+     - jgissing at stevens.edu
+     - reactive molecular dynamics, macro-molecular systems, type labels
+   * - James Goff
+     - SNL
+     - jmgoff at sandia.gov
+     - machine learned potentials, QEq solvers, Python
+   * - Megan McCarthy
+     - SNL
+     - megmcca at sandia.gov
+     - alloys, micro-structure, machine learned potentials
+   * - Stan Moore
+     - SNL
+     - stamoor at sandia.gov
+     - Kokkos, KSpace solvers, ReaxFF
+   * - `Trung Nguyen <tn_>`_
+     - U Chicago
+     - ndactrung at gmail.com
+     - soft matter, GPU package
+
+.. _rb:  https://rbberger.github.io/
+.. _gc:  https://enthalpiste.fr/
+.. _jg:  https://www.nanocipher.org/
+.. _ak:  https://sites.google.com/site/akohlmey/
+.. _tn:  https://sites.google.com/site/ndtrung8/
+.. _at:  https://www2.sandia.gov/~athomps/
 .. _sjp: https://sjplimp.github.io
 .. _lws: https://www.lammps.org
 
-Past developers include Paul Crozier and Mark Stevens, both at Sandia,
+.. raw:: latex
+
+   \normalsize
+
+Past developers include Paul Crozier and Mark Stevens, both at SNL,
 and Ray Shan, now at Materials Design.
 
 ----------

doc/src/Intro_nonfeatures.rst

@@ -25,9 +25,13 @@ Here are suggestions on how to perform these tasks:
   wraps the library interface is provided.  Thus, GUI interfaces can be
   written in Python or C/C++ that run LAMMPS and visualize or plot its
   output.  Examples of this are provided in the python directory and
-  described on the :doc:`Python <Python_head>` doc page.  As of version
-  2 August 2023 :ref:`a GUI tool <lammps_gui>` is included in LAMMPS.
-  Also, there are several external wrappers or GUI front ends.
+  described on the :doc:`Python <Python_head>` doc page.
+
+  Since version 2 August 2023 :ref:`a LAMMPS-GUI tool <lammps_gui>` is
+  included in LAMMPS.  Also, there are several external wrappers or GUI
+  front ends that are mentioned on the `Pre-/post-processing tools page
+  <https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage.
+
 * **Builder:** Several pre-processing tools are packaged with LAMMPS.
   Some of them convert input files in formats produced by other MD codes
   such as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of
@@ -35,12 +39,13 @@ Here are suggestions on how to perform these tasks:
   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>` page for details on tools packaged with
-  LAMMPS.  The `Pre-/post-processing page
+  LAMMPS.  The `Pre-/post-processing tools page
   <https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage
   describes a variety of third party tools for this task.  Furthermore,
   some internal LAMMPS commands allow reconstructing, or selectively adding
   topology information, as well as provide the option to insert molecule
   templates instead of atoms for building bulk molecular systems.
+
 * **Force-field assignment:** The conversion tools described in the previous
   bullet for CHARMM, AMBER, and Insight will also assign force field
   coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
@@ -49,6 +54,7 @@ Here are suggestions on how to perform these tasks:
   `InterMol <https://github.com/shirtsgroup/InterMol>`_ are particularly
   powerful and flexible in converting force field and topology data
   between various MD simulation programs.
+
 * **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
@@ -66,19 +72,38 @@ Here are suggestions on how to perform these tasks:
   extract and massage data in dump files to make it easier to import
   into other programs.  See the :doc:`Tools <Tools>` page for details on
   these various options.
+
+  The `Pre-/post-processing page <https://www.lammps.org/prepost.html>`_
+  on the LAMMPS homepage lists some external packages for analysis of MD
+  simulation data, including data produced by LAMMPS.
+
 * **Visualization:** LAMMPS can produce NETPBM, JPG, or PNG format
   snapshot images on-the-fly via its :doc:`dump image <dump_image>`
-  command and pass them to an external program, `FFmpeg  <https://ffmpeg.org/>`_,
-  to generate movies from them.  For high-quality, interactive visualization,
-  there are many excellent and free tools available.  See the `Visualization Tools
+  command and pass them to an external program, `FFmpeg
+  <https://ffmpeg.org/>`_, to generate movies from them.  The
+  :ref:`LAMMPS-GUI tool <lammps_gui>` has an *Snapshot Image Viewer*
+  which uses :doc:`dump image <dump_image>` and allows to modify the
+  visualization settings interactively.  It also has a *Slide Show*
+  feature where images created by :doc:`dump image <dump_image>` are
+  collected during a simulation and can be animated interactively or
+  exported to a movie with FFmpeg.
+
+  For high-quality, interactive visualization, there are many excellent
+  and free tools available.  See the `Visualization Tools
   <https://www.lammps.org/viz.html>`_ page of the 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>` page for examples of plotting LAMMPS
   output.  Scripts provided with the *python* tool in the ``tools``
   directory will extract and process 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.
+
+  The :ref:`LAMMPS-GUI tool <lammps_gui>` has an *Chart Viewer* where
+  :doc:`thermodynamic data <thermo_style>` computed by LAMMPS is
+  collected during the simulation and plotted immediately.
+
 * **Pizza.py:** Our group has also written a separate toolkit called
   `Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
   setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS