Merge pull request #4297 from akohlmey/next_release

Update version strings for release

.github/CODEOWNERS

@@ -37,7 +37,8 @@ src/MESONT/*          @iafoss
 src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
-src/ML-POD/*          @exapde @rohskopf
+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
@@ -58,17 +60,26 @@ 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
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 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
@@ -80,7 +91,7 @@ src/bond.*                @sjplimp
 src/comm*.*               @sjplimp
 src/compute.*             @sjplimp
 src/dihedral.*            @sjplimp
-src/domain.*              @sjplimp
+src/domain.*              @sjplimp @stanmoore1
 src/dump*.*               @sjplimp
 src/error.*               @sjplimp
 src/finish.*              @sjplimp
@@ -88,9 +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
@@ -98,12 +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/codeql-analysis.yml

@@ -30,12 +30,12 @@ jobs:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -55,4 +55,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/compile-msvc.yml

@@ -24,7 +24,7 @@ jobs:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 

.github/workflows/coverity.yml

@@ -25,7 +25,7 @@ jobs:
 
     - name: Cache Coverity
       id: cache-coverity
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ./download/
         key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
@@ -59,16 +59,13 @@ jobs:
         -D BUILD_SHARED_LIBS=on \
         -D LAMMPS_SIZES=SMALLBIG \
         -D LAMMPS_EXCEPTIONS=off \
-        -D PKG_MESSAGE=on \
-        -D PKG_MPIIO=on \
         -D PKG_ATC=on \
         -D PKG_AWPMD=on \
-        -D PKG_BOCS=on \
-        -D PKG_EFF=on \
         -D PKG_H5MD=on \
         -D PKG_INTEL=on \
         -D PKG_LATBOLTZ=on \
         -D PKG_MANIFOLD=on \
+        -D PKG_MDI=on \
         -D PKG_MGPT=on \
         -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
@@ -77,7 +74,6 @@ jobs:
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
-        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

.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
 
@@ -32,7 +32,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}
@@ -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
@@ -120,6 +126,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+endif()
+
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@@ -150,6 +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 ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -184,18 +219,17 @@ set(LAMMPS_BINARY lmp${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})
@@ -209,6 +243,10 @@ endif()
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+# re-export all symbols for plugins
+if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
+  set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
+endif()
 install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@@ -239,6 +277,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -264,10 +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
@@ -286,6 +326,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -390,6 +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)
@@ -415,6 +457,7 @@ if(BUILD_OMP)
       (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@@ -425,6 +468,21 @@ if(BUILD_OMP)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
+
+  # this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
+  # CrayClang is only directly recognized by version 3.28 and later
+  if(CMAKE_VERSION VERSION_LESS 3.28)
+    get_filename_component(_exe "${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")
+    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")
+    endif()
+  endif()
 endif()
 
 # lower C++ standard for fmtlib sources when using Intel classic compiler
@@ -457,6 +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)
@@ -514,7 +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()
@@ -539,12 +605,12 @@ endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-foreach(HEADER cmath)
-  check_include_file_cxx(${HEADER} FOUND_${HEADER})
-  if(NOT FOUND_${HEADER})
-    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
-  endif(NOT FOUND_${HEADER})
-endforeach(HEADER)
+if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
+  check_include_file_cxx(cmath FOUND_CMATH)
+  if(NOT FOUND_CMATH)
+    message(FATAL_ERROR "Could not find the required 'cmath' header")
+  endif(NOT FOUND_CMATH)
+endif()
 
 # make the standard math library overrideable and autodetected (for systems that don't have it)
 find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
@@ -656,7 +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()
@@ -834,7 +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
@@ -904,6 +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)
@@ -971,34 +1038,37 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  message(STATUS "<<< FFT settings >>>
+  if (FFT_USE_HEFFTE)
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  heFFTe")
+    if (FFT_HEFFTE_BACKEND)
+      message(STATUS "heFFTe backend:  ${FFT_HEFFTE_BACKEND}")
+    else()
+      message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
+    endif()
+    message(STATUS "Using distributed FFT algorithms from heFTTe")
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+  else()
+    message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")
-  if(FFT_SINGLE)
-    message(STATUS "Using single precision FFTs")
-  else()
-    message(STATUS "Using double precision FFTs")
-  endif()
-  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
-    message(STATUS "Using threaded FFTs")
-  else()
-    message(STATUS "Using non-threaded FFTs")
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+    if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+      message(STATUS "Using threaded FFTs")
+    else()
+      message(STATUS "Using non-threaded FFTs")
+    endif()
+    message(STATUS "Using builtin distributed FFT algorithms")
   endif()
   if(PKG_KOKKOS)
-    if(Kokkos_ENABLE_CUDA)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
-      else()
-        message(STATUS "Kokkos FFT: cuFFT")
-      endif()
-    elseif(Kokkos_ENABLE_HIP)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
-      else()
-        message(STATUS "Kokkos FFT: hipFFT")
-      endif()
-    else()
-      message(STATUS "Kokkos FFT: ${FFT}")
-    endif()
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
   endif()
 endif()
 if(BUILD_DOC)
@@ -1007,9 +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/DetectHIPInstallation.cmake

@@ -1,11 +1,3 @@
-if(NOT DEFINED HIP_PATH)
-    if(NOT DEFINED ENV{HIP_PATH})
-        message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
-        "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
-    else()
-        set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
-    endif()
-endif()
 if(NOT DEFINED ROCM_PATH)
     if(NOT DEFINED ENV{ROCM_PATH})
         set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
@@ -13,4 +5,4 @@ if(NOT DEFINED ROCM_PATH)
         set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
     endif()
 endif()
-list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

cmake/Modules/ExternalCMakeProject.cmake

@@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
       "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
   endif()
   add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
 endfunction(ExternalCMakeProject)

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 "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${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)
 
@@ -8,4 +8,3 @@ set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
 include(ExternalCMakeProject)
 ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
 
-add_library(OpenCL::OpenCL ALIAS OpenCL)

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/GPU.cmake

@@ -1,3 +1,10 @@
+
+# Silence CMake warnings about FindCUDA being obsolete.
+# We may need to eventually rewrite this section to use enable_language(CUDA)
+if(POLICY CMP0146)
+  cmake_policy(SET CMP0146 OLD)
+endif()
+
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -151,10 +158,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)

cmake/Modules/Packages/INTEL.cmake

@@ -111,6 +111,9 @@ if(PKG_KSPACE)
   list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
+if(PKG_ML-SNAP)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/sna_intel.cpp)
+endif()
 
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -16,11 +16,6 @@ endif()
 if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
-  else()
-    # NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
-    endif()
   endif()
 endif()
 ########################################################################
@@ -50,8 +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/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" 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)
@@ -76,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.1.00 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)
@@ -131,16 +126,33 @@ if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+  set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
+  set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
+  set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
+  validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
+  string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
+
   if(Kokkos_ENABLE_CUDA)
-    if(NOT (FFT STREQUAL "KISS"))
-      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
-      target_link_libraries(lammps PRIVATE cufft)
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
+      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "CUFFT")
+      find_package(CUDAToolkit REQUIRED)
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
+      target_link_libraries(lammps PRIVATE CUDA::cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
-    if(NOT (FFT STREQUAL "KISS"))
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
+      message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "HIPFFT")
       include(DetectHIPInstallation)
       find_package(hipfft REQUIRED)
-      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
       target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
   endif()

cmake/Modules/Packages/KSPACE.cmake

@@ -46,6 +46,61 @@ else()
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)
 endif()
 
+option(FFT_USE_HEFFTE  "Use heFFTe as the distributed FFT engine, overrides the FFT option."  OFF)
+if(FFT_USE_HEFFTE)
+  # if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
+
+  # map standard FFT choices to available heFFTe backends: FFTW3 -> FFTW, KISS -> BUILTIN
+  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL BUILTIN)
+  string(REPLACE FFTW3 FFTW FFT_HEFFTE_BACKEND_DEFAULT ${FFT})
+  string(REPLACE KISS BUILTIN FFT_HEFFTE_BACKEND_DEFAULT ${FFT_HEFFTE_BACKEND_DEFAULT})
+  set(FFT_HEFFTE_BACKEND "${FFT_HEFFTE_BACKEND_DEFAULT}" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+  set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
+  validate_option(FFT_HEFFTE_BACKEND FFT_HEFFTE_BACKEND_VALUES)
+
+  if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
+    set(HEFFTE_COMPONENTS "FFTW")
+    set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
+  elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
+    set(HEFFTE_COMPONENTS "MKL")
+    set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
+  else()
+    set(HEFFTE_COMPONENTS "BUILTIN")
+    message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
+  endif()
+
+  find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
+  if (NOT Heffte_FOUND) # download and build
+    if(BUILD_SHARED_LIBS)
+      set(BUILD_SHARED_LIBS_WAS_ON YES)
+      set(BUILD_SHARED_LIBS OFF)
+    endif()
+    if(CMAKE_REQUEST_PIC)
+      set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+    endif()
+    set(Heffte_ENABLE_${FFT_HEFFTE_BACKEND} ON)
+    include(FetchContent)
+    FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
+      URL  "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
+      URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
+      )
+    FetchContent_Populate(HEFFTE_PROJECT)
+
+    # fixup git hash to show "(unknown)" to avoid compilation failures.
+    file(READ ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h HEFFTE_CFG_FILE_TEXT)
+    string(REPLACE "@Heffte_GIT_HASH@" "(unknown)" HEFFTE_CFG_FILE_TEXT "${HEFFTE_CFG_FILE_TEXT}")
+    file(WRITE ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h "${HEFFTE_CFG_FILE_TEXT}")
+
+    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR} EXCLUDE_FROM_ALL)
+    add_library(Heffte::Heffte ALIAS Heffte)
+    if(BUILD_SHARED_LIBS_WAS_ON)
+      set(BUILD_SHARED_LIBS ON)
+    endif()
+  endif()
+  target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
+  target_link_libraries(lammps PRIVATE Heffte::Heffte)
+endif()
+
 set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
 set(FFT_PACK_VALUES array pointer memcpy)
 set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)

cmake/Modules/Packages/ML-IAP.cmake

@@ -10,6 +10,14 @@ endif()
 
 option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
+# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
+set(MLIAP_ENABLE_ACE_DEFAULT OFF)
+if(PKG_ML-PACE)
+  set(MLIAP_ENABLE_ACE_DEFAULT ON)
+endif()
+
+option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
+
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
   find_package(Python COMPONENTS NumPy REQUIRED)
@@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON)
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()
+
+if(MLIAP_ENABLE_ACE)
+  if(NOT PKG_ML-PACE)
+    message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
+  endif()
+  target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
+endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,33 +1,46 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+# PACE library support for ML-PACE package
 
-set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+# 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)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-# download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+# to make it easier to check local build without going through the public github releases
+if(LOCAL_ML-PACE)
+ set(lib-pace "${LOCAL_ML-PACE}")
 else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+  # download library sources to build folder
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
 
-# uncompress downloaded sources
-execute_process(
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+
+  # uncompress downloaded sources
+  execute_process(
+    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  )
+  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,14 +18,16 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    # quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
+    string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
     set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")
@@ -56,7 +58,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

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/v2.8.2/plumed-src-2.8.2.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 "599092b6a0aa6fff992612537ad98994" 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/gpu-cuda.cmake

@@ -0,0 +1,11 @@
+# preset that enables GPU and selects CUDA API
+
+set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
+set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
+set(GPU_PREC "mixed" CACHE STRING "" FORCE)
+
+set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -6,6 +6,11 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
+
+# If KSPACE is also enabled, use CUFFT for FFTs
+set(FFT_KOKKOS "CUFFT" CACHE STRING "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -12,6 +12,9 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
 set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
 set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
 
+# If KSPACE is also enabled, use CUFFT for FFTs
+set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
+
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 

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/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

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/Makefile

@@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -231,6 +233,7 @@ role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/github-development-workflow.md

@@ -36,10 +36,10 @@ requests.
 MUST be submitted as a pull request to GitHub.  All changes to the
 "develop" branch must be made exclusively through merging pull requests.
 The "release" and "stable" branches, respectively, are only to be
-updated upon feature or stable releases based on the associated
-tags.  Updates to the stable release in between stable releases
+updated upon "feature releases" or "stable releases" based on the
+associated tags.  Updates to the stable release in between stable releases
 (for example, back-ported bug fixes) are first merged into the "maintenance"
-branch and then into the "stable" branch as update releases.
+branch and then into the "stable" branch as "stable update releases".
 
 Pull requests may also be submitted to (long-running) feature branches
 created by LAMMPS developers inside the LAMMPS project, if needed. Those
@@ -131,7 +131,7 @@ testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time-consuming tests (including regression testing) are
 performed after code is merged to the "develop" branch.  There are feature
-releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
 developers feel, that a sufficient number of changes have been included
 and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch

doc/graphviz/Makefile

@@ -16,8 +16,11 @@ clean:
 	rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
 
 ifeq ($(HAS_DOT),YES)
-$(IMGDIR)/%.png: %.dot
+$(IMGDIR)/lammps-classes.png : lammps-classes.dot
 	dot -Tpng -Kneato -o $@ $<
+
+$(IMGDIR)/%.png: %.dot
+	dot -Tpng -Kdot -o $@ $<
 endif
 
 ifeq ($(HAS_DOT),NO)

doc/graphviz/lammps-releases.dot

@@ -0,0 +1,34 @@
+// LAMMPS branches and releases
+digraph releases {
+    rankdir="LR";
+    github [shape="box" label="Pull Requests\non GitHub" height=0.75];
+    github -> develop [label="Merge commits"];
+    {
+        rank = "same";
+        work [shape="none" label="Development branches:"]
+        develop [label="'develop' branch" height=0.75];
+        maintenance [label="'maintenance' branch" height=0.75];
+    };
+    {
+        rank = "same";
+        upload [shape="none" label="Release branches:"]
+        release [label="'release' branch" height=0.75];
+        stable [label="'stable' branch" height=0.75];
+    };
+    develop -> release [label="Feature release\n(every 4-8 weeks)"];
+    release -> stable [label="Stable release\n(once per year)"];
+    stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
+    develop -> maintenance [label="Backports of bugfixes" style="dashed"];
+    maintenance -> stable [label="Updates to stable release"];
+    {
+        rank = "same";
+        tag [shape="none" label="Applied tags:"];
+        patchtag [shape="box" label="patch_<date>"];
+        stabletag [shape="box" label="stable_<date>"];
+        updatetag [shape="box" label="stable_<date>_update<num>"];
+    };
+    release -> patchtag [label="feature release" style="dotted"];
+    stable -> stabletag [label="stable release" style="dotted"];
+    stable -> updatetag [label="update release" style="dotted"];
+}
+

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "21 November 2023" "2023-11-21"
+.TH LAMMPS "1" "29 August 2024" "2024-08-29"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 21 November 2023
+\- 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
@@ -297,7 +311,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2022 Sandia Corporation
+© 2003--2024 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

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)**
    Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
 
@@ -244,8 +289,17 @@ Bibliography
 **(Cornell)**
    Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 
+**(Cundall, 1987)**
+   Cundall, P. A. Distinct Element Models of Rock and Soil
+
+**(Curk1)**
+   T. Curk, J. Yuan, and E. Luijten, JCP 156 (2022).
+
+**(Curk2)**
+   T. Curk and E. Luijten, PRL 126 (2021)
+
 **(Cusentino)**
-   Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
+   Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
 
 **(Daivis and Todd)**
    Daivis and Todd, J Chem Phys, 124, 194103 (2006).
@@ -268,6 +322,15 @@ Bibliography
 **(Daw2)**
    M.\  S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
 
+**(de Buyl)**
+   de Buyl, Colberg and Hofling, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
+
+**(Deissenbeck)**
+   Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
+
+**(de Koning)**
+   de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
+
 **(DeVane)**
    Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
 
@@ -277,12 +340,24 @@ Bibliography
 **(Destree)**
    M.\  Destree, F. Laupretre, A. Lyulin, and J.-P.  Ryckaert, J Chem Phys, 112, 9632 (2000).
 
+**(Dickel)**
+   Dickel, Francis, and Barrett, Computational Materials Science 171 (2020): 109157.
+
+**(Dietz)**
+   Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).
+
 **(Dobson)**
    Dobson, J Chem Phys, 141, 184103 (2014).
 
+**(Drautz)**
+   Drautz, Phys Rev B, 99, 014104 (2019).
+
 **(Duffy)**
    D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
 
+**(Dufils)**
+   Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
+
 **(Dullweber)**
    Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).
 
@@ -295,6 +370,9 @@ Bibliography
 **(Dunweg)**
    Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
 
+**(EcheverriRestrepo)**
+  Echeverri Restrepo, Andric, Comput Mater Sci, 218, 111978 (2023).
+
 **(EDIP)**
    J F Justo et al, Phys Rev B 58, 2539 (1998).
 
@@ -304,12 +382,21 @@ Bibliography
 **(Elliott)**
    Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
 
+**(Ellis)**
+   Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam,  Phys Rev B, 104, 035120, (2021)
+
+**(Emmrich)**
+   Emmrich, Weckner, Commun. Math. Sci., 5, 851-864 (2007),
+
 **(Elstner)**
    M.\  Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
 
 **(Erdmann)**
    U.\  Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
 
+**(Eshelby)**
+  J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
+
 **(Espanol and Revenga)**
    Espanol, Revenga, Physical Review E, 67, 026705 (2003).
 
@@ -328,9 +415,18 @@ Bibliography
 **(Faken)**
    Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
 
+**(Falk)**
+   Falk and Langer PRE, 57, 7192 (1998).
+
 **(Fath)**
    Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
 
+**(Feng1)**
+   Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
+
+**(Feng2)**
+   Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).
+
 **(Fennell)**
    C.\  J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
 
@@ -367,18 +463,36 @@ Bibliography
 **(Frenkel)**
    Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
 
-**(GLE4MD)**
-   `https://gle4md.org/ <https://gle4md.org/>`_
+**(Fu)**
+   Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
 
 **(Gao)**
    Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
 
+**(Gingrich)**
+   Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
+
+**(Gissinger2017)**
+   Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+
+**(Gissinger2020)**
+   Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
+
 **(Gissinger)**
-   Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
+   Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).
+
+**(Gissinger2024)**
+   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).
+
+**(Gloor)**
+   Gloor, J Chem Phys, 123, 134703 (2005)
 
 **(Glosli)**
    Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
 
+**(Goff)**
+   Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).
+
 **(Goldman1)**
    Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
 
@@ -412,6 +526,9 @@ Bibliography
 **(Guo)**
    Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
 
+**(Gupta)**
+   Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
+
 **(Hardy)**
    David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).
 
@@ -433,6 +550,9 @@ Bibliography
 **(Henrich)**
    O.\  Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
+**(Herman)**
+   M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
+
 **(Hess)**
    Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
 
@@ -454,24 +574,42 @@ Bibliography
 **(Hoover)**
    Hoover, Phys Rev A, 31, 1695 (1985).
 
+**(Huang)**
+   Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
+
+**(Huang2014)**
+   X. Huang, "Exploring critical-state behavior using DEM", Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316
+
+**(Hu)**
+   Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).
+
+**(Hu)**
+   Hu, J. Chem. Theory Comput. 10, 5254 (2014).
+
 **(Hummer)**
    Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
 
 **(Hunt)**
    Hunt, Mol Simul, 42, 347 (2016).
 
+**(Ikeshoji)**
+   Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
+
+**(Ikeshoji2)**
+   Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
+
+**(Ilie)**
+   Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
+
+**(In 't Veld)**
+   In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
+
 **(IPI)**
    `https://ipi-code.org/ <https://ipi-code.org/>`
 
 **(IPI-CPC)**
    Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
 
-**(Ikeshoji)**
-   Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
-
-**(In 't Veld)**
-   In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
-
 **(Isele-Holder)**
    Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
 
@@ -490,6 +628,9 @@ Bibliography
 **(Izvekov)**
    Izvekov, Voth, J Chem Phys 123, 134105 (2005).
 
+**(Jadhao)**
+   Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013)
+
 **(Janssens)**
    Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).
 
@@ -502,6 +643,15 @@ Bibliography
 **(Jiang)**
    Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,  J Phys Chem Lett, 2, 87-92 (2011).
 
+**(Jiang1)**
+   Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
+
+**(Jiang2)**
+   J.-W. Jiang, Nanotechnology 26, 315706 (2015).
+
+**(Jiang3)**
+   J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
+
 **(Johnson et al, 1971)**
    Johnson, K. L., Kendall, K., & Roberts, A. D. (1971).  Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
 
@@ -562,27 +712,33 @@ Bibliography
 **(Kumar)**
    Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
 
+**(Lafourcade)**
+  Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
+
 **(Lamoureux and Roux)**
    G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
 
 **(Lamoureux)**
    Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
 
-**(Larentzos)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+**(Landsgesell)**
+   J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020).
 
 **(Larentzos1)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting
+   J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
 
 **(Larentzos2)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).
 
 **(Larsen)**
    Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
 
-**(Lebedeva et al.)**
+**(Lebedeva1)**
    I.\  V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
 
+**(Lebedeva2)**
+  I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
+
 **(Lechman)**
    Lechman, et al, in preparation (2010).
 
@@ -592,6 +748,9 @@ Bibliography
 **(Lee2)**
    Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
 
+**(Lee2020)**
+   C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.
+
 **(Lenart)**
    Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
 
@@ -616,8 +775,11 @@ Bibliography
 **(Li2015_JCP)**
    Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015).  DOI:10.1063/1.4923254.
 
+**(Liang)**
+   Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
+
 **(Lisal)**
-   M.\  Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
+   M.\  Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
 
 **(Liu1)**
    L.\  Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).
@@ -634,6 +796,15 @@ Bibliography
 **(Luding, 2008)**
    Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.
 
+**(Lysogorskiy)**
+   Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+**(Lysogorskiy21)**
+   Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+**(Lysogorskiy23)**
+   Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
+
 **(Maaravi)**
    T.\  Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
 
@@ -652,12 +823,18 @@ Bibliography
 **(Maginn)**
    Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).
 
+**(Mahoney)**
+   Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
+
 **(Malolepsza)**
    Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).
 
 **(Mandadapu)**
    Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.  Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
 
+**(Mandelli_1)**
+   D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
+
 **(Maras)**
    Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).
 
@@ -673,6 +850,9 @@ Bibliography
 **(Martyna1994)**
    Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
 
+**(Martyna2)**
+  G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
+
 **(Mason)**
    J.\  K. Mason, Acta Cryst A65, 259 (2009).
 
@@ -712,6 +892,9 @@ Bibliography
 **(Mie)**
    G.\  Mie, Ann Phys, 316, 657 (1903).
 
+**(Milano)**
+   G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).
+
 **(Miller1)**
    T.\  F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
@@ -742,12 +925,18 @@ Bibliography
 **(Mitchell2011a)**
    Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).
 
+**(Miyazaki)**
+   Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).
+
 **(Mniszewski)**
    S.\  M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
 
 **(Monaghan)**
    Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).
 
+**(Monti)**
+   Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
+
 **(Moore)**
    Moore, J Chem Phys, 144, 104501 (2016).
 
@@ -767,7 +956,7 @@ Bibliography
    Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
 
 **(Moustafa)**
-   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
 
 **(Muller-Plathe1)**
    Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@@ -787,9 +976,6 @@ Bibliography
 **(Neelov)**
    Neelov, Holm, J Chem Phys 132, 234103 (2010)
 
-**(Negre2016)**
-   C.\  F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
-
 **(Nelson)**
    Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
 
@@ -799,12 +985,24 @@ Bibliography
 **(Neyts)**
    E.\  C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).
 
+**(Nguyen2023)**
+   Nguyen, Physical Review B, 107(14), 144103, (2023).
+
+**(Nguyen2024)**
+   Nguyen, Journal of Computational Physics, 113102, (2024).
+
+**(Nguyen and Rohskopf)**
+  Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
+
+**(Nguyen and Sema)**
+   Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
+
+**(NguyenTD)**
+   Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019)
+
 **(Nicholson and Rutledge)**
    Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
 
-**(Nicklas)**
-   The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
-
 **(Niklasson2002)**
    A.\  M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
 
@@ -817,6 +1015,9 @@ Bibliography
 **(Niklasson2017)**
    A.\  M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
 
+**(Nitol)**
+   Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207.
+
 **(Noid)**
    Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).
 
@@ -838,6 +1039,9 @@ Bibliography
 **(O'Connor)**
    O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
 
+**(O'Hearn)**
+   O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
+
 **(Okabe)**
    T.\  Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
 
@@ -847,6 +1051,8 @@ Bibliography
 **(Omelyan)**
    Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).
 
+**(OPLS-AA96)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
+
 **(Oppelstrup)**
    Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.
 
@@ -868,11 +1074,17 @@ Bibliography
 **(Ouyang2)**
    W.\  Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
 
-**(PASS)**
-   PASS webpage: https://www.sdu.dk/en/DPASS
+**(Ouyang_1)**
+   W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
 
-**(PLUMED)**
-   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+**(Ouyang6)**
+   W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
+
+**(Ouyang7)**
+   W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
+
+**(Palkar)**
+   Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
 
 **(Paquay)**
    Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
@@ -883,21 +1095,33 @@ Bibliography
 **(Parks)**
    Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
 
-**(Parrinello1981)**
+**(Parrinello)**
    Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
 
+**(PASS)**
+   PASS webpage: https://www.sdu.dk/en/DPASS
+
 **(Paula Leite2016)**
    Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
 
 **(Paula Leite2017)**
    Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).
 
+**(Pavlov1)**
+   D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
+
+**(Pavlov2)**
+   Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
+
 **(Pearlman)**
    Pearlman, J Chem Phys, 98, 1487 (1994)
 
 **(Pedersen)**
    Pedersen, J. Chem. Phys., 139, 104102 (2013).
 
+**(Pedone)**
+   A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
+
 **(Peng)**
    Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).
 
@@ -919,6 +1143,9 @@ Bibliography
 **(Pettifor_3)**
    D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).
 
+**(PFC)**
+   PFC Particle Flow Code 6.0 Documentation. Itasca Consulting Group.
+
 **(Phillips)**
    C.\  L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).
 
@@ -928,9 +1155,21 @@ Bibliography
 **(Pisarev)**
    V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).
 
+**(Plimpton)**
+   Plimpton and Knight, JPDC, 147, 184-195 (2021).
+
+**(PLUMED)**
+   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
 **(Pollock)**
    Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
 
+**(Ponder)**
+   Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque,  Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark,  Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
+
+**(Popov1)**
+   A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
+
 **(Price1)**
    Price and Brooks, J Chem Phys, 121, 10096 (2004).
 
@@ -970,6 +1209,12 @@ Bibliography
 **(Rick)**
    S.\  W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).
 
+**(Rick2)**
+   S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+
+**(Roberts)**
+   R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.  `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
+
 **(Rohart)**
    Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
 
@@ -1006,9 +1251,18 @@ Bibliography
 **(Sadigh)**
    B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
 
+**(Sadigh1)**
+   B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
+
+**(Sadigh2)**
+  B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)
+
 **(Safran)**
    Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
 
+**(Salanne)**
+   Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
+
 **(Salerno)**
    Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
 
@@ -1018,9 +1272,18 @@ Bibliography
 **(Sanyal2)**
    Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
 
+**(Scalfi)**
+   Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
+
 **(Schelling)**
    Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
 
+**(Scherer1)**
+   C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
+
+**(Scherer2)**
+   C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
+
 **(Schlitter1)**
    Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).
 
@@ -1039,21 +1302,36 @@ Bibliography
 **(Schroeder)**
    Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).
 
+**(Seleson 2010)**
+   Seleson, Parks, Int J Mult Comp Eng 9(6), pp. 689-706, 2011.
+
 **(Semaev)**
    Semaev, Cryptography and Lattices, 181 (2001).
 
+**(Seo)**
+   Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
+
 **(Sheppard)**
    Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008).  See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.
 
+**(Shi)**
+   Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
+
 **(Shinoda)**
    Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
 
 **(Shinoda)**
    Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
 
+**(Shire)**
+   Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
+
 **(Sides)**
    Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).
 
+**(Siepmann)**
+   Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
+
 **(Silbert)**
    Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).
 
@@ -1063,12 +1341,21 @@ Bibliography
 **(Silling 2000)**
    Silling, J Mech Phys Solids, 48, 175-209 (2000).
 
+**(Silling 2005)**
+   Silling Askari, Computer and Structures, 83, 1526-1535 (2005).
+
 **(Silling 2007)**
    Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
 
 **(Singh)**
    Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
 
+**(Singraber, Behler and Dellago 2019)**
+   Singraber, A.; Behler, J.; Dellago, C. J., Chem.  Theory Comput. 2019, 15 (3), 1827-1840
+
+**(Singraber et al 2019)**
+   Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput.  2019, 15 (5), 3075-3092.
+
 **(Sirk1)**
    Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.
 
@@ -1081,6 +1368,9 @@ Bibliography
 **(Snodin)**
    B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
+**(Son)**
+   Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).
+
 **(Srivastava)**
    Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
 
@@ -1090,6 +1380,12 @@ Bibliography
 **(Steinhardt)**
    P.\  Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
 
+**(Steward)**
+   Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
+
+**(Stewart2018)**
+   J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
+
 **(Stiles)**
    Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).
 
@@ -1147,12 +1443,21 @@ Bibliography
 **(Tainter 2015)**
    Tainter, Shi, and Skinner, 11, 2268 (2015)
 
+**(Tang and Toennies)**
+   J Chem Phys, 80, 3726 (1984).
+
+**(Tee)**
+   Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
+
 **(Templeton2010)**
    Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
 
 **(Templeton2011)**
    Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
 
+**(tenWolde)**
+   P.\  R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
+
 **(Tersoff_1)**
    J.\  Tersoff, Phys Rev B, 37, 6991 (1988).
 
@@ -1195,6 +1500,9 @@ Bibliography
 **(Tranchida)**
    Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).
 
+**(Tribello)**
+   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
 **(Tsuji et al, 1992)**
    Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),
 
@@ -1213,6 +1521,9 @@ Bibliography
 **(Tuckerman4)**
    Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).
 
+**(Tyagi)**
+   Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010)
+
 **(Ulomek)**
    Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
 
@@ -1222,6 +1533,15 @@ Bibliography
 **(Valone)**
    Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
 
+**(vanWijk)**
+   M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)
+
+**(Van Workum)**
+   K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
+
+**(Vargas and McCarthy 2001)**
+   Vargas, W.L. and McCarthy, J.J. (2001).
+
 **(Varshalovich)**
    Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).
 
@@ -1234,6 +1554,9 @@ Bibliography
 **(Veld)**
    In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
 
+**(Verstraelen)**
+   Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).
+
 **(Volkov1)**
    Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
 
@@ -1258,6 +1581,9 @@ Bibliography
 **(Wang et al, 2015)**
    Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015).  Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.
 
+**(Wang2020)**
+   X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
+
 **(Wang1)**
    J.\  Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
 
@@ -1297,6 +1623,9 @@ Bibliography
 **(Wicaksono2)**
    Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
 
+**(Winkler)**
+   Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
+
 **(Wirnsberger)**
    Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).
 
@@ -1309,9 +1638,27 @@ Bibliography
 **(Wood)**
    Wood and Thompson, J Chem Phys, 148, 241721, (2018)
 
+**(Xie23)**
+   Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7
+
+**(Yade-DEM)**
+   V. Smilauer et al. (2021), Yade Documentation 3rd ed.
+
+**(Yanxon2020)**
+   Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).
+
 **(Yeh)**
    Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
 
+**(Yuan2010a)**
+   Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
+
+**(Yuan2010b)**
+   Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
+
+**(Zagaceta2020)**
+   Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
+
 **(ZBL)**
    J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.
 
@@ -1381,17 +1728,6 @@ Bibliography
 **(Zimmerman2010)**
    Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
 
-**(de Buyl)**
-   de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
-
-**(de Koning)**
-   de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
-
 **(electronic stopping)**
    Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
 
-**(tenWolde)**
-   P.\  R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
-
-**(vanWijk)**
-   M.\  M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)

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
@@ -122,32 +123,44 @@ Code Coverage and Unit Testing (CMake only)
 -------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
-during development: integration testing (i.e. whether the code compiles
-on various platforms and with a variety of settings), unit testing
-(i.e. whether certain individual parts of the code produce the expected
-results for given inputs), run testing (whether selected complete input
-decks run without crashing for multiple configurations), and regression
-testing (i.e. whether selected input examples reproduce the same
-results over a given number of steps and operations within a given
-error margin).  The status of this automated testing can be viewed on
-`https://ci.lammps.org <https://ci.lammps.org>`_.
+during development:
+
+- Integration testing (i.e. whether the code compiles
+  on various platforms and with a variety of compilers and settings),
+- Unit testing (i.e. whether certain functions or classes of the code
+  produce the expected results for given inputs),
+- Run testing (i.e. whether selected input decks can run to completion
+  without crashing for multiple configurations),
+- Regression testing (i.e. whether selected input examples reproduce the
+  same results over a given number of steps and operations within a
+  given error margin).
+
+The status of this automated testing can be viewed on `https://ci.lammps.org
+<https://ci.lammps.org>`_.
 
 The scripts and inputs for integration, run, and regression testing
 are maintained in a
 `separate repository <https://github.com/lammps/lammps-testing>`_
-of the LAMMPS project on GitHub.
+of the LAMMPS project on GitHub.  A few tests are also run as GitHub
+Actions and their configuration files are in the ``.github/workflows/``
+folder of the LAMMPS git tree.
 
-The unit testing facility is integrated into the CMake build process
-of the LAMMPS source code distribution itself.  It can be enabled by
+The unit testing facility is integrated into the CMake build process of
+the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <https://pyyaml.org/>`_ library and development
-headers (if those are not found locally a recent version will be
-downloaded and compiled along with LAMMPS and the test program) to
-compile and will download and compile a specific recent version of the
-`Googletest <https://github.com/google/googletest/>`_ C++ test framework
-for implementing the tests.
+It requires the `YAML <https://pyyaml.org/>`_ library and matching
+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.  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 requirements for testing
+.. admonition:: Software version and LAMMPS configuration requirements
    :class: note
 
    The compiler and library version requirements for the testing
@@ -155,7 +168,7 @@ for implementing the tests.
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
    to detect incompatible versions and either skip incompatible tests or
-   stop with an error.  Also the number of tests will depend on
+   stop with an error.  Also the number of available tests will depend on
    installed LAMMPS packages, development environment, operating system,
    and configuration settings.
 
@@ -168,24 +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
 
@@ -200,24 +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
@@ -234,12 +248,31 @@ will be skipped if prerequisite features are not available in LAMMPS.
    time.  Preference is given to parts of the code base that are easy to
    test or commonly used.
 
-Tests for styles of the same kind of style (e.g. pair styles or bond
-styles) are performed with the same test executable using different
-input files in YAML format.  So to add a test for another style of the
-same kind it may be sufficient to add a suitable YAML file.
-:doc:`Detailed instructions for adding tests <Developer_unittest>` are
-provided in the Programmer Guide part of the manual.
+Tests as shown by the ``ctest`` program are command lines defined in the
+``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
+tests simply execute LAMMPS with specific command line flags and check
+the output to the screen for expected content.  A large number of unit
+tests are special tests programs using the `GoogleTest framework
+<https://github.com/google/googletest/>`_ and linked to the LAMMPS
+library that test individual functions or create a LAMMPS class
+instance, execute one or more commands and check data inside the LAMMPS
+class hierarchy.  There are also tests for the C-library, Fortran, and
+Python module interfaces to LAMMPS.  The Python tests use the Python
+"unittest" module in a similar fashion than the others use `GoogleTest`.
+These special test programs are structured to perform multiple
+individual tests internally and each of those contains several checks
+(aka assertions) for internal data being changed as expected.
+
+Tests for force computing or modifying styles (e.g. styles for non-bonded
+and bonded interactions and selected fixes) are run by using a more generic
+test program that reads its input from files in YAML format. The YAML file
+provides the information on how to customized the test program to test
+a specific style and - if needed - with specific settings.
+To add a test for another, similar style (e.g. a new pair style) it is
+usually sufficient to add a suitable YAML file.  :doc:`Detailed
+instructions for adding tests <Developer_unittest>` are provided in the
+Programmer Guide part of the manual.  A description of what happens
+during the tests is given below.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -255,16 +288,18 @@ A test run is then a a collection multiple individual test runs each
 with many comparisons to reference results based on template input
 files, individual command settings, relative error margins, and
 reference data stored in a YAML format file with ``.yaml``
-suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
-``test_angle_style`` are implemented.  They will compare forces, energies and
-(global) stress for all atoms after a ``run 0`` calculation and after a
-few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
-with different settings and also for multiple accelerated styles. If a
-prerequisite style or package is missing, the individual tests are
-skipped.  All tests will be executed on a single MPI process, so using
-the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
-since this will skip the MPI initialization for each test run.
-Below is an example command and output:
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
+``test_angle_style``, ``test_dihedral_style``, and
+``test_improper_style`` are implemented.  They will compare forces,
+energies and (global) stress for all atoms after a ``run 0`` calculation
+and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
+multiple variants with different settings and also for multiple
+accelerated styles. If a prerequisite style or package is missing, the
+individual tests are skipped.  All force style tests will be executed on
+a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
+significantly speed up testing, since this will skip the MPI
+initialization for each test run.  Below is an example command and
+output:
 
 .. code-block:: console
 
@@ -302,16 +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
@@ -325,10 +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
@@ -416,15 +452,16 @@ When compiling LAMMPS with enabled tests, most test executables will
 need to be linked against the LAMMPS library.  Since this can be a very
 large library with many C++ objects when many packages are enabled, link
 times can become very long on machines that use the GNU BFD linker (e.g.
-Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
-or the ``gold`` linker available with GNU binutils can speed up this step
-substantially. CMake will by default test if any of the two can be
-enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
-selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
-Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
-``default`` option will use the system default linker otherwise, the
-linker is chosen explicitly.  This option is only available for the
-GNU or Clang C++ compiler.
+Linux systems).  Alternatives like the ``mold`` linker, the ``lld``
+linker of the LLVM project, or the ``gold`` linker available with GNU
+binutils can speed up this step substantially (in this order).  CMake
+will by default test if any of the three can be enabled and use it when
+``ENABLE_TESTING`` is active.  It can also be selected manually through
+the ``CMAKE_CUSTOM_LINKER`` CMake variable.  Allowed values are
+``mold``, ``lld``, ``gold``, ``bfd``, or ``default``.  The ``default``
+option will use the system default linker otherwise, the linker is
+chosen explicitly.  This option is only available for the GNU or Clang
+C++ compilers.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -477,27 +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
 ----------------------
@@ -518,6 +579,8 @@ The following options are available.
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
+   make check-docs          # search for several issues in the manual
+   make check-version       # list files with pending release version tags
    make check               # run all check targets from above
 
 These should help to make source and documentation files conforming

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
@@ -533,9 +569,6 @@ They must be specified in uppercase.
    *  - A64FX
       - HOST
       - ARMv8.2 with SVE Support
-   *  - WSM
-      - HOST
-      - Intel Westmere CPU (SSE 4.2)
    *  - SNB
       - HOST
       - Intel Sandy/Ivy Bridge CPU (AVX 1)
@@ -566,18 +599,15 @@ They must be specified in uppercase.
    *  - KNL
       - HOST
       - Intel Knights Landing Xeon Phi
-   *  - BGQ
-      - HOST
-      - IBM Blue Gene/Q CPU
-   *  - POWER7
-      - HOST
-      - IBM POWER7 CPU
    *  - POWER8
       - HOST
       - IBM POWER8 CPU
    *  - POWER9
       - HOST
       - IBM POWER9 CPU
+   *  - RISCV_SG2042
+      - HOST
+      - SG2042 (RISC-V) CPU
    *  - KEPLER30
       - GPU
       - NVIDIA Kepler generation CC 3.0 GPU
@@ -626,24 +656,27 @@ They must be specified in uppercase.
    *  - HOPPER90
       - GPU
       - NVIDIA Hopper generation CC 9.0 GPU
-   *  - VEGA900
+   *  - AMD_GFX906
       - GPU
-      - AMD GPU MI25 GFX900
-   *  - VEGA906
+      - AMD GPU MI50/MI60
+   *  - AMD_GFX908
       - GPU
-      - AMD GPU MI50/MI60 GFX906
-   *  - VEGA908
+      - AMD GPU MI100
+   *  - AMD_GFX90A
       - GPU
-      - AMD GPU MI100 GFX908
-   *  - VEGA90A
+      - AMD GPU MI200
+   *  - AMD_GFX942
       - GPU
-      - AMD GPU MI200 GFX90A
-   *  - NAVI1030
+      - AMD GPU MI300
+   *  - AMD_GFX1030
       - GPU
       - AMD GPU V620/W6800
-   *  - NAVI1100
+   *  - 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
@@ -666,7 +699,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.0.1 of the Kokkos library.
+This list was last updated for version 4.3.0 of the Kokkos library.
 
 .. tabs::
 
@@ -731,7 +764,8 @@ This list was last updated for version 4.0.1 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:
@@ -759,9 +793,10 @@ This list was last updated for version 4.0.1 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
 
@@ -789,10 +824,11 @@ This list was last updated for version 4.0.1 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -876,11 +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``
@@ -902,7 +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
@@ -920,9 +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
@@ -996,7 +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.
 
 ----------
@@ -1023,10 +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
@@ -1090,9 +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
@@ -1112,12 +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
@@ -1191,10 +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
@@ -1213,10 +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++"
 
 ----------
 
@@ -1242,10 +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
@@ -1264,10 +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++"
 
 ----------
 
@@ -1300,10 +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
@@ -1322,8 +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
@@ -1370,9 +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
@@ -1383,10 +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``
@@ -1403,6 +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
@@ -1426,8 +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.
 
@@ -1454,10 +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
@@ -1467,10 +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``.
 
@@ -1493,10 +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
@@ -1567,29 +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.
@@ -1618,14 +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
@@ -1640,17 +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.
 
 ----------
@@ -1724,8 +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
@@ -1742,12 +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.
@@ -1794,19 +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
@@ -1835,7 +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
 
@@ -1864,7 +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
@@ -2023,10 +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
@@ -2039,10 +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.
 
 ----------
 
@@ -2082,11 +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
@@ -44,21 +53,36 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
+.. versionadded:: 7Feb2024
+
+Alternatively, LAMMPS can use the `heFFTe
+<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
+communication algorithms, which comes with many optimizations for
+special cases, e.g. leveraging available 2D and 3D FFTs in the back end
+libraries and better pipelining for packing and communication.
+
 .. tabs::
 
    .. tab:: CMake build
 
       .. code-block:: bash
 
-         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else 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
 
       .. note::
 
-         The values for the FFT variable must be in upper-case.  This is
-         an exception to the rule that all CMake variables can be specified
-         with lower-case values.
+         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 variable applies.
+         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``.
 
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
@@ -76,6 +100,17 @@ LAMMPS can use them if they are available on your system.
          -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 Heffte_ROOT=path         # path to an existing heFFTe installation
+
+      .. note::
+
+         heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
+         default internal FFT implementation; however, this stock back
+         end is intended for testing purposes only and is not optimized
+         for production runs.
+
 
    .. tab:: Traditional make
 
@@ -85,32 +120,74 @@ LAMMPS can use them if they are available on your system.
 
       .. 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_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 =       -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
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
+      Traditional make can also link to heFFTe using an existing installation
+
+      .. code-block:: make
+
+         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
+         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
+         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
+      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``,
+      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.
+
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -134,13 +211,18 @@ 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
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
+The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
+AMD's HIP installations, respectively. These FFT libraries require the
+Kokkos acceleration package to be enabled and the Kokkos back end to be
+GPU-resident (i.e., HIP or CUDA).
+
 Performing 3d FFTs in parallel can be time-consuming due to data access
 and required communication.  This cost can be reduced by performing
 single-precision FFTs instead of double precision.  Single precision
@@ -152,11 +234,11 @@ generally less than the difference in precision. Using the
 ``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
 use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
-library a second time with support for single-precision.
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
+the FFTW3 installation includes support for single-precision.
 
-For FFTW3, do the following, which should produce the additional
-library ``libfftw3f.a`` or ``libfftw3f.so``\ .
+When compiler FFTW3 from source, you can do the following, which should
+produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 
@@ -165,13 +247,27 @@ library ``libfftw3f.a`` 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.
 
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing
+install with hints provided by ``-DHeffte_ROOT``, as recommended by the
+CMake standard and note that the name is case sensitive. If CMake cannot
+find a heFFTe installation with the correct back end (e.g., FFTW or
+MKL), it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific
+variables listed in the `heFFTe documentation
+<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+and those variables will be passed into the heFFTe build.
+
 ----------
 
+.. raw:: latex
+
+    \clearpage
+
 .. _size:
 
 Size of LAMMPS integer types and size limits
@@ -212,7 +308,7 @@ LAMMPS system size restrictions
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 18 27 28 27
    :align: center
 
    * -
@@ -281,8 +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
@@ -295,12 +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
@@ -322,8 +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``,
@@ -354,8 +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::
 
@@ -363,8 +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
 
@@ -386,18 +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.
@@ -411,9 +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
 
@@ -422,7 +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
@@ -463,8 +608,8 @@ Exception handling when using LAMMPS as a library
 
 LAMMPS errors do not kill the calling code, but throw an exception.  In
 the C-library interface, the call stack is unwound and control returns
-to the caller, e.g. to Python or a code that is coupled to LAMMPS and
-the error status can be queried.  When using C++ directly, the calling
+to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
+error status can then be queried.  When using C++ directly, the calling
 code has to be set up to *catch* exceptions thrown from within LAMMPS.
 
 .. note::

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>`
+   *
+   *
    *
    *
    *
@@ -89,6 +80,7 @@ OPT.
    * :doc:`cosine/shift (o) <angle_cosine_shift>`
    * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
    * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
    * :doc:`cross <angle_cross>`
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
@@ -99,13 +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
@@ -113,20 +105,23 @@ 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>`
+   *
+   *
    *
    *
    *
    *
    *
    * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`charmmfsw (k) <dihedral_charmm>`
    * :doc:`class2 (ko) <dihedral_class2>`
    * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
@@ -141,8 +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
@@ -150,11 +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>`
@@ -100,6 +86,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
+   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -107,6 +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>`
@@ -115,12 +106,16 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
+   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :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:`slice <compute_slice>`
    * :doc:`smd/contact/radius <compute_smd_contact_radius>`
    * :doc:`smd/damage <compute_smd_damage>`

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>`
@@ -61,6 +48,7 @@ OPT.
    * :doc:`controller <fix_controller>`
    * :doc:`damping/cundall <fix_damping_cundall>`
    * :doc:`deform (k) <fix_deform>`
+   * :doc:`deform/pressure <fix_deform_pressure>`
    * :doc:`deposit <fix_deposit>`
    * :doc:`dpd/energy (k) <fix_dpd_energy>`
    * :doc:`drag <fix_drag>`
@@ -122,6 +110,7 @@ OPT.
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
@@ -202,6 +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>`
@@ -238,10 +232,10 @@ OPT.
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`
-   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`
    * :doc:`temp/csvr <fix_temp_csvr>`
-   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale (k) <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
    * :doc:`tgnpt/drude <fix_tgnh_drude>`
@@ -261,6 +255,7 @@ OPT.
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
+   * :doc:`wall/flow (k) <fix_wall_flow>`
    * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`

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>`
@@ -87,16 +73,17 @@ OPT.
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
-   * :doc:`coul/slater/long <pair_coul_slater>`
+   * :doc:`coul/slater/long (g) <pair_coul_slater>`
    * :doc:`coul/shield <pair_coul_shield>`
    * :doc:`coul/streitz <pair_coul>`
    * :doc:`coul/tt <pair_coul_tt>`
    * :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>`
@@ -110,7 +97,7 @@ OPT.
    * :doc:`eam/he <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
-   * :doc:`edpd <pair_mesodpd>`
+   * :doc:`edpd (g) <pair_mesodpd>`
    * :doc:`eff/cut <pair_eff>`
    * :doc:`eim (o) <pair_eim>`
    * :doc:`exp6/rx (k) <pair_exp6_rx>`
@@ -146,7 +133,7 @@ OPT.
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
    * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
-   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
    * :doc:`lj/class2 (gko) <pair_class2>`
    * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
    * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
@@ -158,14 +145,14 @@ OPT.
    * :doc:`lj/cut (gikot) <pair_lj>`
    * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/cut/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
    * :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/long/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
@@ -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>`
@@ -202,7 +189,7 @@ OPT.
    * :doc:`lubricate/poly (o) <pair_lubricate>`
    * :doc:`lubricateU <pair_lubricateU>`
    * :doc:`lubricateU/poly <pair_lubricateU>`
-   * :doc:`mdpd <pair_mesodpd>`
+   * :doc:`mdpd (g) <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
    * :doc:`meam (k) <pair_meam>`
    * :doc:`meam/ms (k) <pair_meam>`
@@ -245,7 +232,8 @@ OPT.
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
-   * :doc:`pod <pair_pod>`
+   * :doc:`pedone (o) <pair_pedone>`
+   * :doc:`pod (k) <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -256,7 +244,10 @@ OPT.
    * :doc:`rann <pair_rann>`
    * :doc:`reaxff (ko) <pair_reaxff>`
    * :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>`
@@ -267,12 +258,12 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (ik) <pair_snap>`
-   * :doc:`soft (go) <pair_soft>`
-   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`soft (gko) <pair_soft>`
+   * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
-   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/lj (g) <pair_sph_lj>`
    * :doc:`sph/rhosum <pair_sph_rhosum>`
-   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater (g) <pair_sph_taitwater>`
    * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
    * :doc:`spin/dipole/cut <pair_spin_dipole>`
    * :doc:`spin/dipole/long <pair_spin_dipole>`
@@ -301,6 +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
 ------------------------------------------
 
@@ -126,6 +138,17 @@ syntax compatible with the removed reax pair style, so input files will
 have to be adapted.  The REAXFF package was originally called
 USER-REAXC.
 
+USER-REAXC package
+------------------
+
+.. deprecated:: 7Feb2024
+
+The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
+In the process also the pair style and related fixes were renamed to use
+the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
+backward compatibility by providing aliases for the styles.  These have
+been removed, so using "reaxff" is now *required*.
+
 USER-CUDA package
 -----------------
 
@@ -137,12 +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_platform.rst

@@ -70,6 +70,9 @@ File and path functions and global constants
 .. doxygenfunction:: is_console
    :project: progguide
 
+.. doxygenfunction:: disk_free
+   :project: progguide
+
 .. doxygenfunction:: path_is_directory
    :project: progguide
 

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:
@@ -121,7 +121,7 @@ will be suppressed and only a summary printed, but adding
 the '-V' option will then produce output from the tests
 above like the following:
 
-.. code-block::
+.. code-block:: console
 
    [...]
    1: [ RUN      ] Tokenizer.empty_string
@@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
 environment variable, ``TEST_ARGS=-v``) it can be printed and used to
 understand why tests fail unexpectedly.
 
-Another complexity of these tests stems from the need to capture
-situations where LAMMPS will stop with an error, i.e. handle so-called
-"death tests".  Here the LAMMPS code will operate differently depending
-on whether it was configured to throw C++ exceptions on errors or call
-either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
-also needs to detect whether LAMMPS was compiled with the OpenMPI
-library, as OpenMPI is **only** compatible the death test options of the
-GoogleTest library when C++ exceptions are enabled; otherwise those
-"death tests" must be skipped to avoid reporting bogus failures.  The
-specifics of this step are implemented in the ``TEST_FAILURE()``
-macro. These tests operate by capturing the screen output when executing
-the failing command and then comparing that with a provided regular
-expression string pattern.  Example:
+The specifics of so-called "death tests", i.e. conditions where LAMMPS
+should fail and throw an exception, are implemented in the
+``TEST_FAILURE()`` macro. These tests operate by capturing the screen
+output when executing the failing command and then comparing that with a
+provided regular expression string pattern.  Example:
 
 .. code-block:: c++
 
@@ -235,12 +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
@@ -266,7 +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).
@@ -280,11 +272,9 @@ 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.  This part of the
-unit tests is incomplete since the Fortran module it is based on is
-incomplete as well.
+turn call the functions in the LAMMPS Fortran module.
 
 Tests for the C++-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -303,7 +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
@@ -405,10 +395,10 @@ compare with the reference and also start from the data file.  A final
 check will use multi-cutoff r-RESPA (if supported by the pair style) at
 a 1:1 split and compare to the Verlet results.  These sets of tests are
 run with multiple test fixtures for accelerated styles (OPT, OPENMP,
-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
-these tests the relative error (epsilon) is lowered by a common factor
-due to the additional numerical noise, but the tests are still comparing
-to the same reference data.
+INTEL, KOKKOS (OpenMP only)) and for the latter three with 4 OpenMP
+threads enabled.  For these tests the relative error (epsilon) is lowered
+by a common factor due to the additional numerical noise, but the tests
+are still comparing to the same reference data.
 
 Additional tests will check whether all listed extract keywords are
 supported and have the correct dimensionality and the final set of tests
@@ -421,7 +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:
 
@@ -442,17 +432,19 @@ The ``test_pair_style`` tester is used with 4 categories of test inputs:
   pair style is defined, but the computation of the pair style contributions
   is disabled.
 
-The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
-fashion and share support functions with the pair style tester.  The final
-group of tests in this section is for fix styles that add/manipulate forces
-and velocities, e.g. for time integration, thermostats and more.
+The ``test_bond_style``, ``test_angle_style``, ``test_dihedral_style``, and
+``test_improper_style`` tester programs are set up in a similar fashion and
+share support functions with the pair style tester.  The final group of
+tests in this section is for fix styles that add/manipulate forces and
+velocities, e.g. for time integration, thermostats and more.
 
-Adding a new test is easiest done by copying and modifying an existing test
-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 they do not diverge.
+Adding a new test is easiest done by copying and modifying an existing YAML
+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, as long as
+they do not diverge.
 
 The template input files define a large number of index variables at the top
 that can be modified inside the YAML file to control the behavior.  For example,
@@ -480,7 +472,7 @@ Note that this disables computing the kspace contribution, but still will run
 the setup.  The "gewald" parameter should be set explicitly to speed up the run.
 For styles with long-range electrostatics, typically two tests are added one using
 the (slower) analytic approximation of the erfc() function and the other using
-the tabulated coulomb, to test both code paths. The reference results in the YAML
+the tabulated coulomb, to test both code paths.  The reference results in the YAML
 files then should be compared manually, if they agree well enough within the limits
 of those two approximations.
 
@@ -534,3 +526,101 @@ The ``unittest/tools`` folder contains tests for programs in the
 shell, which are implemented as a python scripts using the ``unittest``
 Python module and launching the tool commands through the ``subprocess``
 Python module.
+
+
+Troubleshooting failed unit tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+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 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
+*after* a merge, or when a special label, ``gpu_unit_tests`` is added
+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 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"
+symbol near the ``Logout`` button on the top right of that page to go to
+the "classic view".  In the classic view, there is a list of the
+individual runs that make up this test run (they are shown but cannot be
+inspected in the default view).  You can click on any of those.
+Clicking on ``Test Result`` will display the list of failed tests. Click
+on the "Status" column to sort the tests based on their Failed or Passed
+status.  Then click on the failed test to expand its output.
+
+For example, the following output snippet shows the failed unit test
+
+.. code-block:: console
+
+   [ RUN      ] PairStyle.gpu
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:63: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00018957912910606503 vs 0.0001
+   Google Test trace:
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:56: EXPECT_FORCES: init_forces (newton off)
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:64: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00022892713393549854 vs 0.0001
+
+The failed assertions provide line numbers in the test source
+(e.g. ``test_main.cpp:56``), from which one can understand what
+specific assertion failed.
+
+Note that the force style engine runs one of a small number of systems
+in a rather off-equilibrium configuration with a few atoms for a few
+steps, writes data and restart files, uses :doc:`the clear command
+<clear>` to reset LAMMPS, and then runs from those files with different
+settings (e.g. newton on/off) and integrators (e.g. verlet vs. respa).
+Beyond potential issues/bugs in the source code, the mismatch between
+the expected and actual values could be that force arrays are not
+properly cleared between multiple run commands or that class members are
+not correctly initialized or written to or read from a data or restart
+file.
+
+While the epsilon (relative precision) for a single, `IEEE 754 compliant
+<https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
+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.  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.
+For tests of accelerated styles, the per-test epsilon is multiplied
+by empirical factors that take into account the differences in the order
+of floating point operations or that some or most intermediate operations
+may be done using approximations or with single precision floating point
+math.
+
+To rerun the failed unit test individually, change to the ``build`` directory
+and run the test with verbose output. For example,
+
+.. code-block:: bash
+
+    env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
+
+``ctest`` with the ``-V`` flag also shows the exact command line
+of the test. One can then use ``gdb --args`` to further debug and
+catch exceptions with the test command, for example,
+
+.. code-block:: bash
+
+    gdb --args /path/to/lammps/build/test_pair_style /path/to/lammps/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml
+
+
+It is recommended to configure the build with ``-D
+BUILD_SHARED_LIBS=on`` and use a custom linker to shorten the build time
+during recompilation.  Installing `ccache` in your development
+environment helps speed up recompilation by caching previous
+compilations and detecting when the same compilation is being done
+again.  Please see :doc:`Build_development` for further details.

doc/src/Developer_updating.rst

@@ -18,8 +18,10 @@ Available topics in mostly chronological order are:
 - `Setting flags in the constructor`_
 - `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
 - `Use ev_init() to initialize variables derived from eflag and vflag`_
+- `Use utils::count_words() functions instead of atom->count_words()`_
 - `Use utils::numeric() functions instead of force->numeric()`_
 - `Use utils::open_potential() function to open potential files`_
+- `Use symbolic Atom and AtomVec constants instead of numerical values`_
 - `Simplify customized error messages`_
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
@@ -50,10 +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
@@ -107,7 +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:
@@ -129,6 +130,41 @@ Not applying this change will not cause a compilation error, but
 can lead to inconsistent behavior and incorrect tallying of
 energy or virial.
 
+Use utils::count_words() functions instead of atom->count_words()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 2Jun2020
+
+The "count_words()" functions for parsing text have been moved from the
+Atom class to the :doc:`utils namespace <Developer_utils>`.  The
+"count_words()" function in "utils" uses the Tokenizer class internally
+to split a line into words and count them, thus it will not modify the
+argument string as the function in the Atoms class did and thus had a
+variant using a copy buffer.  Unlike the old version, the new version
+does not remove comments. For that you can use the
+:cpp:func:`utils::trim_comment() function
+<LAMMPS_NS::utils::trim_comment>` as shown in the example below.
+
+Old:
+
+.. code-block:: c++
+
+   nwords = atom->count_words(line);
+   int nwords = atom->count_words(buf);
+
+New:
+
+.. code-block:: c++
+
+   nwords = utils::count_words(line);
+   int nwords = utils::count_words(utils::trim_comment(buf));
+
+.. seealso::
+
+   :cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
+   :cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
+
+
 Use utils::numeric() functions instead of force->numeric()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -136,11 +172,12 @@ Use utils::numeric() functions instead of force->numeric()
 
 The "numeric()" conversion functions (including "inumeric()",
 "bnumeric()", and "tnumeric()") have been moved from the Force class to
-the utils namespace.  Also they take an additional argument that selects
-whether the ``Error::all()`` or ``Error::one()`` function should be
-called in case of an error.  The former should be used when *all* MPI
-processes call the conversion function and the latter *must* be used
-when they are called from only one or a subset of the MPI processes.
+the :doc:`utils namespace <Developer_utils>`.  Also they take an
+additional argument that selects whether the ``Error::all()`` or
+``Error::one()`` function should be called in case of an error.  The
+former should be used when *all* MPI processes call the conversion
+function and the latter *must* be used when they are called from only
+one or a subset of the MPI processes.
 
 Old:
 
@@ -173,14 +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:
@@ -196,6 +233,73 @@ New:
 
    fp = utils::open_potential(filename, lmp);
 
+Use symbolic Atom and AtomVec constants instead of numerical values
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+Properties in LAMMPS that were represented by integer values (0, 1,
+2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
+classes derived from it) (and its derived classes) have been converted
+to use scoped enumerators instead.
+
+.. list-table::
+   :header-rows: 1
+   :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
+   * - AtomVec::PER_ATOM
+     - 0
+     - AtomVec::PER_TYPE
+     - 1
+     - Atom::MAP_YES
+     - 3
+
+Old:
+
+.. code-block:: c++
+
+   molecular = 0;
+   mass_type = 1;
+   if (atom->molecular == 2)
+   if (atom->map_style == 2)
+   atom->add_callback(0);
+   atom->delete_callback(id,1);
+
+New:
+
+.. code-block:: c++
+
+   molecular = Atom::ATOMIC;
+   mass_type = AtomVec::PER_TYPE;
+   if (atom->molecular == Atom::TEMPLATE)
+   if (atom->map_style == Atom::MAP_HASH)
+   atom->add_callback(Atom::GROW);
+   atom->delete_callback(id,Atom::RESTART);
+
 Simplify customized error messages
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -203,7 +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:
 
@@ -229,7 +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
@@ -267,7 +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.
@@ -635,10 +638,10 @@ Tohoku University (under MIT license)
 
 ----------
 
-.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
+.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
    :project: progguide
 
-.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
+.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
    :project: progguide
 
 ---------------------------

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_details.rst

@@ -13,15 +13,44 @@ discussions of such cases.
 Unknown identifier in data file
 -------------------------------
 
-This error happens when LAMMPS encounters a line of text in an unexpected format
-while reading a data file. This is most commonly cause by inconsistent header and
-section data.  The header section informs LAMMPS how many entries or lines are expected in the
-various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
-If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
-or stop reading before the section has ended.
+This error happens when LAMMPS encounters a line of text with an
+unexpected keyword while :doc:`reading a data file <read_data>`.  This
+would be either header keywords or section header keywords.  This is
+most commonly due to a mistyped keyword or due to a keyword that is
+inconsistent with the :doc:`atom style <atom_style>` used.
 
-Such a mismatch can happen unexpectedly when the first line of the data
-is *not* a comment as required by the format.  That would result in
-LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
-is treated as a comment.
+The header section informs LAMMPS how many entries or lines are expected
+in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
+the data file.  If there is a mismatch, LAMMPS will either keep reading
+beyond the end of a section or stop reading before the section has
+ended.  In that case the next line will not contain a recognized keyword.
 
+Such a mismatch can also happen when the first line of the data
+is *not* a comment as required by the format, but a line with a valid
+header keyword.  That would result in LAMMPS expecting, for instance,
+0 atoms because the "atoms" header line is the first line and thus
+treated as a comment.
+
+Another possibility to trigger this error is to have a keyword in the
+data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
+but the :doc:`read_data <read_data>` command is missing the (optional)
+arguments that identify the fix and the header keyword and section
+keyword or those arguments are inconsistent with the keywords in the
+data file.
+
+.. _err0002:
+
+Incorrect format in ... section of data file
+--------------------------------------------
+
+This error happens when LAMMPS reads the contents of a section of a
+:doc:`data file <read_data>` and the number of parameters in the line
+differs from what is expected.  This most commonly happens, when the
+atom style is different from what is expected for a specific data file
+since changing the atom style usually changes the format of the line.
+
+This error can also happen when the number of entries indicated in the
+header of a data file (e.g. the number of atoms) is larger than the
+number of lines provided (e.g. in the corresponding Atoms section)
+and then LAMMPS will continue reading into the next section and that
+would have a completely different format.

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.
 
@@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed
    Fix poems cannot (yet) work with coupled bodies whose joints connect
    the bodies in a tree structure.
 
-*Triclinic box skew is too large*
-   The displacement in a skewed direction must be less than half the box
-   length in that dimension.  E.g. the xy tilt must be between -half and
-   +half of the x box length.  This constraint can be relaxed by using
-   the box tilt command.
-
 *Tried to convert a double to int, but input_double > INT_MAX*
    Self-explanatory.
 

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
@@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations.
    More than the maximum # of neighbors was found multiple times.  This
    was unexpected.
 
-*Triclinic box skew is large*
-   The displacement in a skewed direction is normally required to be less
-   than half the box length in that dimension.  E.g. the xy tilt must be
-   between -half and +half of the x box length.  You have relaxed the
-   constraint using the box tilt command, but the warning means that a
-   LAMMPS simulation may be inefficient as a result.
-
 *Use special bonds = 0,1,1 with bond style fene*
    Most FENE models need this setting for the special_bonds command.
 

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`
@@ -315,6 +317,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype extract_variable: function
    :f set_variable: :f:subr:`set_variable`
    :ftype set_variable: subroutine
+   :f set_string_variable: :f:subr:`set_set_string_variable`
+   :ftype set_string_variable: subroutine
+   :f set_internal_variable: :f:subr:`set_internal_variable`
+   :ftype set_internal_variable: subroutine
    :f gather_atoms: :f:subr:`gather_atoms`
    :ftype gather_atoms: subroutine
    :f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@@ -1071,7 +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
@@ -1161,7 +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
@@ -1251,8 +1257,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    three elements of the global vector calculated by fix recenter into the
    variables *dx*, *dy*, and *dz*, respectively.
 
-   If asked for per-atom or local data, :f:func:`extract_compute` returns a
-   pointer to actual LAMMPS data. The pointer so returned will have the
+   If asked for per-atom or local data, :f:func:`extract_fix` returns a
+   pointer to actual LAMMPS data.  The pointer returned will have the
    appropriate size to match the internal data, and will be
    type/kind/rank-checked at the time of the assignment. For example,
 
@@ -1398,7 +1404,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    Set the value of a string-style variable.
 
-   .. versionadded:: 3Nov2022
+   .. deprecated:: 7Feb2024
+
+   This function assigns a new value from the string *str* to the string-style
+   variable *name*\ . If *name* does not exist or is not a string-style
+   variable, an error is generated.
+
+   .. warning::
+
+      This subroutine is deprecated and :f:subr:`set_string_variable`
+      should be used instead.
+
+   :p character(len=*) name: name of the variable
+   :p character(len=*) str:  new value to assign to the variable
+   :to: :cpp:func:`lammps_set_variable`
+
+--------
+
+.. f:subroutine:: set_string_variable(name, str)
+
+   Set the value of a string-style variable.
+
+   .. versionadded:: 7Feb2024
 
    This function assigns a new value from the string *str* to the string-style
    variable *name*\ . If *name* does not exist or is not a string-style
@@ -1406,7 +1433,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    :p character(len=*) name: name of the variable
    :p character(len=*) str:  new value to assign to the variable
-   :to: :cpp:func:`lammps_set_variable`
+   :to: :cpp:func:`lammps_set_string_variable`
+
+--------
+
+.. f:subroutine:: set_internal_variable(name, val)
+
+   Set the value of a internal-style variable.
+
+   .. versionadded:: 7Feb2024
+
+   This function assigns a new value from the floating-point number *val* to
+   the internal-style variable *name*\ . If *name* does not exist or is not
+   an internal-style variable, an error is generated.
+
+   :p character(len=*) name: name of the variable
+   :p read(c_double) val:  new value to assign to the variable
+   :to: :cpp:func:`lammps_set_internal_variable`
 
 --------
 
@@ -2284,7 +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:
@@ -3038,14 +3081,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This function can be used to query if an error inside of LAMMPS
    has thrown a :ref:`C++ exception <exceptions>`.
 
-   .. note::
-
-      This function will always report "no error" when the LAMMPS library
-      has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
-      errors aborting LAMMPS into C++ exceptions. You can use the library
-      function :cpp:func:`lammps_config_has_exceptions` to check if this is
-      the case.
-
    :to: :cpp:func:`lammps_has_error`
    :r has_error: ``.TRUE.`` if there is an error.
    :rtype has_error: logical
@@ -3068,13 +3103,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    would happen only in a single MPI rank and thus may not be recoverable, as
    other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
 
-   .. note::
-
-      This function will do nothing when the LAMMPS library has been
-      compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
-      LAMMPS into C++ exceptions.  You can use the function
-      :f:func:`config_has_exceptions` to check whether this is the case.
-
    :p character(len=\*) buffer: string buffer to copy the error message into
    :o integer(c_int) status [optional]: 1 when all ranks had the error,
     2 on a single-rank error.

doc/src/Howto.rst

@@ -89,6 +89,7 @@ Packages howto
    Howto_drude2
    Howto_peri
    Howto_manifold
+   Howto_rheo
    Howto_spins
 
 Tutorials howto
@@ -101,6 +102,7 @@ Tutorials howto
    Howto_cmake
    Howto_github
    Howto_lammps_gui
+   Howto_moltemplate
    Howto_pylammps
    Howto_wsl
 

doc/src/Howto_2d.rst

@@ -1,42 +1,112 @@
-2d simulations
-==============
+================
+ 2d simulations
+================
 
-Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
+You must use the :doc:`dimension <dimension>` command to specify a 2d
+simulation.  The default is 3d.
 
-Make the simulation box periodic in z via the :doc:`boundary <boundary>`
-command.  This is the default.
+A 2d simulation box must be periodic in z as set by the :doc:`boundary
+<boundary>` command.  This is the default.
 
-If using the :doc:`create_box <create_box>` command to define a
-simulation box, set the z dimensions narrow, but finite, so that the
-:doc:`create_atoms <create_atoms>` command will fill the 3d simulation
-box with a single z plane of atoms - e.g.
+Simulation boxes in LAMMPS can be either orthogonal or triclinic in
+shape.  Orthogonal boxes in 2d are a rectangle with 4 edges that are
+each perpendicular to either the x or y coordinate axes.  Triclinic
+boxes in 2d are a parallelogram with opposite pairs of faces parallel
+to each other.  LAMMPS supports two forms of triclinic boxes,
+restricted and general, which for 2d differ in how the box is oriented
+with respect to the xy coordinate axes.  See the :doc:`Howto triclinic
+<Howto_triclinic>` for a detailed description of all 3 kinds of
+simulation boxes.
+
+Here are examples of using the :doc:`create_box <create_box>` command
+to define the simulation box for a 2d system.
 
 .. code-block:: LAMMPS
 
-   create_box 1 -10 10 -10 10 -0.25 0.25
+   # 2d orthogonal box using a block-style region
+   region mybox block -10 10 0 10 -0.5 0.5
+   create_box 1 mybox
 
-If using the :doc:`read_data <read_data>` command to read in a file of
-atom coordinates, set the "zlo zhi" values to be finite but narrow,
-similar to the create_box command settings just described.  For each
-atom in the file, assign a z coordinate so it falls inside the
-z-boundaries of the box - e.g. 0.0.
+   # 2d restricted triclinic box using a prism-style region with only xy tilt
+   region mybox prism 0 10 0 10 -0.5 0.5 2.0 0.0 0.0
+   create_box 1 mybox
 
-Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
-defined fix to ensure that the z-components of velocities and forces
-are zeroed out every timestep.  The reason to make it the last fix is
-so that any forces induced by other fixes will be zeroed out.
+   # 2d general triclinic box using a primitive cell for a 2d hex lattice
+   lattice       custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
+                 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
+   create_box    1 NULL 0 5 0 5 -0.5 0.5
 
-Many of the example input scripts included in the LAMMPS distribution
+Note that for 2d orthogonal or restricted triclinic boxes, the box has
+a 3rd dimension which must straddle z = 0.0 in the z dimension.
+Typically the width of box in the z dimension should be narrow,
+e.g. -0.5 to 0.5, but that is not required.  For a 2d general
+triclinic box, the *a3* vector defined by the :doc:`lattice <lattice>`
+command must be (0.0,0.0,1.0), which is its default value.  Also the
+*clo* and *chi* arguments of the :doc:`create_box <create_box>`
+command must be -0.5 and 0.5.
+
+Here are examples of using the :doc:`read_data <read_data>` command
+to define the simulation box for a 2d system via keywords in the
+header section of the data file.  These are the same boxes as the examples
+for the :doc:`create_box <create_box>` command
+
+.. code-block:: LAMMPS
+
+   # 2d orthogonal box
+   -10 10   xlo xhi
+   0 10     ylo yhi
+   -0.5 0.5 zlo zhi       # this is the default, so no need to specify
+
+   # 2d restricted triclinic box with only xy tilt
+   -10 10   xlo xhi
+   0 10     ylo yhi
+   -0.5 0.5 zlo zhi       # this is the default, so no need to specify
+   2.0 0.0 0.0 xy xz yz
+
+   # 3d general triclinic box using a primitive cell for a 2d hex lattice
+   5 0 0              avec
+   2.5 4.3301270189 0 bvec
+   0 0 1              cvec           # this is the default, so no need to specify
+   0 0 -0.5           abc origin     # this is the default for 2d, so no need to specify
+
+Note that for 2d orthogonal or restricted triclinic boxes, the box has
+a 3rd dimension specified by the *zlo zhi* values, which must straddle
+z = 0.0.  Typically the width of box in the z dimension should be
+narrow, e.g. -0.5 to 0.5, but that is not required.  For a 2d general
+triclinic box, the z component of *avec* and *bvec* must be zero, and
+*cvec* must be (0,0,1), which is the default.  The z component of *abc
+origin* must also be -0.5, which is the default.
+
+If using the :doc:`create_atoms <create_atoms>` command to create
+atoms in the 2d simulation box, all the z coordinates of created atoms
+will be zero.
+
+If using the :doc:`read_data <read_data>` command to read in a data
+file of atom coordinates for a 2d system, the z coordinates of all
+atoms should be zero.  A value within epsilon of zero is also allowed
+in case the data file was generated by another program with finite
+numeric precision, in which case the z coord for the atom will be set
+to zero.
+
+Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last fix
+defined in the input script.  It ensures that the z-components of
+velocities and forces are zeroed out every timestep.  The reason to
+make it the last fix is so that any forces added by other fixes will
+also be zeroed out.
+
+Many of the example input scripts included in the examples directory
 are for 2d models.
 
 .. note::
 
    Some models in LAMMPS treat particles as finite-size spheres, as
-   opposed to point particles.  See the :doc:`atom_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
-   commands for details.  By default, for 2d simulations, such particles
-   will still be modeled as 3d spheres, not 2d discs (circles), meaning
+   opposed to point particles.  See the :doc:`atom_style sphere
+   <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>` commands
+   for details.  By default, for 2d simulations, such particles will
+   still be modeled as 3d spheres, not 2d discs (circles), meaning
    their moment of inertia will be that of a sphere.  If you wish to
-   model them as 2d discs, see the :doc:`set density/disc <set>` command
-   and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
-   :doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
-   commands.
+   model them as 2d discs, see the :doc:`set density/disc <set>`
+   command and the *disc* option for the :doc:`fix nve/sphere
+   <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
+   :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
+   <fix_npt_sphere>` commands.

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_body.rst

@@ -102,8 +102,19 @@ particles of different styles
 | :doc:`dump image <dump_image>`                 | output body particle attributes as an image         |
 +------------------------------------------------+-----------------------------------------------------+
 
-The pair styles defined for use with specific body styles are listed
-in the sections below.
+The pair styles currently defined for use with specific body styles
+are listed in the sections below.
+
+Note that for all the body styles, if the data file defines a general
+triclinic box, then the orientation of the body particle and its
+corresponding 6 moments of inertia and other orientation-dependent
+values should reflect the fact the body is defined withing a general
+triclinic box with edge vectors **A**,**B**,**C**.  LAMMPS will rotate
+the box to convert it to a restricted triclinic box.  This operation
+will also rotate the orientation of the body particles.  See the
+:doc:`Howto triclinic <Howto_triclinic>` doc page for more details.
+The sections below highlight the orientation-dependent values specific
+to each body style.
 
 ----------
 
@@ -154,12 +165,18 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each sub-particle are specified as its x,y,z
 displacement from the center-of-mass of the body particle.  The
 center-of-mass position of the particle is specified by the x,y,z
 values in the *Atoms* section of the data file, as is the total mass
 of the body particle.
 
+Note that if the data file defines a general triclinic simulation box,
+these sub-particle displacements are orientation-dependent and, as
+mentioned above, should reflect the body particle's orientation within
+the general triclinic box.
+
 The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
 with this body style to compute body/body and body/non-body interactions.
 
@@ -226,6 +243,7 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass
 position of the particle is specified by the x,y,z values in the
@@ -270,6 +288,11 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
    0 0 0
    3.0
 
+Note that if the data file defines a general triclinic simulation box,
+these polygon vertex displacements are orientation-dependent and, as
+mentioned above, should reflect the body particle's orientation within
+the general triclinic box.
+
 The :doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>`
 command can be used with this body style to compute body/body
 interactions.  The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
@@ -335,7 +358,7 @@ faces are listed, so that M = 6 + 3\*N + 1.
 The integer line has three values: number of vertices (N), number of
 edges (E) and number of faces (F). The floating point line(s) list 6
 moments of inertia followed by the coordinates of the N vertices (x1
-to zN) as 3N values, followed by 2N vertex indices corresponding to
+to zN) as 3N values, followed by 2E vertex indices corresponding to
 the end points of the E edges, then 4\*F vertex indices defining F
 faces.  The last value is the diameter value = the rounded diameter of
 the sphere that surrounds each vertex. The diameter value can be
@@ -366,6 +389,7 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass
 position of the particle is specified by the x,y,z values in the
@@ -435,6 +459,11 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
 The number of edges and faces for a rod or sphere must be listed,
 but is ignored.
 
+Note that if the data file defines a general triclinic simulation box,
+these polyhedron vertex displacements are orientation-dependent and,
+as mentioned above, should reflect the body particle's orientation
+within the general triclinic box.
+
 The :doc:`pair_style body/rounded/polhedron
 <pair_body_rounded_polyhedron>` command can be used with this body
 style to compute body/body interactions.  The :doc:`fix

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``
@@ -349,6 +347,8 @@ Some common LAMMPS specific variables
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
    * - ``FFT``
      - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
+   * - ``FFT_KOKKOS``
+     - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
    * - ``FFT_SINGLE``
      - select whether to use single precision FFTs (default: ``off``)
    * - ``WITH_JPEG``

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`.