Merge branch 'develop' into pace-mliap

# Conflicts:
#	src/ML-IAP/compute_mliap.cpp

.github/CODEOWNERS

@@ -37,7 +37,7 @@ 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/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -65,9 +65,12 @@ src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
 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
 
 # core LAMMPS classes

.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.*') }}

.github/workflows/unittest-macos.yml

@@ -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 }}

cmake/CMakeLists.txt

@@ -120,6 +120,19 @@ 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")
@@ -209,6 +222,10 @@ 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)
@@ -415,6 +432,7 @@ 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 +443,21 @@ 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
@@ -539,12 +572,12 @@ endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-foreach(HEADER cmath)
+if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
-  check_include_file_cxx(${HEADER} FOUND_${HEADER})
+  check_include_file_cxx(cmath FOUND_CMATH)
-  if(NOT FOUND_${HEADER})
+  if(NOT FOUND_CMATH)
-    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+    message(FATAL_ERROR "Could not find the required 'cmath' header")
-  endif(NOT FOUND_${HEADER})
+  endif(NOT FOUND_CMATH)
-endforeach(HEADER)
+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")
@@ -971,14 +1004,15 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  if (LMP_HEFFTE)
+  if (FFT_USE_HEFFTE)
     message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  heFFTe")
-    if (HEFFTE_BACKEND)
+    if (FFT_HEFFTE_BACKEND)
-      message(STATUS "heFFTe backend:  ${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()
@@ -997,28 +1031,10 @@ if(PKG_KSPACE)
     else()
       message(STATUS "Using non-threaded FFTs")
     endif()
-    if (FFT_HEFFTE)
+    message(STATUS "Using builtin distributed FFT algorithms")
-      message(STATUS "Using distributed algorithms from heFTTe")
+  endif()
-    else()
+  if(PKG_KOKKOS)
-      message(STATUS "Using builtin distributed algorithms")
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
-    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()
-    endif()
   endif()
 endif()
 if(BUILD_DOC)

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/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.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_MD5 "f3573cf9daa3558ba46fd5866517f38f" 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/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

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

@@ -45,8 +45,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "16b9b09ae947d434dfb58fc5c87c2b76" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.2.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.2.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -126,16 +126,36 @@ 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"))
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
-      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
+      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
-      target_link_libraries(lammps PRIVATE 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_library(CUFFT_LIBRARY cufft)
+      if (CUFFT_LIBRARY STREQUAL "CUFFT_LIBRARY-NOTFOUND")
+        message(FATAL_ERROR "Required cuFFT library not found. Check your environment or set CUFFT_LIBRARY to its location")
+      endif()
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
+      target_link_libraries(lammps PRIVATE ${CUFFT_LIBRARY})
     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

@@ -48,10 +48,15 @@ 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, switch the builtin FFT engine with Heffte
+  # if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
-  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
+
-  set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+  # 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")
@@ -60,24 +65,38 @@ if(FFT_USE_HEFFTE)
     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)
-    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
-    set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-    set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-    add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
-    target_link_libraries(Heffte::Heffte INTERFACE Heffte)
-  endif()
 
+    # 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()

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_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum 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-QUIP.cmake

@@ -18,7 +18,9 @@ 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")
@@ -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

@@ -21,9 +21,9 @@ 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"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)

cmake/presets/kokkos-cuda.cmake

@@ -9,5 +9,8 @@ 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)
 

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/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "21 November 2023" "2023-11-21"
+.TH LAMMPS "1" "7 February 2024" "2024-02-07"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 21 November 2023
+\- Molecular Dynamics Simulator.  Version 7 February 2024
 
 .SH SYNOPSIS
 .B lmp

doc/src/Bibliography.rst

@@ -877,6 +877,9 @@ Bibliography
 **(PLUMED)**
    G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
+**(Pavlov)**
+D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
+
 **(Paquay)**
    Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
 

doc/src/Build_development.rst

@@ -122,32 +122,39 @@ 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
+during development:
-on various platforms and with a variety of settings), unit testing
+
-(i.e. whether certain individual parts of the code produce the expected
+- Integration testing (i.e. whether the code compiles
-results for given inputs), run testing (whether selected complete input
+  on various platforms and with a variety of compilers and settings),
-decks run without crashing for multiple configurations), and regression
+- Unit testing (i.e. whether certain functions or classes of the code
-testing (i.e. whether selected input examples reproduce the same
+  produce the expected results for given inputs),
-results over a given number of steps and operations within a given
+- Run testing (i.e. whether selected input decks can run to completion
-error margin).  The status of this automated testing can be viewed on
+  without crashing for multiple configurations),
-`https://ci.lammps.org <https://ci.lammps.org>`_.
+- 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
+The unit testing facility is integrated into the CMake build process of
-of the LAMMPS source code distribution itself.  It can be enabled by
+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
+It requires the `YAML <https://pyyaml.org/>`_ library and matching
-headers (if those are not found locally a recent version will be
+development headers to compile (if those are not found locally a recent
-downloaded and compiled along with LAMMPS and the test program) to
+version of that library will be downloaded and compiled along with
-compile and will download and compile a specific recent version of the
+LAMMPS and the test programs) and will download and compile a specific
-`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
-for implementing the tests.
+test framework that is used to implement the tests.
 
-.. 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 +162,7 @@ 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.
 
@@ -234,12 +241,31 @@ 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
+Tests as shown by the ``ctest`` program are command lines defined in the
-styles) are performed with the same test executable using different
+``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
-input files in YAML format.  So to add a test for another style of the
+tests simply execute LAMMPS with specific command line flags and check
-same kind it may be sufficient to add a suitable YAML file.
+the output to the screen for expected content.  A large number of unit
-:doc:`Detailed instructions for adding tests <Developer_unittest>` are
+tests are special tests programs using the `GoogleTest framework
-provided in the Programmer Guide part of the manual.
+<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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Build_settings.rst

@@ -44,7 +44,7 @@ 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:: TBD
+.. versionadded:: 7Feb2024
 
 Alternatively, LAMMPS can use the `heFFTe
 <https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
@@ -59,15 +59,19 @@ libraries and better pipelining for packing and communication.
       .. code-block:: bash
 
          -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
          -D FFT_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
+         When the Kokkos variant of a package is compiled and selected at run time,
-         an exception to the rule that all CMake variables can be specified
+         the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
-         with lower-case values.
+         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
@@ -106,6 +110,8 @@ libraries and better pipelining for packing and communication.
 
          FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                                        # default is KISS if not specified
+         FFT_INC = -DFFT_KOKKOS_CUFFT  # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
+                                       # default is KISS if not specified
          FFT_INC = -DFFT_SINGLE        # do not specify for double precision
          FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
          FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
@@ -116,6 +122,8 @@ libraries and better pipelining for packing and communication.
 
          FFT_INC =       -I/usr/local/include
          FFT_PATH =      -L/usr/local/lib
+         FFT_LIB =       -lhipfft            # hipFFT either precision
+         FFT_LIB =       -lcufft             # cuFFT either precision
          FFT_LIB =       -lfftw3             # FFTW3 double precision
          FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
          FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
@@ -178,6 +186,11 @@ 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
@@ -189,11 +202,11 @@ 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
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
-library a second time with support for single-precision.
+the FFTW3 installation includes support for single-precision.
 
-For FFTW3, do the following, which should produce the additional
+When compiler FFTW3 from source, you can do the following, which should
-library ``libfftw3f.a`` or ``libfftw3f.so``\ .
+produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 

doc/src/Commands_bond.rst

@@ -124,7 +124,7 @@ OPT.
    *
    *
    * :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:`fourier (io) <dihedral_fourier>`

doc/src/Commands_fix.rst

@@ -61,6 +61,7 @@ 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>`
@@ -262,6 +263,7 @@ 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_pair.rst

@@ -146,7 +146,7 @@ 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>`
@@ -256,6 +256,7 @@ 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:`saip/metal (t) <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Commands_removed.rst

@@ -129,7 +129,7 @@ USER-REAXC.
 USER-REAXC package
 ------------------
 
-.. deprecated:: TBD
+.. 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

doc/src/Developer_updating.rst

@@ -18,6 +18,7 @@ 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`_
@@ -130,6 +131,41 @@ 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()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -137,11 +173,12 @@ 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
+the :doc:`utils namespace <Developer_utils>`.  Also they take an
-whether the ``Error::all()`` or ``Error::one()`` function should be
+additional argument that selects whether the ``Error::all()`` or
-called in case of an error.  The former should be used when *all* MPI
+``Error::one()`` function should be called in case of an error.  The
-processes call the conversion function and the latter *must* be used
+former should be used when *all* MPI processes call the conversion
-when they are called from only one or a subset of the MPI processes.
+function and the latter *must* be used when they are called from only
+one or a subset of the MPI processes.
 
 Old:
 

doc/src/Fortran.rst

@@ -315,6 +315,10 @@ 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`
@@ -1398,7 +1402,28 @@ 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 +1431,23 @@ 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`
 
 --------
 

doc/src/Howto_cmake.rst

@@ -349,6 +349,8 @@ 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_granular.rst

@@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
 
 To model heat conduction, one must add the temperature and heatflow
 atom variables with:
+
 * :doc:`fix property/atom <fix_property_atom>`
+
 a temperature integration fix
+
 * :doc:`fix heat/flow <fix_heat_flow>`
+
 and a heat conduction option defined in both
+
 * :doc:`pair_style granular <pair_granular>`
 * :doc:`fix wall/gran <fix_wall_gran>`
 

doc/src/Howto_structured_data.rst

@@ -52,8 +52,8 @@ JSON
      "ke": 2.4962152903997174569
    }
 
-YAML format thermo_style output
+YAML format thermo_style or dump_style output
-===============================
+=============================================
 
 Extracting data from log file
 -----------------------------
@@ -112,6 +112,9 @@ of that run:
    Number of runs:  2
    TotEng  =  -4.62140097780047
 
+Extracting data from dump file
+------------------------------
+
 .. versionadded:: 4May2022
 
 YAML format output has been added to multiple commands in LAMMPS,

doc/src/Library_objects.rst

@@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
 - :cpp:func:`lammps_extract_variable_datatype`
 - :cpp:func:`lammps_extract_variable`
 - :cpp:func:`lammps_set_variable`
+- :cpp:func:`lammps_set_string_variable`
+- :cpp:func:`lammps_set_internal_variable`
 - :cpp:func:`lammps_variable_info`
 
 -----------------------
@@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_set_string_variable
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_set_internal_variable
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_variable_info
    :project: progguide
 

doc/src/Modify_style.rst

@@ -96,6 +96,39 @@ list all non-conforming lines.  By adding the `-f` flag to the command
 line, they will modify the flagged files to try to remove the detected
 issues.
 
+Constants (strongly preferred)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Global or per-file constants should be declared as `static constexpr`
+variables rather than via the pre-processor with `#define`.  The name of
+constants should be all uppercase.  This has multiple advantages:
+
+- constants are easily identified as such by their all upper case name
+- rather than a pure text substitution during pre-processing, `constexpr
+  variables` have a type associated with them and are processed later in
+  the parsing process where the syntax checks and type specific
+  processing (e.g. via overloads) can be applied to them.
+- compilers can emit a warning if the constant is not used and thus can
+  be removed (we regularly check for and remove dead code like this)
+- there are no unexpected substitutions and thus confusing syntax errors
+  when compiling leading to, for instance, conflicts so that LAMMPS
+  cannot be compiled with certain combinations of packages (this *has*
+  happened multiple times in the past).
+
+Pre-processor defines should be limited to macros (but consider C++
+templates) and conditional compilation.  If a per-processor define must
+be used, it should be defined at the top of the .cpp file after the
+include statements and at all cost it should be avoided to put them into
+header files.
+
+Some sets of commonly used constants are provided in the ``MathConst``
+and ``EwaldConst`` namespaces and implemented in the files
+``math_const.h`` and ``ewald_const.h``, respectively.
+
+There are always exceptions, special cases, and legacy code in LAMMPS,
+so please contact the LAMMPS developers if you are not sure.
+
+
 Placement of braces (strongly preferred)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Speed_kokkos.rst

@@ -20,11 +20,28 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
 (Sandia). For more information on developing using Kokkos abstractions
 see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
 
-Kokkos currently provides support for 4 modes of execution (per MPI
+.. note::
+
+   The Kokkos library is under active development and tracking the
+   availability of accelerator hardware, so is the KOKKOS package in
+   LAMMPS.  This means that only a certain range of versions of the
+   Kokkos library are compatible with the KOKKOS package of a certain
+   range of LAMMPS versions.  For that reason LAMMPS comes with a
+   bundled version of the Kokkos library that has been validated on
+   multiple platforms and may contain selected back-ported bug fixes
+   from upstream Kokkos versions.  While it is possible to build LAMMPS
+   with an external version of Kokkos, it is untested and may result in
+   incorrect execution or crashes.
+
+Kokkos currently provides full support for 4 modes of execution (per MPI
 task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
-(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA
+(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA GPUs) and
-GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
+HIP (for AMD GPUs).  Additional modes (e.g. OpenMP target, Intel data
-produce an executable compatible with a specific hardware.
+center GPUs) are under development.  You choose the mode at build time
+to produce an executable compatible with a specific hardware.
+
+The following compatibility notes have been last updated for LAMMPS
+version 23 November 2023 and Kokkos version 4.2.
 
 .. admonition:: C++17 support
    :class: note
@@ -54,22 +71,22 @@ produce an executable compatible with a specific hardware.
    :class: note
 
    Kokkos with CUDA currently implicitly assumes that the MPI library is
-   GPU-aware. This is not always the case, especially when using
+   GPU-aware.  This is not always the case, especially when using
    pre-compiled MPI libraries provided by a Linux distribution. This is
    not a problem when using only a single GPU with a single MPI
-   rank. When running with multiple MPI ranks, you may see segmentation
+   rank.  When running with multiple MPI ranks, you may see segmentation
    faults without GPU-aware MPI support. These can be avoided by adding
    the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
    LAMMPS command line or by using the command :doc:`package kokkos
    gpu/aware off <package>` in the input file.
 
-.. admonition:: AMD GPU support
+.. admonition:: Intel Data Center GPU support
    :class: note
 
-   To build with Kokkos the HIPCC compiler from the AMD ROCm software
+   Support for Kokkos with Intel Data Center GPU accelerators (formerly
-   version 3.5 or later is required.  Supporting this Kokkos mode in
+   known under the code name "Ponte Vecchio") in LAMMPS is still a work
-   LAMMPS is still work in progress.  Please contact the LAMMPS developers
+   in progress.  Only a subset of the functionality works correctly.
-   if you run into problems.
+   Please contact the LAMMPS developers if you run into problems.
 
 Building LAMMPS with the KOKKOS package
 """""""""""""""""""""""""""""""""""""""
@@ -292,6 +309,10 @@ one or more nodes, each with two GPUs:
    settings. Experimenting with its options can provide a speed-up for
    specific calculations. For example:
 
+.. code-block:: bash
+
+   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
+
 .. note::
 
    The default binsize for :doc:`atom sorting <atom_modify>` on GPUs
@@ -302,9 +323,15 @@ one or more nodes, each with two GPUs:
    frequent sorting than default (e.g. sorting every 100 time steps
    instead of 1000) may improve performance.
 
-.. code-block:: bash
+.. note::
 
-   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
+   When running on GPUs with many MPI ranks (tens of thousands and
+   more), the creation of the atom map (required for molecular systems)
+   on the GPU can slow down significantly or run out of GPU memory and
+   thus slow down the whole calculation or cause a crash.  You can use
+   the "-pk kokkos atom/map no" :doc:`command-line switch <Run_options>`
+   of the :doc:`package kokkos atom/map no <package>` command to create
+   the atom map on the CPU instead.
 
 .. note::
 
@@ -416,15 +443,22 @@ Generally speaking, the following rules of thumb apply:
   performance of a KOKKOS style is a bit slower than the OPENMP
   package.
 * When running large number of atoms per GPU, KOKKOS is typically faster
-  than the GPU package when compiled for double precision. The benefit
+  than the GPU package when compiled for double precision.  The benefit
   of using single or mixed precision with the GPU package depends
   significantly on the hardware in use and the simulated system and pair
   style.
-* When running on Intel hardware, KOKKOS is not as fast as
+* When running on Intel Phi hardware, KOKKOS is not as fast as
   the INTEL package, which is optimized for x86 hardware (not just
   from Intel) and compilation with the Intel compilers.  The INTEL
   package also can increase the vector length of vector instructions
   by switching to single or mixed precision mode.
+* The KOKKOS package by default assumes that you are using exactly one
+  MPI rank per GPU. When trying to use multiple MPI ranks per GPU it is
+  mandatory to enable `CUDA Multi-Process Service (MPS)
+  <https://docs.nvidia.com/deploy/mps/index.html>`_ to get good
+  performance.  In this case it is better to not use all available
+  MPI ranks in order to avoid competing with the MPS daemon for
+  CPU resources.
 
 See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
 LAMMPS website for performance of the KOKKOS package on different

doc/src/angle_charmm.rst

@@ -70,7 +70,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`angle_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`dihedral_style charmm <dihedral_charmm>`,
+:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

doc/src/angle_lepton.rst

@@ -11,7 +11,16 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   angle_style lepton
+   angle_style style args
+
+* style = *lepton*
+* args = optional arguments
+
+.. parsed-literal::
+
+   args = *auto_offset* or *no_offset*
+     *auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
+     *no_offset* = do not offset the potential energy
 
 Examples
 """"""""
@@ -19,6 +28,7 @@ Examples
 .. code-block:: LAMMPS
 
    angle_style lepton
+   angle_style lepton no_offset
 
    angle_coeff  1  120.0  "k*theta^2; k=250.0"
    angle_coeff  2   90.0  "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@@ -41,6 +51,13 @@ angle coefficient.  For example `"200.0*theta^2"` represents a
 
    U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
 
+.. versionchanged:: 7Feb2024
+
+By default the potential energy U is shifted so that the value U is 0.0
+for $theta = theta_0$.  This is equivalent to using the optional keyword
+*auto_offset*.  When using the keyword *no_offset* instead, the
+potential energy is not shifted.
+
 The `Lepton library <https://simtk.org/projects/lepton>`_, that the
 *lepton* angle style interfaces with, evaluates this expression string
 at run time to compute the pairwise energy.  It also creates an

doc/src/atom_style.rst

@@ -49,248 +49,221 @@ Examples
 Description
 """""""""""
 
-Define what style of atoms to use in a simulation.  This determines
+The *atom_style* command selects which per-atom attributes are
-what attributes are associated with the atoms.  This command must be
+associated with atoms in a LAMMPS simulation and thus stored and
-used before a simulation is setup via a :doc:`read_data <read_data>`,
+communicated with those atoms as well as read from and stored in data
-:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
+and restart files.  Different models (e.g. :doc:`pair styles
-command.
+<pair_style>`) require access to specific per-atom attributes and thus
+require a specific atom style.  For example, to compute Coulomb
+interactions, the atom must have a "charge" (aka "q") attribute.
+
+A number of distinct atom styles exist that combine attributes.  Some
+atom styles are a superset of other atom styles.  Further attributes
+may be added to atoms either via using a hybrid style which provides a
+union of the attributes of the sub-styles, or via the :doc:`fix
+property/atom <fix_property_atom>` command.  The *atom_style* command
+must be used before a simulation is setup via a :doc:`read_data
+<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
+<create_box>` command.
 
 .. note::
 
-   Many of the atom styles discussed here are only enabled if
+   Many of the atom styles discussed here are only enabled if LAMMPS was
-   LAMMPS was built with a specific package, as listed below in the
+   built with a specific package, as listed below in the Restrictions
-   Restrictions section.
+   section.
 
-Once a style is assigned, it cannot be changed, so use a style general
+Once a style is selected and the simulation box defined, it cannot be
-enough to encompass all attributes.  E.g. with style *bond*, angular
+changed but only augmented with the :doc:`fix property/atom
-terms cannot be used or added later to the model.  It is OK to use a
+<fix_property_atom>` command.  So one should select an atom style
-style more general than needed, though it may be slightly inefficient.
+general enough to encompass all attributes required.  E.g. with atom
+style *bond*, it is not possible to define angles and use angle styles.
 
-The choice of style affects what quantities are stored by each atom,
+It is OK to use a style more general than needed, though it may be
-what quantities are communicated between processors to enable forces
+slightly inefficient because it will allocate and communicate
-to be computed, and what quantities are listed in the data file read
+additional unused data.
-by the :doc:`read_data <read_data>` command.
 
-These are the additional attributes of each style and the typical
+Atom style attributes
-kinds of physical systems they are used to model.  All styles store
+"""""""""""""""""""""
-coordinates, velocities, atom IDs and types.  See the
+
+The atom style *atomic* has the minimum subset of per-atom attributes
+and is also the default setting.  It encompasses the following per-atom
+attributes (name of the vector or array in the :doc:`Atom class
+<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
+position (x), velocities (v), forces (f), image flags (image), group
+membership (mask).  Since all atom styles are a superset of atom style
+*atomic*\ , they all include these attributes.
+
+This table lists all the available atom styles, which attributes they
+provide, which :doc:`package <Packages>` is required to use them, and
+what the typical applications are that use them.  See the
 :doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
-:doc:`set <set>` commands for info on how to set these various
+:doc:`set <set>` commands for details on how to set these various
-quantities.
+quantities.  More information about many of the styles is provided in
+the Additional Information section below.
 
-+--------------+-----------------------------------------------------+--------------------------------------+
+.. list-table::
-| *amoeba*     | molecular + charge + 1/5 neighbors                  | AMOEBA/HIPPO polarized force fields  |
+   :header-rows: 1
-+--------------+-----------------------------------------------------+--------------------------------------+
+   :widths: auto
-| *angle*      | bonds and angles                                    | bead-spring polymers with stiffness  |
+
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - Atom style
-| *atomic*     | only the default values                             | coarse-grain liquids, solids, metals |
+     - Attributes
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - Required package
-| *body*       | mass, inertia moments, quaternion, angular momentum | arbitrary bodies                     |
+     - Applications
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *amoeba*
-| *bond*       | bonds                                               | bead-spring polymers                 |
+     - *full* + "1-5 special neighbor data"
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`AMOEBA <PKG-AMOEBA>`
-| *charge*     | charge                                              | atomic system with charges           |
+     - AMOEBA/HIPPO force fields
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *angle*
-| *dielectric* | normx normy normz area/patch ed em epsilon curv     | system with surface polarization     |
+     - *bond* + "angle data"
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`MOLECULE <PKG-MOLECULE>`
-| *dipole*     | charge and dipole moment                            | system with dipolar particles        |
+     - bead-spring polymers with stiffness
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *atomic*
-| *dpd*        | internal temperature and internal energies          | DPD particles                        |
+     - tag, type, x, v, f, image, mask
-+--------------+-----------------------------------------------------+--------------------------------------+
+     -
-| *edpd*       | temperature and heat capacity                       | eDPD particles                       |
+     - atomic liquids, solids, metals
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *body*
-| *electron*   | charge and spin and eradius                         | electronic force field               |
+     - *atomic* + radius, rmass, angmom, torque, body
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`BODY <PKG-BODY>`
-| *ellipsoid*  | shape, quaternion, angular momentum                 | aspherical particles                 |
+     - arbitrary bodies, see :doc:`body howto <Howto_body>`
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *bond*
-| *full*       | molecular + charge                                  | bio-molecules                        |
+     - *atomic* + molecule, nspecial, special + "bond data"
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`MOLECULE <PKG-MOLECULE>`
-| *line*       | end points, angular velocity                        | rigid bodies                         |
+     - bead-spring polymers
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *bpm/sphere*
-| *mdpd*       | density                                             | mDPD particles                       |
+     - *bond* + radius, rmass, omega, torque, quat
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`BPM <PKG-BPM>`
-| *molecular*  | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
+     - granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *charge*
-| *oxdna*      | nucleotide polarity                                 | coarse-grained DNA and RNA models    |
+     - *atomic* + q
-+--------------+-----------------------------------------------------+--------------------------------------+
+     -
-| *peri*       | mass, volume                                        | mesoscopic Peridynamic models        |
+     - atomic systems with charges
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *dielectric*
-| *smd*        | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
+     - *full* + mu, area, ed, em, epsilon, curvature, q_scaled
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DIELECTRIC <PKG-DIELECTRIC>`
-| *sph*        | rho, esph, cv                                       | SPH particles                        |
+     - systems with surface polarization
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *dipole*
-| *sphere*     | diameter, mass, angular velocity                    | granular models                      |
+     - *charge* + mu
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DIPOLE <PKG-DIPOLE>`
-| *bpm/sphere* | diameter, mass, angular velocity, quaternion        | granular bonded particle models (BPM)|
+     - atomic systems with charges and point dipoles
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *dpd*
-| *spin*       | magnetic moment                                     | system with magnetic particles       |
+     - *atomic* + rho + "reactive DPD data"
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DPD-REACT <PKG-DPD-REACT>`
-| *tdpd*       | chemical concentration                              | tDPD particles                       |
+     - reactive DPD
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *edpd*
-| *template*   | template index, template atom                       | small molecules with fixed topology  |
+     - *atomic* + "eDPD data"
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
-| *tri*        | corner points, angular momentum                     | rigid bodies                         |
+     - Energy conservative DPD (eDPD)
-+--------------+-----------------------------------------------------+--------------------------------------+
+   * - *electron*
-| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im           | AWPMD                                |
+     - *charge* + espin, eradius, ervel, erforce
-+--------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`EFF <PKG-EFF>`
+     - Electron force field systems
+   * - *ellipsoid*
+     - *atomic* + rmass, angmom, torque, ellipsoid
+     -
+     - aspherical particles
+   * - *full*
+     - *molecular* + q
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - molecular force fields
+   * - *line*
+     - *atomic* + molecule, radius, rmass, omega, torque, line
+     -
+     - 2-d rigid body particles
+   * - *mdpd*
+     - *atomic* + rho, drho, vest
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
+     - Many-body DPD (mDPD)
+   * - *molecular*
+     - *angle* + "dihedral and improper data"
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - apolar and uncharged molecules
+   * - *oxdna*
+     - *atomic* + id5p
+     - :ref:`CG-DNA <PKG-CG-DNA>`
+     - coarse-grained DNA and RNA models
+   * - *peri*
+     - *atomic* + rmass, vfrac, s0, x0
+     - :ref:`PERI <PKG-PERI>`
+     - mesoscopic Peridynamics models
+   * - *smd*
+     - *atomic* + molecule, radius, rmass + "smd data"
+     - :ref:`MACHDYN <PKG-MACHDYN>`
+     - Smooth Mach Dynamics models
+   * - *sph*
+     - *atomic* + "sph data"
+     - :ref:`SPH <PKG-SPH>`
+     - Smoothed particle hydrodynamics models
+   * - *sphere*
+     - *atomic* + radius, rmass, omega, torque
+     -
+     - finite size spherical particles, e.g. granular models
+   * - *spin*
+     - *atomic* + "magnetic moment data"
+     - :ref:`SPIN <PKG-SPIN>`
+     - magnetic particles
+   * - *tdpd*
+     - *atomic* + cc, cc_flux, vest
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
+     - Transport DPD (tDPD)
+   * - *template*
+     - *atomic* + molecule, molindex, molatom
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - molecular systems where attributes are taken from :doc:`molecule files <molecule>`
+   * - *tri*
+     - *sphere* + molecule, angmom, tri
+     -
+     - 3-d triangulated rigid body LJ particles
+   * - *wavepacket*
+     - *charge* + "wavepacket data"
+     - :ref:`AWPMD <PKG-AWPMD>`
+     - Antisymmetrized wave packet MD
 
 .. note::
 
-   It is possible to add some attributes, such as a molecule ID, to
+   It is possible to add some attributes, such as a molecule ID and
-   atom styles that do not have them via the :doc:`fix property/atom
+   charge, to atom styles that do not have them built in using the
-   <fix_property_atom>` command.  This command also allows new custom
+   :doc:`fix property/atom <fix_property_atom>` command.  This command
-   attributes consisting of extra integer or floating-point values to
+   also allows new custom-named attributes consisting of extra integer
-   be added to atoms.  See the :doc:`fix property/atom
+   or floating-point values or vectors to be added to atoms.  See the
-   <fix_property_atom>` page for examples of cases where this is
+   :doc:`fix property/atom <fix_property_atom>` page for examples of
-   useful and details on how to initialize, access, and output the
+   cases where this is useful and details on how to initialize,
-   custom values.
+   access, and output these custom values.
 
-All of the above styles define point particles, except the *sphere*,
+----------
-*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
-*tri*, and *body* styles, which define finite-size particles.  See the
-:doc:`Howto spherical <Howto_spherical>` page for an overview of using
-finite-size particle models with LAMMPS.
 
-All of the point-particle styles assign mass to particles on a
+Particle size and mass
-per-type basis, using the :doc:`mass <mass>` command, The finite-size
+""""""""""""""""""""""
-particle styles assign mass to individual particles on a per-particle
-basis.
 
-For the *sphere* and *bpm/sphere* styles, the particles are spheres
+All of the atom styles define point particles unless they (1) define
-and each stores a per-particle diameter and mass.  If the diameter >
+finite-size spherical particles via the *radius* attribute, or (2)
-0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
+define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
-is a point particle.  Note that by use of the *disc* keyword with the
+*line*, and *tri* styles).  Most of these styles can also be used with
-:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
+mixtures of point and finite-size particles.
-<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
-:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
-spheres can be effectively treated as 2d discs for a 2d simulation if
-desired.  See also the :doc:`set density/disc <set>` command.  These
-styles take an optional 0 or 1 argument.  A value of 0 means the
-radius of each sphere is constant for the duration of the simulation.
-A value of 1 means the radii may vary dynamically during the simulation,
-e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
 
-For the *ellipsoid* style, the particles are ellipsoids and each
+Note that the *radius* property may need to be provided as a
-stores a flag which indicates whether it is a finite-size ellipsoid or
+*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
-a point particle.  If it is an ellipsoid, it also stores a shape
+files <read_data>`).  See the :doc:`Howto spherical <Howto_spherical>`
-vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
+page for an overview of using finite-size spherical and aspherical
-with its orientation.
+particle models with LAMMPS.
 
-For the *dielectric* style, each particle can be either a physical
+Unless an atom style defines the per-atom *rmass* attribute, particle
-particle (e.g. an ion), or an interface particle representing a boundary
+masses are defined on a per-type basis, using the :doc:`mass <mass>`
-element between two regions of different dielectric constant. For
+command.  This means each particle's mass is indexed by its atom
-interface particles, in addition to the properties associated with
+*type*.
-atom_style full, each particle also should be assigned a normal unit
-vector (defined by normx, normy, normz), an area (area/patch), the
-difference and mean of the dielectric constants of two sides of the
-interface along the direction of the normal vector (ed and em), the
-local dielectric constant at the boundary element (epsilon), and a mean
-local curvature (curv).  Physical particles must be assigned these
-values, as well, but only their local dielectric constants will be used;
-see documentation for associated :doc:`pair styles <pair_dielectric>`
-and :doc:`fixes <fix_polarize>`.  The distinction between the physical
-and interface particles is only meaningful when :doc:`fix polarize
-<fix_polarize>` commands are applied to the interface particles. This
-style is part of the DIELECTRIC package.
 
-For the *dipole* style, a point dipole is defined for each point
+A few styles define the per-atom *rmass* attribute which can also be
-particle.  Note that if you wish the particles to be finite-size
+added using the :doc:`fix property/atom <fix_property_atom>` command.
-spheres as in a Stockmayer potential for a dipolar fluid, so that the
+In this case each particle stores its own mass.  Atom styles that have
-particles can rotate due to dipole-dipole interactions, then you need
+a per-atom rmass may define it indirectly through setting particle
-to use atom_style hybrid sphere dipole, which will assign both a
+diameter and density on a per-particle basis.  If both per-type mass
-diameter and dipole moment to each particle.
+and per-atom *rmass* are defined (e.g. in a hybrid style), the
+per-atom mass will take precedence in any operation which which works
+with both flavors of mass.
 
-For the *electron* style, the particles representing electrons are 3d
+----------
-Gaussians with a specified position and bandwidth or uncertainty in
-position, which is represented by the eradius = electron size.
 
-For the *peri* style, the particles are spherical and each stores a
+Additional information about specific atom styles
-per-particle mass and volume.
+"""""""""""""""""""""""""""""""""""""""""""""""""
-
-The *bpm/sphere* style is part of the BPM package.
-
-The *oxdna* style is for coarse-grained nucleotides and stores the
-3'-to-5' polarity of the nucleotide strand, which is set through
-the bond topology in the data file. The first (second) atom in a
-bond definition is understood to point towards the 3'-end (5'-end)
-of the strand. Note that this style is part of the CG-DNA package.
-
-The *dpd* style is for dissipative particle dynamics (DPD) particles.
-Note that it is part of the DPD-REACT package, and is not for use with
-the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
-simply use atom_style atomic.  Atom_style dpd extends DPD particle
-properties with internal temperature (dpdTheta), internal conductive
-energy (uCond), internal mechanical energy (uMech), and internal
-chemical energy (uChem).
-
-The *edpd* style is for energy-conserving dissipative particle
-dynamics (eDPD) particles which store a temperature (edpd_temp), and
-heat capacity(edpd_cv).
-
-The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
-particles which store a density (rho) for considering
-density-dependent many-body interactions.
-
-The *tdpd* style is for transport dissipative particle dynamics (tDPD)
-particles which store a set of chemical concentration. An integer
-"cc_species" is required to specify the number of chemical species
-involved in a tDPD system.
-
-The *sph* style is for smoothed particle hydrodynamics (SPH)
-particles which store a density (rho), energy (esph), and heat capacity
-(cv).
-
-The *smd* style is for a general formulation of Smooth Particle
-Hydrodynamics.  Both fluids and solids can be modeled.  Particles
-store the mass and volume of an integration point, a kernel diameter
-used for calculating the field variables (e.g. stress and deformation)
-and a contact radius for calculating repulsive forces which prevent
-individual physical bodies from penetrating each other.
-
-For the *spin* style, a magnetic spin is associated to each atom.
-Those spins have a norm (their magnetic moment) and a direction.
-
-The *wavepacket* style is similar to *electron*, but the electrons may
-consist of several Gaussian wave packets, summed up with coefficients
-cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
-particle in LAMMPS, wave packets belonging to the same electron must
-have identical *etag* values.
-
-For the *line* style, the particles are idealized line segments and
-each stores a per-particle mass and length and orientation (i.e. the
-end points of the line segment).
-
-For the *tri* style, the particles are planar triangles and each
-stores a per-particle mass and size and orientation (i.e. the corner
-points of the triangle).
-
-The *template* style allows molecular topology (bonds,angles,etc) to be
-defined via a molecule template using the :doc:`molecule <molecule>`
-command.  The template stores one or more molecules with a single copy
-of the topology info (bonds,angles,etc) of each.  Individual atoms
-only store a template index and template atom to identify which
-molecule and which atom-within-the-molecule they represent.  Using the
-*template* style instead of the *bond*, *angle*, *molecular* styles
-can save memory for systems comprised of a large number of small
-molecules, all of a single type (or small number of types).  See the
-paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
-can be advantageous for large-scale coarse-grained systems.
-The ``examples/template`` directory has a few demo inputs and examples
-showing the use of the *template* atom style versus *molecular*.
-
-.. note::
-
-   When using the *template* style with a :doc:`molecule template
-   <molecule>` that contains multiple molecules, you should ensure the
-   atom types, bond types, angle_types, etc in all the molecules are
-   consistent.  E.g. if one molecule represents H2O and another CO2,
-   then you probably do not want each molecule file to define 2 atom
-   types and a single bond type, because they will conflict with each
-   other when a mixture system of H2O and CO2 molecules is defined,
-   e.g. by the :doc:`read_data <read_data>` command.  Rather the H2O
-   molecule should define atom types 1 and 2, and bond type 1.  And
-   the CO2 molecule should define atom types 3 and 4 (or atom types 3
-   and 2 if a single oxygen type is desired), and bond type 2.
 
 For the *body* style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
@@ -309,6 +282,148 @@ Note that there may be additional arguments required along with the
 *bstyle* specification, in the atom_style body command.  These
 arguments are described on the :doc:`Howto body <Howto_body>` doc page.
 
+For the *dielectric* style, each particle can be either a physical
+particle (e.g. an ion), or an interface particle representing a boundary
+element between two regions of different dielectric constant. For
+interface particles, in addition to the properties associated with
+atom_style full, each particle also should be assigned a normal unit
+vector (defined by normx, normy, normz), an area (area/patch), the
+difference and mean of the dielectric constants of two sides of the
+interface along the direction of the normal vector (ed and em), the
+local dielectric constant at the boundary element (epsilon), and a mean
+local curvature (curv).  Physical particles must be assigned these
+values, as well, but only their local dielectric constants will be used;
+see documentation for associated :doc:`pair styles <pair_dielectric>`
+and :doc:`fixes <fix_polarize>`.  The distinction between the physical
+and interface particles is only meaningful when :doc:`fix polarize
+<fix_polarize>` commands are applied to the interface particles. This
+style is part of the DIELECTRIC package.
+
+For the *dipole* style, a point dipole vector mu is defined for each
+point particle.  Note that if you wish the particles to be finite-size
+spheres as in a Stockmayer potential for a dipolar fluid, so that the
+particles can rotate due to dipole-dipole interactions, then you need
+to use the command `atom_style hybrid sphere dipole`, which will
+assign both a diameter and dipole moment to each particle.  This also
+requires using an integrator with a "/sphere" suffix like :doc:`fix
+nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
+and the "update dipole" or "update dlm" parameters to the fix
+commands.
+
+The *dpd* style is for reactive dissipative particle dynamics (DPD)
+particles.  Note that it is part of the DPD-REACT package, and is not
+required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
+commands, which only require the attributes from atom_style *atomic*.
+Atom_style *dpd* extends DPD particle properties with internal
+temperature (dpdTheta), internal conductive energy (uCond), internal
+mechanical energy (uMech), and internal chemical energy (uChem).
+
+The *edpd* style is for energy-conserving dissipative particle
+dynamics (eDPD) particles which store a temperature (edpd_temp), and
+heat capacity (edpd_cv).
+
+For the *electron* style, the particles representing electrons are 3d
+Gaussians with a specified position and bandwidth or uncertainty in
+position, which is represented by the eradius = electron size.
+
+For the *ellipsoid* style, particles can be ellipsoids which each
+stores a shape vector with the 3 diameters of the ellipsoid and a
+quaternion 4-vector with its orientation.  Each particle stores a flag
+in the ellipsoid vector which indicates whether it is an ellipsoid (1)
+or a point particle (0).
+
+For the *line* style, particles can be are idealized line segments
+which store a per-particle mass and length and orientation (i.e. the
+end points of the line segment).  Each particle stores a flag in the
+line vector which indicates whether it is a line segment (1) or a
+point particle (0).
+
+The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
+particles which store a density (rho) for considering density-dependent
+many-body interactions.
+
+The *oxdna* style is for coarse-grained nucleotides and stores the
+3'-to-5' polarity of the nucleotide strand, which is set through
+the bond topology in the data file. The first (second) atom in a
+bond definition is understood to point towards the 3'-end (5'-end)
+of the strand.
+
+For the *peri* style, the particles are spherical and each stores a
+per-particle mass and volume.
+
+The *smd* style is for Smooth Particle Mach dynamics.  Both fluids and
+solids can be modeled.  Particles store the mass and volume of an
+integration point, a kernel diameter used for calculating the field
+variables (e.g. stress and deformation) and a contact radius for
+calculating repulsive forces which prevent individual physical bodies
+from penetrating each other.
+
+The *sph* style is for smoothed particle hydrodynamics (SPH) particles
+which store a density (rho), energy (esph), and heat capacity (cv).
+
+For the *spin* style, a magnetic spin is associated with each atom.
+Those spins have a norm (their magnetic moment) and a direction.
+
+The *tdpd* style is for transport dissipative particle dynamics (tDPD)
+particles which store a set of chemical concentration. An integer
+"cc_species" is required to specify the number of chemical species
+involved in a tDPD system.
+
+The *wavepacket* style is similar to the *electron* style, but the
+electrons may consist of several Gaussian wave packets, summed up with
+coefficients cs= (cs_re,cs_im).  Each of the wave packets is treated
+as a separate particle in LAMMPS, wave packets belonging to the same
+electron must have identical *etag* values.
+
+The *sphere* and *bpm/sphere* styles allow particles to be either point
+particles or finite-size particles.  If the *radius* attribute is >
+0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
+is a point particle.  Note that by using the *disc* keyword with 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 for the *sphere* style, spheres
+can be effectively treated as 2d discs for a 2d simulation if desired.
+See also the :doc:`set density/disc <set>` command.  These styles also
+take an optional 0 or 1 argument.  A value of 0 means the radius of
+each sphere is constant for the duration of the simulation (this is
+the default).  A value of 1 means the radii may vary dynamically
+during the simulation, e.g. due to use of the :doc:`fix adapt
+<fix_adapt>` command.
+
+The *template* style allows molecular topology (bonds,angles,etc) to be
+defined via a molecule template using the :doc:`molecule <molecule>`
+command.  The template stores one or more molecules with a single copy
+of the topology info (bonds,angles,etc) of each.  Individual atoms only
+store a template index and template atom to identify which molecule and
+which atom-within-the-molecule they represent.  Using the *template*
+style instead of the *bond*, *angle*, *molecular* styles can save memory
+for systems comprised of a large number of small molecules, all of a
+single type (or small number of types).  See the paper by Grime and
+Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
+advantageous for large-scale coarse-grained systems.  The
+``examples/template`` directory has a few demo inputs and examples
+showing the use of the *template* atom style versus *molecular*.
+
+.. note::
+
+   When using the *template* style with a :doc:`molecule template
+   <molecule>` that contains multiple molecules, you should ensure the
+   atom types, bond types, angle_types, etc in all the molecules are
+   consistent.  E.g. if one molecule represents H2O and another CO2,
+   then you probably do not want each molecule file to define 2 atom
+   types and a single bond type, because they will conflict with each
+   other when a mixture system of H2O and CO2 molecules is defined,
+   e.g. by the :doc:`read_data <read_data>` command.  Rather the H2O
+   molecule should define atom types 1 and 2, and bond type 1.  And
+   the CO2 molecule should define atom types 3 and 4 (or atom types 3
+   and 2 if a single oxygen type is desired), and bond type 2.
+
+For the *tri* style, particles can be planar triangles which each
+stores a per-particle mass and size and orientation (i.e. the corner
+points of the triangle).  Each particle stores a flag in the tri
+vector which indicates whether it is a triangle (1) or a point
+particle (0).
+
 ----------
 
 Typically, simulations require only a single (non-hybrid) atom style.
@@ -326,11 +441,12 @@ dipole".  When a hybrid style is used, atoms store and communicate the
 union of all quantities implied by the individual styles.
 
 When using the *hybrid* style, you cannot combine the *template* style
-with another molecular style that stores bond,angle,etc info on a
+with another molecular style that stores bond, angle, etc info on a
 per-atom basis.
 
-LAMMPS can be extended with new atom styles as well as new body
+LAMMPS can be extended with new atom styles as well as new body styles;
-styles; see the :doc:`Modify <Modify>` doc page.
+see the corresponding manual page on :doc:`modifying & extending LAMMPS
+<Modify_atom>`.
 
 ----------
 
@@ -346,54 +462,20 @@ This command cannot be used after the simulation box is defined by a
 
 Many of the styles listed above are only enabled if LAMMPS was built
 with a specific package, as listed below.  See the :doc:`Build package
-<Build_package>` page for more info.
+<Build_package>` page for more info.  The table above lists which package
-
+is required for individual atom styles.
-The *amoeba* style is part of the AMOEBA package.
-
-The *angle*, *bond*, *full*, *molecular*, and *template* styles are
-part of the MOLECULE package.
-
-The *line* and *tri* styles are part of the ASPHERE package.
-
-The *body* style is part of the BODY package.
-
-The *dipole* style is part of the DIPOLE package.
-
-The *peri* style is part of the PERI package for Peridynamics.
-
-The *oxdna* style is part of the CG-DNA package for coarse-grained
-simulation of DNA and RNA.
-
-The *electron* style is part of the EFF package for :doc:`electronic
-force fields <pair_eff>`.
-
-The *dpd* style is part of the DPD-REACT package for dissipative
-particle dynamics (DPD).
-
-The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
-for energy-conserving dissipative particle dynamics (eDPD), many-body
-dissipative particle dynamics (mDPD), and transport dissipative particle
-dynamics (tDPD), respectively.
-
-The *sph* style is part of the SPH package for smoothed particle
-hydrodynamics (SPH).  See `this PDF guide
-<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
-
-The *spin* style is part of the SPIN package.
-
-The *wavepacket* style is part of the AWPMD package for the
-:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
 
 Related commands
 """"""""""""""""
 
-:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
+:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
+:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
 
 Default
 """""""
 
-The default atom style is atomic.  If atom_style sphere is used its
+The default atom style is *atomic*.  If atom_style *sphere* or
-default argument is 0.
+*bpm/sphere* is used, its default argument is 0.
 
 ----------
 

doc/src/bond_lepton.rst

@@ -11,7 +11,16 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   bond_style lepton
+   bond_style style args
+
+* style = *lepton*
+* args = optional arguments
+
+.. parsed-literal::
+
+   args = *auto_offset* or *no_offset*
+     *auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
+     *no_offset* = do not offset the potential energy
 
 Examples
 """"""""
@@ -19,6 +28,7 @@ Examples
 .. code-block:: LAMMPS
 
    bond_style lepton
+   bond_style lepton no_offset
 
    bond_coeff  1  1.5 "k*r^2; k=250.0"
    bond_coeff  2  1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@@ -40,6 +50,13 @@ constant *K* of 200.0 energy units:
 
    U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
 
+.. versionchanged:: 7Feb2024
+
+By default the potential energy U is shifted so that he value U is 0.0
+for $r = r_0$.  This is equivalent to using the optional keyword
+*auto_offset*.  When using the keyword *no_offset* instead, the
+potential energy is not shifted.
+
 The `Lepton library <https://simtk.org/projects/lepton>`_, that the
 *lepton* bond style interfaces with, evaluates this expression string at
 run time to compute the pairwise energy.  It also creates an analytical

doc/src/compute_adf.rst

@@ -204,8 +204,23 @@ angles per atom satisfying the ADF criteria.
 Restrictions
 """"""""""""
 
-This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
+This compute is part of the EXTRA-COMPUTE package.  It is only enabled
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+By default, the ADF is not computed for distances longer than the
+largest force cutoff, since the neighbor list creation will only contain
+pairs up to that distance (plus neighbor list skin).  If you use outer
+cutoffs larger than that, you must use :doc:`neighbor style 'bin' or
+'nsq' <neighbor>`.
+
+If you want an ADF for a larger outer cutoff, you can also use the
+:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
+style zero <pair_zero>` and set the force cutoff to be larger in the
+rerun script.  Note that in the rerun context, the force cutoff is
+arbitrary and with pair style zero you are not computing any forces, and
+since you are not running dynamics you are not changing the model that
+generated the trajectory.
 
 The ADF is not computed for neighbors outside the force cutoff,
 since processors (in parallel) don't know about atom coordinates for

doc/src/compute_ave_sphere_atom.rst

@@ -102,6 +102,8 @@ This compute is part of the EXTRA-COMPUTE package.  It is only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_composition_atom.rst

@@ -107,6 +107,8 @@ This compute is part of the EXTRA-COMPUTE package.  It is only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_efield_wolf_atom.rst

@@ -106,6 +106,8 @@ Restrictions
 This compute is part of the EXTRA-COMPUTE package. It is only enabled if
 LAMMPS was built with that package.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_fabric.rst

@@ -64,7 +64,7 @@ tangential force tensor. The contact tensor is calculated as
 
 .. math::
 
-   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab})
+   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \frac{1}{3} \mathrm{Tr}(\phi) \delta_{ab})
 
 where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z`
 directions, :math:`\delta_{ab}` is the Kronecker delta function, and
@@ -83,7 +83,7 @@ The branch tensor is calculated as
 
 .. math::
 
-   B_{ab}  =  \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab})
+   B_{ab}  =  \frac{15}{2\, \mathrm{Tr}(D)} (D_{ab} - \frac{1}{3} \mathrm{Tr}(D) \delta_{ab})
 
 where the tensor :math:`D` is defined as
 
@@ -101,7 +101,7 @@ The normal force fabric tensor is calculated as
 
 .. math::
 
-   F^n_{ab}  =  \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab})
+   F^n_{ab}  =  \frac{15}{2\, \mathrm{Tr}(N)} (N_{ab} - \frac{1}{3} \mathrm{Tr}(N) \delta_{ab})
 
 where the tensor :math:`N` is defined as
 
@@ -119,7 +119,7 @@ as
 
 .. math::
 
-   F^t_{ab}  =  \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab})
+   F^t_{ab}  =  \frac{5}{\mathrm{Tr}(N)} (T_{ab} - \frac{1}{3} \mathrm{Tr}(T) \delta_{ab})
 
 where the tensor :math:`T` is defined as
 

doc/src/compute_pace.rst

@@ -36,7 +36,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 This compute calculates a set of quantities related to the atomic
 cluster expansion (ACE) descriptors of the atoms in a group.  ACE

doc/src/compute_pressure.rst

@@ -153,7 +153,8 @@ Related commands
 Default
 """""""
 
-none
+By default the compute includes contributions from the keywords:
+``ke pair bond angle dihedral improper kspace fix``
 
 ----------
 

doc/src/compute_property_atom.rst

@@ -23,8 +23,9 @@ Syntax
                              spx, spy, spz, sp, fmx, fmy, fmz,
                              nbonds,
                              radius, diameter, omegax, omegay, omegaz,
+                             temperature, heatflow,
                              angmomx, angmomy, angmomz,
-                             shapex,shapey, shapez,
+                             shapex, shapey, shapez,
                              quatw, quati, quatj, quatk, tqx, tqy, tqz,
                              end1x, end1y, end1z, end2x, end2y, end2z,
                              corner1x, corner1y, corner1z,
@@ -56,6 +57,8 @@ Syntax
            *nbonds* = number of bonds assigned to an atom
            *radius,diameter* = radius,diameter of spherical particle
            *omegax,omegay,omegaz* = angular velocity of spherical particle
+           *temperature* = internal temperature of spherical particle
+           *heatflow* = internal heat flow of spherical particle
            *angmomx,angmomy,angmomz* = angular momentum of aspherical particle
            *shapex,shapey,shapez* = 3 diameters of aspherical particle
            *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

doc/src/compute_rattlers_atom.rst

@@ -32,7 +32,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a compute that identifies rattlers in a system. Rattlers are often
 identified in granular or glassy packings as under-coordinated atoms that

doc/src/compute_rdf.rst

@@ -176,22 +176,29 @@ also numbers :math:`\ge 0.0`.
 Restrictions
 """"""""""""
 
-The RDF is not computed for distances longer than the force cutoff,
+By default, the RDF is not computed for distances longer than the
-since processors (in parallel) do not know about atom coordinates for
+largest force cutoff, since the neighbor list creation will only contain
-atoms further away than that distance.  If you want an RDF for larger
+pairs up to that distance (plus neighbor list skin).  This distance can
-distances, you can use the :doc:`rerun <rerun>` command to post-process
+be increased using the *cutoff* keyword but this keyword is only valid
-a dump file and set the cutoff for the potential to be longer in the
+with :doc:`neighbor styles 'bin' and 'nsq' <neighbor>`.
+
+If you want an RDF for larger distances, you can also use the
+:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
+style zero <pair_zero>` and set the force cutoff to be longer in the
 rerun script.  Note that in the rerun context, the force cutoff is
-arbitrary, since you are not running dynamics and thus are not changing
+arbitrary and with pair style zero you are not computing any forces, and
-your model.  The definition of :math:`g(r)` used by LAMMPS is only appropriate
+you are not running dynamics you are not changing the model that
-for characterizing atoms that are uniformly distributed throughout the
+generated the trajectory.
-simulation cell. In such cases, the coordination number is still
+
-correct and meaningful.  As an example, if a large simulation cell
+The definition of :math:`g(r)` used by LAMMPS is only appropriate for
-contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)`
+characterizing atoms that are uniformly distributed throughout the
-will register an arbitrarily large spike at whatever distance they
+simulation cell. In such cases, the coordination number is still correct
-happen to be at, and zero everywhere else.
+and meaningful.  As an example, if a large simulation cell contains only
-The function :math:`\text{coord}(r)` will show a step
+one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` will
-change from zero to one at the location of the spike in :math:`g(r)`.
+register an arbitrarily large spike at whatever distance they happen to
+be at, and zero everywhere else.  The function :math:`\text{coord}(r)`
+will show a step change from zero to one at the location of the spike in
+:math:`g(r)`.
 
 .. note::
 

doc/src/compute_reaxff_atom.rst

@@ -40,7 +40,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a computation that extracts bond information computed by the ReaxFF
 potential specified by :doc:`pair_style reaxff <pair_reaxff>`.

doc/src/compute_reduce.rst

@@ -56,8 +56,9 @@ Examples
    compute 1 all reduce sum c_force
    compute 1 all reduce/region subbox sum c_force
    compute 2 all reduce min c_press[2] f_ave v_myKE
-   compute 2 all reduce min c_press[*] f_ave v_myKE
+   compute 2 all reduce min c_press[*] f_ave v_myKE inputs peratom
    compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+   compute 4 all reduce max c_bond inputs local
 
 Description
 """""""""""

doc/src/compute_slcsa_atom.rst

@@ -32,7 +32,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a computation that performs the Supervised Learning Crystal
 Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`

doc/src/compute_stress_atom.rst

@@ -289,7 +289,8 @@ Related commands
 Default
 """""""
 
-none
+By default the compute includes contributions from the keywords:
+``ke pair bond angle dihedral improper kspace fix``
 
 ----------
 

doc/src/compute_stress_mop.rst

@@ -132,10 +132,13 @@ size does not change in time, and axis-aligned planes.
 The method only works with two-body pair interactions, because it
 requires the class method ``Pair::single()`` to be implemented, which is
 not possible for manybody potentials.  In particular, compute
-*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
+*stress/mop/profile* and *stress/mop* do not work with more than two-body
-interactions, long range (kspace) interactions and
+pair interactions, long range (kspace) interactions and
 improper intramolecular interactions.
 
+The impact of fixes that affect the stress (e.g. fix langevin) is
+also not included in the stress computed here.
+
 Related commands
 """"""""""""""""
 

doc/src/create_atoms.rst

@@ -268,6 +268,12 @@ molecule can be specified in the molecule file.  See the
 required to be in this file are the coordinates and types of atoms in
 the molecule.
 
+.. note::
+
+  If you are using the *mol* keyword in combination with the
+  :doc:`atom style template <atom_style>` command, they must use
+  the same molecule template-ID.
+
 Using a lattice to add molecules, e.g. via the *box* or *region* or
 *single* styles, is exactly the same as adding atoms on lattice
 points, except that entire molecules are added at each point, i.e. on
@@ -536,6 +542,11 @@ command.
 A rotation vector specified for a single molecule must be in
 the z-direction for a 2d model.
 
+For :doc:`molecule templates <molecule>` that are created from multiple
+files, i.e. contain multiple molecule *sets*, only the first set is
+used.  To create multiple molecules the files currently need to be
+merged and different molecule IDs assigned with a Molecules section.
+
 Related commands
 """"""""""""""""
 

doc/src/dihedral_charmm.rst

@@ -3,6 +3,7 @@
 .. index:: dihedral_style charmm/kk
 .. index:: dihedral_style charmm/omp
 .. index:: dihedral_style charmmfsw
+.. index:: dihedral_style charmmfsw/kk
 
 dihedral_style charmm command
 =============================
@@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
 dihedral_style charmmfsw command
 ================================
 
+Accelerator Variants: *charmmfsw/kk*
+
 Syntax
 """"""
 
@@ -144,7 +147,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`dihedral_coeff <dihedral_coeff>`
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

doc/src/dump.rst

@@ -104,7 +104,6 @@ Syntax
                                q, mux, muy, muz, mu,
                                radius, diameter, omegax, omegay, omegaz,
                                angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                               heatflow, temperature,
                                c_ID, c_ID[I], f_ID, f_ID[I], v_name,
                                i_name, d_name, i2_name[I], d2_name[I]
 
@@ -131,8 +130,6 @@ Syntax
            omegax,omegay,omegaz = angular velocity of spherical particle
            angmomx,angmomy,angmomz = angular momentum of aspherical particle
            tqx,tqy,tqz = torque on finite-size particles
-           heatflow = rate of heat flow into particle
-           temperature = temperature of particle
            c_ID = per-atom vector calculated by a compute with ID
            c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
            f_ID = per-atom vector calculated by a fix with ID

doc/src/fix.rst

@@ -226,6 +226,7 @@ accelerated styles exist.
 * :doc:`controller <fix_controller>` - apply control loop feedback mechanism
 * :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations
 * :doc:`deform <fix_deform>` - change the simulation box size/shape
+* :doc:`deform/pressure <fix_deform_pressure>` - change the simulation box size/shape with additional loading conditions
 * :doc:`deposit <fix_deposit>` - add new atoms above a surface
 * :doc:`dpd/energy <fix_dpd_energy>` - constant energy dissipative particle dynamics
 * :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
@@ -427,6 +428,7 @@ accelerated styles exist.
 * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
 * :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
 * :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
+* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
 * :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
 * :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
 * :doc:`wall/harmonic <fix_wall>` - harmonic spring wall

doc/src/fix_balance.rst

@@ -14,15 +14,15 @@ Syntax
 * balance = style name of this fix command
 * Nfreq = perform dynamic load balancing every this many steps
 * thresh = imbalance threshold that must be exceeded to perform a re-balance
-* style = *shift* or *rcb*
+* style = *shift* or *rcb* or *report*
-
   .. parsed-literal::
 
-       shift args = dimstr Niter stopthresh
+       *shift* args = dimstr Niter stopthresh
          dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once
          Niter = # of times to iterate within each dimension of dimstr sequence
          stopthresh = stop balancing when this imbalance threshold is reached
        *rcb* args = none
+       *report* args = none
 
 * zero or more keyword/arg pairs may be appended
 * keyword = *weight* or *out*
@@ -70,6 +70,13 @@ re-balancing is performed periodically during the simulation.  To
 perform "static" balancing, before or between runs, see the
 :doc:`balance <balance>` command.
 
+.. versionadded:: TBD
+
+The *report* balance style only computes the load imbalance but
+does not attempt any re-balancing.  This way the load imbalance
+information can be used otherwise, for instance for stopping a
+run with :doc:`fix halt <fix_halt>`.
+
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or
 where the computational cost varies significantly between different

doc/src/fix_charge_regulation.rst

@@ -253,11 +253,11 @@ built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
 The :doc:`atom_style <atom_style>`, used must contain the charge
-property, for example, the style could be *charge* or *full*. Only
+property and have per atom type masses, for example, the style could be
-usable for 3D simulations. Atoms specified as free ions cannot be part
+*charge* or *full*. Only usable for 3D simulations.  Atoms specified as
-of rigid bodies or molecules and cannot have bonding interactions. The
+free ions cannot be part of rigid bodies or molecules and cannot have
-scheme is limited to integer charges, any atoms with non-integer charges
+bonding interactions.  The scheme is limited to integer charges, any
-will not be considered by the fix.
+atoms with non-integer charges will not be considered by the fix.
 
 All interaction potentials used must be continuous, otherwise the MD
 integration and the particle exchange MC moves do not correspond to the

doc/src/fix_deform.rst

@@ -4,6 +4,9 @@
 fix deform command
 ==================
 
+:doc:`fix deform/pressure <fix_deform_pressure>` command
+========================================================
+
 Accelerator Variants: *deform/kk*
 
 Syntax
@@ -11,18 +14,18 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   fix ID group-ID deform N parameter args ... keyword value ...
+   fix ID group-ID fix_style N parameter style args ... keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* deform = style name of this fix command
+* fix_style = *deform* or *deform/pressure*
 * N = perform box deformation every this many timesteps
-* one or more parameter/arg pairs may be appended
+* one or more parameter/style/args sequences of arguments may be appended
 
   .. parsed-literal::
 
      parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
        *x*, *y*, *z* args = style value(s)
-         style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
+         style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
            *final* values = lo hi
              lo hi = box boundaries at end of run (distance units)
            *delta* values = dlo dhi
@@ -43,8 +46,15 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for box length change as function of time
              v_name2 = variable with name2 for change rate as function of time
+           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+           *pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+
        *xy*, *xz*, *yz* args = style value
-         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle*
+         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
            *final* value = tilt
              tilt = tilt factor at end of run (distance units)
            *delta* value = dtilt
@@ -62,9 +72,12 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for tilt change as function of time
              v_name2 = variable with name2 for change rate as function of time
+           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
 
 * zero or more keyword/value pairs may be appended
-* keyword = *remap* or *flip* or *units*
+* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
 
   .. parsed-literal::
 
@@ -77,6 +90,15 @@ Syntax
        *units* value = *lattice* or *box*
          lattice = distances are defined in lattice units
          box = distances are defined in simulation box units
+       *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+         couple pressure values of various dimensions
+       *vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+         Modifies the behavior of the *volume* option to try and balance pressures
+       *max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+         rate = maximum strain rate for pressure control
+       *normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+         Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
+
 
 Examples
 """"""""
@@ -88,6 +110,8 @@ Examples
    fix 1 all deform 1 xy erate 0.001 remap v
    fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
 
+See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
+
 Description
 """""""""""
 
@@ -95,29 +119,46 @@ Change the volume and/or shape of the simulation box during a dynamics
 run.  Orthogonal simulation boxes have 3 adjustable parameters
 (x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
-adjusted independently and simultaneously by this command.
+adjusted independently and simultaneously.
 
-This fix can be used to perform non-equilibrium MD (NEMD) simulations
+The fix deform command allows use of all the arguments listed above,
-of a continuously strained system.  See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details.  Note
+except those flagged as available ONLY for the :doc:`fix
-that simulation of a continuously extended system (extensional flow)
+deform/pressure <fix_deform_pressure>` command, which are
-can be modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
+pressure-based controls.  The fix deform/pressure command allows use
+of all the arguments listed above.
+
+The rest of this doc page explains the options common to both
+commands.  The :doc:`fix deform/pressure <fix_deform_pressure>` doc
+page explains the options available ONLY with the fix deform/pressure
+command.  Note that a simulation can define only a single deformation
+command: fix deform or fix deform/pressure.
+
+Both these fixes can be used to perform non-equilibrium MD (NEMD)
+simulations of a continuously strained system.  See the :doc:`fix
+nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform
+<compute_temp_deform>` commands for more details.  Note that
+simulation of a continuously extended system (extensional flow) can be
+modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
+commands <fix_nh_uef>`.
 
 For the *x*, *y*, *z* parameters, the associated dimension cannot be
 shrink-wrapped.  For the *xy*, *yz*, *xz* parameters, the associated
-second dimension cannot be shrink-wrapped.  Dimensions not varied by this
+second dimension cannot be shrink-wrapped.  Dimensions not varied by
-command can be periodic or non-periodic.  Dimensions corresponding to
+this command can be periodic or non-periodic.  Dimensions
-unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
+corresponding to unspecified parameters can also be controlled by a
+:doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
 
 The size and shape of the simulation box at the beginning of the
-simulation run were either specified by the
+simulation run were either specified by the :doc:`create_box
-:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
+<create_box>` or :doc:`read_data <read_data>` or :doc:`read_restart
-:doc:`read_restart <read_restart>` command used to setup the simulation
+<read_restart>` command used to setup the simulation initially if it
-initially if it is the first run, or they are the values from the end
+is the first run, or they are the values from the end of the previous
-of the previous run.  The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` commands
+run.  The :doc:`create_box <create_box>`, :doc:`read data
-specify whether the simulation box is orthogonal or non-orthogonal
+<read_data>`, and :doc:`read_restart <read_restart>` commands specify
-(triclinic) and explain the meaning of the xy,xz,yz tilt factors.  If
+whether the simulation box is orthogonal or non-orthogonal (triclinic)
-fix deform changes the xy,xz,yz tilt factors, then the simulation box
+and explain the meaning of the xy,xz,yz tilt factors.  If fix deform
-must be triclinic, even if its initial tilt factors are 0.0.
+changes the xy,xz,yz tilt factors, then the simulation box must be
+triclinic, even if its initial tilt factors are 0.0.
 
 As described below, the desired simulation box size and shape at the
 end of the run are determined by the parameters of the fix deform
@@ -258,21 +299,22 @@ of the units keyword below.
 
 The *variable* style changes the specified box length dimension by
 evaluating a variable, which presumably is a function of time.  The
-variable with *name1* must be an :doc:`equal-style variable <variable>`
+variable with *name1* must be an :doc:`equal-style variable
-and should calculate a change in box length in units of distance.
+<variable>` and should calculate a change in box length in units of
-Note that this distance is in box units, not lattice units; see the
+distance.  Note that this distance is in box units, not lattice units;
-discussion of the *units* keyword below.  The formula associated with
+see the discussion of the *units* keyword below.  The formula
-variable *name1* can reference the current timestep.  Note that it
+associated with variable *name1* can reference the current timestep.
-should return the "change" in box length, not the absolute box length.
+Note that it should return the "change" in box length, not the
-This means it should evaluate to 0.0 when invoked on the initial
+absolute box length.  This means it should evaluate to 0.0 when
-timestep of the run following the definition of fix deform.  It should
+invoked on the initial timestep of the run following the definition of
-evaluate to a value > 0.0 to dilate the box at future times, or a
+fix deform.  It should evaluate to a value > 0.0 to dilate the box at
-value < 0.0 to compress the box.
+future times, or a value < 0.0 to compress the box.
 
-The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of box length
+The variable *name2* must also be an :doc:`equal-style variable
-change, in units of distance/time, i.e. the time-derivative of the
+<variable>` and should calculate the rate of box length change, in
-*name1* variable.  This quantity is used internally by LAMMPS to reset
+units of distance/time, i.e. the time-derivative of the *name1*
-atom velocities when they cross periodic boundaries.  It is computed
+variable.  This quantity is used internally by LAMMPS to reset atom
+velocities when they cross periodic boundaries.  It is computed
 internally for the other styles, but you must provide it when using an
 arbitrary variable.
 
@@ -414,12 +456,13 @@ can reference the current timestep.  Note that it should return the
 should evaluate to 0.0 when invoked on the initial timestep of the run
 following the definition of fix deform.
 
-The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of tilt change,
+The variable *name2* must also be an :doc:`equal-style variable
-in units of distance/time, i.e. the time-derivative of the *name1*
+<variable>` and should calculate the rate of tilt change, in units of
-variable.  This quantity is used internally by LAMMPS to reset atom
+distance/time, i.e. the time-derivative of the *name1* variable.  This
-velocities when they cross periodic boundaries.  It is computed
+quantity is used internally by LAMMPS to reset atom velocities when
-internally for the other styles, but you must provide it when using an
+they cross periodic boundaries.  It is computed internally for the
-arbitrary variable.
+other styles, but you must provide it when using an arbitrary
+variable.
 
 Here is an example of using the *variable* style to perform the same
 box deformation as the *wiggle* style formula listed above, where we
@@ -510,33 +553,40 @@ box without explicit remapping of their coordinates.
 .. note::
 
    For non-equilibrium MD (NEMD) simulations using "remap v" it is
-   usually desirable that the fluid (or flowing material, e.g. granular
+   usually desirable that the fluid (or flowing material,
-   particles) stream with a velocity profile consistent with the
+   e.g. granular particles) stream with a velocity profile consistent
-   deforming box.  As mentioned above, using a thermostat such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin <fix_langevin>`
+   with the deforming box.  As mentioned above, using a thermostat
-   (with a bias provided by :doc:`compute temp/deform <compute_temp_deform>`), will typically accomplish
+   such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin
-   that.  If you do not use a thermostat, then there is no driving force
+   <fix_langevin>` (with a bias provided by :doc:`compute temp/deform
-   pushing the atoms to flow in a manner consistent with the deforming
+   <compute_temp_deform>`), will typically accomplish that.  If you do
-   box.  E.g. for a shearing system the box deformation velocity may vary
+   not use a thermostat, then there is no driving force pushing the
+   atoms to flow in a manner consistent with the deforming box.
+   E.g. for a shearing system the box deformation velocity may vary
    from 0 at the bottom to 10 at the top of the box.  But the stream
-   velocity profile of the atoms may vary from -5 at the bottom to +5 at
+   velocity profile of the atoms may vary from -5 at the bottom to +5
-   the top.  You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands.  One way to induce
+   at the top.  You can monitor these effects using the :doc:`fix
-   atoms to stream consistent with the box deformation is to give them an
+   ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform
+   <compute_temp_deform>`, and :doc:`compute temp/profile
+   <compute_temp_profile>` commands.  One way to induce atoms to
+   stream consistent with the box deformation is to give them an
    initial velocity profile, via the :doc:`velocity ramp <velocity>`
-   command, that matches the box deformation rate.  This also typically
+   command, that matches the box deformation rate.  This also
-   helps the system come to equilibrium more quickly, even if a
+   typically helps the system come to equilibrium more quickly, even
-   thermostat is used.
+   if a thermostat is used.
 
 .. note::
 
    If a :doc:`fix rigid <fix_rigid>` is defined for rigid bodies, and
    *remap* is set to *x*, then the center-of-mass coordinates of rigid
-   bodies will be remapped to the changing simulation box.  This will be
+   bodies will be remapped to the changing simulation box.  This will
-   done regardless of whether atoms in the rigid bodies are in the fix
+   be done regardless of whether atoms in the rigid bodies are in the
-   deform group or not.  The velocity of the centers of mass are not
+   fix deform group or not.  The velocity of the centers of mass are
-   remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod <fix_nvt_sllod>` does not currently do anything special
+   not remapped even if *remap* is set to *v*, since :doc:`fix
+   nvt/sllod <fix_nvt_sllod>` does not currently do anything special
    for rigid particles.  If you wish to perform a NEMD simulation of
    rigid particles, you can either thermostat them independently or
-   include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod <fix_nvt_sllod>`.
+   include a background fluid and thermostat the fluid via :doc:`fix
+   nvt/sllod <fix_nvt_sllod>`.
 
 The *flip* keyword allows the tilt factors for a triclinic box to
 exceed half the distance of the parallel box length, as discussed
@@ -568,7 +618,8 @@ command if you want to include lattice spacings in a variable formula.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
+This fix will restore the initial box settings from :doc:`binary
+restart files <restart>`, which allows the fix to be properly continue
 deformation, when using the start/stop options of the :doc:`run <run>`
 command.  None of the :doc:`fix_modify <fix_modify>` options are
 relevant to this fix.  No global or per-atom quantities are stored by
@@ -586,12 +637,14 @@ Restrictions
 You cannot apply x, y, or z deformations to a dimension that is
 shrink-wrapped via the :doc:`boundary <boundary>` command.
 
-You cannot apply xy, yz, or xz deformations to a second dimension (y in
+You cannot apply xy, yz, or xz deformations to a second dimension (y
-xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
+in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
+command.
 
 Related commands
 """"""""""""""""
 
+:doc:`fix deform/pressure <fix_deform_pressure>`,
 :doc:`change_box <change_box>`
 
 Default

doc/src/fix_deform_pressure.rst

@@ -0,0 +1,319 @@
+.. index:: fix deform/pressure
+
+fix deform/pressure command
+===========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID deform/pressure N parameter style args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* deform/pressure = style name of this fix command
+* N = perform box deformation every this many timesteps
+* one or more parameter/arg sequences may be appended
+
+  .. parsed-literal::
+
+     parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
+       *x*, *y*, *z* args = style value(s)
+         style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
+           *pressure* values = target gain
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+           *pressure/mean* values = target gain
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
+
+       *xy*, *xz*, *yz* args = style value
+         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure*
+           *pressure* values = target gain
+             target = target pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
+
+       *box* = style value
+         style = *volume* or *pressure*
+           *volume* value = none = isotropically adjust system to preserve volume of system
+           *pressure* values = target gain
+             target = target mean pressure (pressure units)
+             gain = proportional gain constant (1/(time * pressure) or 1/time units)
+
+* zero or more keyword/value pairs may be appended
+* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
+
+  .. parsed-literal::
+
+       *couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
+         couple pressure values of various dimensions
+       *vol/balance/p* value = *yes* or *no*
+         Modifies the behavior of the *volume* option to try and balance pressures
+       *max/rate* value = *rate*
+         rate = maximum strain rate for pressure control
+       *normalize/pressure* value = *yes* or *no*
+         Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
+       NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all deform/pressure 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001
+   fix 1 all deform/pressure 1 x trate 0.1 y volume z volume vol/balance/p yes
+   fix 1 all deform/pressure 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix is an extension of the :doc:`fix deform <fix_deform>`
+command, which allows all of its options to be used as well as new
+pressure-based controls implemented by this command.
+
+All arguments described on the :doc:`fix deform <fix_deform>` doc page
+also apply to this fix unless otherwise noted below.  The rest of this
+doc page explains the arguments specific to this fix.  Note that a
+simulation can define only a single deformation command: fix deform or
+fix deform/pressure.
+
+----------
+
+For the *x*, *y*, and *z* parameters, this is the meaning of the
+styles and values provided by this fix.
+
+The *pressure* style adjusts a dimension's box length to control the
+corresponding component of the pressure tensor. This option attempts to
+maintain a specified target pressure using a linear controller where the
+box length :math:`L` evolves according to the equation
+
+.. parsed-literal::
+
+   \frac{d L(t)}{dt} = L(t) k (P_t - P)
+
+where :math:`k` is a proportional gain constant, :math:`P_t` is the target
+pressure, and :math:`P` is the current pressure along that dimension. This
+approach is similar to the method used to control the pressure by
+:doc:`fix press/berendsen <fix_press_berendsen>`. The target pressure
+accepts either a constant numeric value or a LAMMPS :ref:`variable <variable>`.
+Notably, this variable can be a function of time or other components of
+the pressure tensor. By default, :math:`k` has units of 1/(time * pressure)
+although this will change if the *normalize/pressure* option is set as
+:ref:`discussed below <deform_normalize>`. There is no proven method
+to choosing an appropriate value of :math:`k` as it will depend on the
+specific details of a simulation. Testing different values is recommended.
+
+By default, there is no limit on the resulting strain rate in any dimension.
+A maximum limit can be applied using the :ref:`max/rate <deform_max_rate>`
+option. Akin to :doc:`fix nh <fix_nh>`, pressures in different dimensions
+can be coupled using the :ref:`couple <deform_couple>` option. This means
+the instantaneous pressure along coupled dimensions are averaged and the box
+strains identically along the coupled dimensions.
+
+The *pressure/mean* style changes a dimension's box length to maintain
+a constant mean pressure defined as the trace of the pressure tensor.
+This option has identical arguments to the *pressure* style and a similar
+functional equation, except the current and target pressures refer to the
+mean trace of the pressure tensor. All options for the *pressure* style
+also apply to the *pressure/mean* style except for the
+:ref:`couple <deform_couple>` option.
+
+Note that while this style can be identical to coupled *pressure* styles,
+it is generally not the same. For instance in 2D, a coupled *pressure*
+style in the *x* and *y* dimensions would be equivalent to using the
+*pressure/mean* style with identical settings in each dimension. However,
+it would not be the same if settings (e.g. gain constants) were used in
+the *x* and *y* dimensions or if the *pressure/mean* command was only applied
+along one dimension.
+
+----------
+
+For the *xy*, *xz*, and *yz* parameters, this is the meaning of the
+styles and values provided by this fix.  Note that changing the
+tilt factors of a triclinic box does not change its volume.
+
+The *pressure* style adjusts a tilt factor to control the corresponding
+off-diagonal component of the pressure tensor. This option attempts to
+maintain a specified target value using a linear controller where the
+tilt factor T evolves according to the equation
+
+.. parsed-literal::
+
+   \frac{d T(t)}{dt} = L(t) k (P - P_t)
+
+where :math:`k` is a proportional gain constant, :math:`P_t` is the
+target pressure, :math:`P` is the current pressure, and :math:`L` is
+the perpendicular box length. The target pressure accepts either a
+constant numeric value or a LAMMPS :ref:`variable
+<variable>`. Notably, this variable can be a function of time or other
+components of the pressure tensor. By default, :math:`k` has units of
+1/(time * pressure) although this will change if the
+*normalize/pessure* option is set as :ref:`discussed below
+<deform_normalize>`.  There is no proven method to choosing an
+appropriate value of :math:`k` as it will depend on the specific
+details of a simulation and testing different values is
+recommended. One can also apply a maximum limit to the magnitude of
+the applied strain using the :ref:`max/rate <deform_max_rate>` option.
+
+----------
+
+The *box* parameter provides an additional control over the *x*, *y*,
+and *z* box lengths by isotropically dilating or contracting the box
+to either maintain a fixed mean pressure or volume. This isotropic
+scaling is applied after the box is deformed by the above *x*, *y*,
+*z*, *xy*, *xz*, and *yz* styles, acting as a second deformation
+step. This parameter will change the overall strain rate in the *x*,
+*y*, or *z* dimensions.  This parameter can only be used in
+combination with the *x*, *y*, or *z* commands: *vel*, *erate*,
+*trate*, *pressure*, or *wiggle*. This is the meaning of its styles
+and values.
+
+The *volume* style isotropically scales box lengths to maintain a constant
+box volume in response to deformation from other parameters. This style
+may be useful in scenarios where one wants to apply a constant deviatoric
+pressure using *pressure* styles in the *x*, *y*, and *z* dimensions (
+deforming the shape of the box), while maintaining a constant volume.
+
+The *pressure* style isotropically scales box lengths in an attempt to
+maintain a target mean pressure (the trace of the pressure tensor) of the
+system. This is accomplished by isotropically scaling all box lengths
+:math:`L` by an additional factor of :math:`k (P_t - P_m)` where :math:`k`
+is the proportional gain constant, :math:`P_t` is the target pressure, and
+:math:`P_m` is the current mean pressure. This style may be useful in
+scenarios where one wants to apply a constant deviatoric strain rate
+using various strain-based styles (e.g. *trate*) along the *x*, *y*, and *z*
+dimensions (deforming the shape of the box), while maintaining a mean pressure.
+
+----------
+
+The optional keywords provided by this fix are described below.
+
+.. _deform_normalize:
+
+The *normalize/pressure* keyword changes how box dimensions evolve when
+using the *pressure* or *pressure/mean* deformation styles. If the
+*deform/normalize* value is set to *yes*, then the deviation from the
+target pressure is normalized by the absolute value of the target
+pressure such that the proportional gain constant scales a percentage
+error and has units of 1/time. If the target pressure is ever zero, this
+will produce an error unless the *max/rate* keyword is defined,
+described below, which will cap the divergence.
+
+.. _deform_max_rate:
+
+The *max/rate* keyword sets an upper threshold, *rate*, that limits the
+maximum magnitude of the instantaneous strain rate applied in any dimension.
+This keyword only applies to the *pressure* and *pressure/mean* options. If
+a pressure-controlled rate is used for both *box* and either *x*, *y*, or
+*z*, then this threshold will apply separately to each individual controller
+such that the cumulative strain rate on a box dimension may be up to twice
+the value of *rate*.
+
+.. _deform_couple:
+
+The *couple* keyword allows two or three of the diagonal components of
+the pressure tensor to be "coupled" together for the *pressure* option.
+The value specified with the keyword determines which are coupled. For
+example, *xz* means the *Pxx* and *Pzz* components of the stress tensor
+are coupled. *Xyz* means all 3 diagonal components are coupled. Coupling
+means two things: the instantaneous stress will be computed as an average
+of the corresponding diagonal components, and the coupled box dimensions
+will be changed together in lockstep, meaning coupled dimensions will be
+dilated or contracted by the same percentage every timestep. If a *pressure*
+style is defined for more than one coupled dimension, the target pressures
+and gain constants must be identical. Alternatively, if a *pressure*
+style is only defined for one of the coupled dimensions, its settings are
+copied to other dimensions with undefined styles. *Couple xyz* can be used
+for a 2d simulation; the *z* dimension is simply ignored.
+
+.. _deform_balance:
+
+The *vol/balance/p* keyword modifies the behavior of the *volume* style when
+applied to two of the *x*, *y*, and *z* dimensions. Instead of straining
+the two dimensions in lockstep, the two dimensions are allowed to
+separately dilate or contract in a manner to maintain a constant
+volume while simultaneously trying to keep the pressure along each
+dimension equal using a method described in :ref:`(Huang2014) <Huang2014>`.
+
+----------
+
+If any pressure controls are used, this fix computes a temperature and
+pressure each timestep. To do this, the fix creates its own computes
+of style "temp" and "pressure", as if these commands had been issued:
+
+.. code-block:: LAMMPS
+
+   compute fix-ID_temp group-ID temp
+   compute fix-ID_press group-ID pressure fix-ID_temp
+
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure
+<compute_pressure>` commands for details.  Note that the IDs of the
+new computes are the fix-ID + underscore + "temp" or fix_ID
++ underscore + "press", and the group for the new computes is the same
+as the fix group.
+
+Note that these are NOT the computes used by thermodynamic output (see
+the :doc:`thermo_style <thermo_style>` command) with ID =
+*thermo_temp* and *thermo_press*.  This means you can change the
+attributes of this fix's temperature or pressure via the
+:doc:`compute_modify <compute_modify>` command or print this
+temperature or pressure during thermodynamic output via the
+:doc:`thermo_style custom <thermo_style>` command using the
+appropriate compute-ID. It also means that changing attributes of
+*thermo_temp* or *thermo_press* will have no effect on this fix.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This fix will restore the initial box settings from :doc:`binary
+restart files <restart>`, which allows the fix to be properly continue
+deformation, when using the start/stop options of the :doc:`run <run>`
+command.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.
+
+If any pressure controls are used, the :doc:`fix_modify <fix_modify>`
+*temp* and *press* options are supported by this fix, unlike in
+:doc:`fix deform <fix_deform>`.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be
+used in its temperature and pressure calculations.  If you do this,
+note that the kinetic energy derived from the compute temperature
+should be consistent with the virial term computed using all atoms for
+the pressure.  LAMMPS will warn you if you choose to compute
+temperature on a subset of atoms.
+
+This fix can perform deformation over multiple runs, using the *start*
+and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+You cannot apply x, y, or z deformations to a dimension that is
+shrink-wrapped via the :doc:`boundary <boundary>` command.
+
+You cannot apply xy, yz, or xz deformations to a second dimension (y
+in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
+command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix deform <fix_deform>`, :doc:`change_box <change_box>`
+
+Default
+"""""""
+
+The option defaults are normalize/pressure = no.
+
+----------
+
+.. _Huang2014:
+
+**(Huang2014)** X. Huang, "Exploring critical-state behavior using DEM",
+Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316

doc/src/fix_electrode.rst

@@ -45,7 +45,7 @@ Syntax
                 rng_v = integer used to initialize random number generator
 
 * zero or more keyword/value pairs may be appended
-* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
+* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal* or *eta*
 
 .. parsed-literal::
 
@@ -68,6 +68,10 @@ Syntax
         filename = file from which to read elastance matrix
     *read_inv* value = filename
         filename = file from which to read inverted matrix
+    *qtotal* value = number or *v_* equal-style variable
+        add overall potential so that all electrode charges add up to *qtotal*
+    *eta* value = d_propname
+        d_propname = a custom double vector defined via fix property/atom
 
 Examples
 """"""""
@@ -249,6 +253,26 @@ be enabled if any electrode particle has the same type as any
 electrolyte particle (which would be unusual in a typical simulation)
 and the fix will issue an error in that case.
 
+.. versionadded:: TBD
+
+The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
+to add an overall potential to all electrodes so that the total charge on
+the electrodes is a specified amount (which may be an equal-style variable).
+For example, if a user wanted to simulate a solution of excess cations
+such that the total electrolyte charge is +2, setting *qtotal -2* would cause
+the total electrode charge to be -2, so that the simulation box remains overall
+electroneutral. Since *fix electrode/conq* constrains the total charges of
+individual electrodes, and since *symm on* constrains the total charge of all
+electrodes to be zero, either option is incompatible with the *qtotal* keyword
+(even if *qtotal* is set to zero).
+
+.. versionadded:: TBD
+
+The keyword *eta* takes the name of a custom double vector defined via fix
+property/atom.  The values will be used instead of the standard eta value.  The
+property/atom fix must be for vector of double values and use the *ghost on*
+option.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_gcmc.rst

@@ -440,8 +440,11 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 Do not set "neigh_modify once yes" or else this fix will never be
-called.  Reneighboring is required.
+called.  Reneighboring is **required**.
 
 Only usable for 3D simulations.
 

doc/src/fix_indent.rst

@@ -8,33 +8,44 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   fix ID group-ID indent K keyword values ...
+   fix ID group-ID indent K gstyle args keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * indent = style name of this fix command
 * K = force constant for indenter surface (force/distance\^2 units)
-* one or more keyword/value pairs may be appended
+* gstyle = *sphere* or *cylinder* or *cone* or *plane*
-* keyword = *sphere* or *cylinder* or *plane* or *side* or *units*
 
   .. parsed-literal::
 
        *sphere* args = x y z R
-         x,y,z = position of center of indenter (distance units)
+         x, y, z = position of center of indenter (distance units)
          R = sphere radius of indenter (distance units)
-         any of x,y,z,R can be a variable (see below)
+         any of x, y, z, R can be a variable (see below)
        *cylinder* args = dim c1 c2 R
          dim = *x* or *y* or *z* = axis of cylinder
-         c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+         c1, c2 = coords of cylinder axis in other 2 dimensions (distance units)
          R = cylinder radius of indenter (distance units)
          any of c1,c2,R can be a variable (see below)
+       *cone* args = dim c1 c2 radlo radhi lo hi
+         dim = *x* or *y* or *z* = axis of cone
+         c1, c2 = coords of cone axis in other 2 dimensions (distance units)
+         radlo,radhi = cone radii at lo and hi end (distance units)
+         lo,hi = bounds of cone in dim (distance units)
+         any of c1, c2, radlo, radhi, lo, hi can be a variable (see below)
        *plane* args = dim pos side
          dim = *x* or *y* or *z* = plane perpendicular to this dimension
          pos = position of plane in dimension x, y, or z (distance units)
          pos can be a variable (see below)
          side = *lo* or *hi*
+
+* zero or more keyword/value pairs may be appended
+* keyword = *side* or *units*
+
+  .. parsed-literal::
+
        *side* value = *in* or *out*
-         *in* = the indenter acts on particles inside the sphere or cylinder
+         *in* = the indenter acts on particles inside the sphere or cylinder or cone
-         *out* = the indenter acts on particles outside the sphere or cylinder
+         *out* = the indenter acts on particles outside the sphere or cylinder or cone
        *units* value = *lattice* or *box*
          lattice = the geometry is defined in lattice units
          box = the geometry is defined in simulation box units
@@ -53,12 +64,12 @@ Description
 
 Insert an indenter within a simulation box.  The indenter repels all
 atoms in the group that touch it, so it can be used to push into a
-material or as an obstacle in a flow.  Or it can be used as a
+material or as an obstacle in a flow.  Alternatively, it can be used as a
 constraining wall around a simulation; see the discussion of the
 *side* keyword below.
 
-The indenter can either be spherical or cylindrical or planar.  You
+The *gstyle* geometry of the indenter can either be a sphere, a
-must set one of those 3 keywords.
+cylinder, a cone, or a plane.
 
 A spherical indenter exerts a force of magnitude
 
@@ -75,15 +86,20 @@ A cylindrical indenter exerts the same force, except that *r* is the
 distance from the atom to the center axis of the cylinder.  The
 cylinder extends infinitely along its axis.
 
-Spherical and cylindrical indenters account for periodic boundaries in
+A conical indenter is similar to a cylindrical indenter except that it
-two ways.  First, the center point of a spherical indenter (x,y,z) or
+has a finite length (between *lo* and *hi*), and that two different
-axis of a cylindrical indenter (c1,c2) is remapped back into the
+radii (one at each end, *radlo* and *radhi*) can be defined.
-simulation box, if the box is periodic in a particular dimension.
+
-This occurs every timestep if the indenter geometry is specified with
+Spherical, cylindrical, and conical indenters account for periodic
-a variable (see below), e.g. it is moving over time.  Second, the
+boundaries in two ways.  First, the center point of a spherical
-calculation of distance to the indenter center or axis accounts for
+indenter (x,y,z) or axis of a cylindrical/conical indenter (c1,c2) is
-periodic boundaries.  Both of these mean that an indenter can
+remapped back into the simulation box, if the box is periodic in a
-effectively move through and straddle one or more periodic boundaries.
+particular dimension.  This occurs every timestep if the indenter
+geometry is specified with a variable (see below), e.g. it is moving
+over time.  Second, the calculation of distance to the indenter center
+or axis accounts for periodic boundaries.  Both of these mean that an
+indenter can effectively move through and straddle one or more
+periodic boundaries.
 
 A planar indenter is really an axis-aligned infinite-extent wall
 exerting the same force on atoms in the system, where *R* is the
@@ -97,9 +113,13 @@ is specified as *hi*\ .
 
 Any of the 4 quantities defining a spherical indenter's geometry can
 be specified as an equal-style :doc:`variable <variable>`, namely *x*,
-*y*, *z*, or *R*\ .  Similarly, for a cylindrical indenter, any of *c1*,
+*y*, *z*, or *R*\ .  For a cylindrical indenter, any of the 3
-*c2*, or *R*, can be a variable.  For a planar indenter, *pos* can be
+quantities *c1*, *c2*, or *R*, can be a variable.  For a conical
-a variable.  If the value is a variable, it should be specified as
+indenter, any of the 6 quantities *c1*, *c2*, *radlo*, *radhi*, *lo*,
+or *hi* can be a variable.  For a planar indenter, the single value
+*pos* can be a variable.
+
+If any of these values is a variable, it should be specified as
 v_name, where name is the variable name.  In this case, the variable
 will be evaluated each timestep, and its value used to define the
 indenter geometry.
@@ -110,7 +130,8 @@ command keywords for the simulation box parameters and timestep and
 elapsed time.  Thus it is easy to specify indenter properties that
 change as a function of time or span consecutive runs in a continuous
 fashion.  For the latter, see the *start* and *stop* keywords of the
-:doc:`run <run>` command and the *elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
+:doc:`run <run>` command and the *elaplong* keyword of
+:doc:`thermo_style custom <thermo_style>` for details.
 
 For example, if a spherical indenter's x-position is specified as v_x,
 then this variable definition will keep it's center at a relative
@@ -141,12 +162,13 @@ rate.
 
 If the *side* keyword is specified as *out*, which is the default,
 then particles outside the indenter are pushed away from its outer
-surface, as described above.  This only applies to spherical or
+surface, as described above.  This only applies to spherical,
-cylindrical indenters.  If the *side* keyword is specified as *in*,
+cylindrical, and conical indenters.  If the *side* keyword is
-the action of the indenter is reversed.  Particles inside the indenter
+specified as *in*, the action of the indenter is reversed.  Particles
-are pushed away from its inner surface.  In other words, the indenter
+inside the indenter are pushed away from its inner surface.  In other
-is now a containing wall that traps the particles inside it.  If the
+words, the indenter is now a containing wall that traps the particles
-radius shrinks over time, it will squeeze the particles.
+inside it.  If the radius shrinks over time, it will squeeze the
+particles.
 
 The *units* keyword determines the meaning of the distance units used
 to define the indenter geometry.  A *box* value selects standard
@@ -166,10 +188,10 @@ lattice spacings in a variable formula.
 
 The force constant *K* is not affected by the *units* keyword.  It is
 always in force/distance\^2 units where force and distance are defined
-by the :doc:`units <units>` command.  If you wish K to be scaled by the
+by the :doc:`units <units>` command.  If you wish K to be scaled by
-lattice spacing, you can define K with a variable whose formula
+the lattice spacing, you can define K with a variable whose formula
-contains *xlat*, *ylat*, *zlat* keywords of the
+contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style
-:doc:`thermo_style <thermo_style>` command, e.g.
+<thermo_style>` command, e.g.
 
 .. code-block:: LAMMPS
 

doc/src/fix_neb.rst

@@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
 force/distance units.
 
 With a value of *ideal*, the spring force is computed as suggested in
-ref`(WeinanE) <WeinanE>`
+:ref:`(WeinanE) <WeinanE>`
 
 .. math::
 
@@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
 equally spaced.  I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
 climbing replica is off, where *i* is the replica number).  The
 *meanDist* is the average distance between replicas.  Note that in this
-case the specified *Kspring* is in force units. When the climbing replica
+case the specified *Kspring* is in force units. When the climbing
-is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
+replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
-each side of the climbing image. Note that the *ideal* form of nudging
+separately each side of the climbing image. Note that the *ideal* form
-can often be more effective at keeping the replicas equally spaced before
+of nudging can often be more effective at keeping the replicas equally
-climbing, then equally spaced either side of the climbing image whilst
+spaced before climbing, then equally spaced either side of the climbing
-climbing.
+image whilst climbing.
 
-With a value of *equal* the spring force is computed as for *ideal*
+With a value of *equal* the spring force is computed as for *ideal* when
-when the climbing replica is off, promoting equidistance. When the climbing
+the climbing replica is off, promoting equidistance. When the climbing
 replica is on, the spring force is computed to promote equidistant
-absolute differences in energy, rather than distance, each side of
+absolute differences in energy, rather than distance, each side of the
-the climbing image:
+climbing image:
 
 .. math::
 
@@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
 
    ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
 
-*meanEdist* is the average absolute energy difference between
+*meanEdist* is the average absolute energy difference between replicas
-replicas up to the climbing image or from the climbing image
+up to the climbing image or from the climbing image to the final image,
-to the final image, for images before or after the climbing
+for images before or after the climbing image
-image respectively. :math:`ED_{ideal}` is the corresponding
+respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
-cumulative sum of average absolute energy differences in
+average absolute energy differences in each case, in close analogy to
-each case, in close analogy to *ideal*. This form of nudging
+*ideal*. This form of nudging is to aid schemes which integrate forces
-is to aid schemes which integrate forces along, or near to,
+along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
-NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
 
 ----------
 
-The keyword *perp* specifies if and how a perpendicular nudging force
+The keyword *perp* specifies if and how a perpendicular nudging force is
-is computed.  It adds a spring force perpendicular to the path in
+computed.  It adds a spring force perpendicular to the path in order to
-order to prevent the path from becoming too strongly kinked.  It can
+prevent the path from becoming too strongly kinked.  It can
 significantly improve the convergence of the NEB calculation when the
-resolution is poor.  I.e. when few replicas are used; see
+resolution is poor.  I.e. when few replicas are used; see :ref:`(Maras)
-:ref:`(Maras) <Maras1>` for details.
+<Maras1>` for details.
 
 The perpendicular spring force is given by
 
@@ -181,10 +180,10 @@ force is added.
 
 By default, no additional forces act on the first and last replicas
 during the NEB relaxation, so these replicas simply relax toward their
-respective local minima.  By using the key word *end*, additional
+respective local minima.  By using the key word *end*, additional forces
-forces can be applied to the first and/or last replicas, to enable
+can be applied to the first and/or last replicas, to enable them to
-them to relax toward a MEP while constraining their energy E to the
+relax toward a MEP while constraining their energy E to the target
-target energy ETarget.
+energy ETarget.
 
 If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
 specified replica becomes:
@@ -197,33 +196,33 @@ specified replica becomes:
 The "spring" constant on the difference in energies is the specified
 *Kspring3* value.
 
-When *estyle* is specified as *first*, the force is applied to the
+When *estyle* is specified as *first*, the force is applied to the first
-first replica.  When *estyle* is specified as *last*, the force is
+replica.  When *estyle* is specified as *last*, the force is applied to
-applied to the last replica.  Note that the *end* keyword can be used
+the last replica.  Note that the *end* keyword can be used twice to add
-twice to add forces to both the first and last replicas.
+forces to both the first and last replicas.
 
 For both these *estyle* settings, the target energy *ETarget* is set
 to the initial energy of the replica (at the start of the NEB
 calculation).
 
 If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
-force is applied to the last replica, but the target energy *ETarget*
+force is applied to the last replica, but the target energy *ETarget* is
-is continuously set to the energy of the first replica, as it evolves
+continuously set to the energy of the first replica, as it evolves
 during the NEB relaxation.
 
 The difference between these two *estyle* options is as follows.  When
 *estyle* is specified as *last/efirst*, no change is made to the
-inter-replica force applied to the intermediate replicas (neither
+inter-replica force applied to the intermediate replicas (neither first
-first or last).  If the initial path is too far from the MEP, an
+or last).  If the initial path is too far from the MEP, an intermediate
-intermediate replica may relax "faster" and reach a lower energy than
+replica may relax "faster" and reach a lower energy than the last
-the last replica.  In this case the intermediate replica will be
+replica.  In this case the intermediate replica will be relaxing toward
-relaxing toward its own local minima.  This behavior can be prevented
+its own local minima.  This behavior can be prevented by specifying
-by specifying *estyle* as *last/efirst/middle* which will alter the
+*estyle* as *last/efirst/middle* which will alter the inter-replica
-inter-replica force applied to intermediate replicas by removing the
+force applied to intermediate replicas by removing the contribution of
-contribution of the gradient to the inter-replica force.  This will
+the gradient to the inter-replica force.  This will only be done if a
-only be done if a particular intermediate replica has a lower energy
+particular intermediate replica has a lower energy than the first
-than the first replica.  This should effectively prevent the
+replica.  This should effectively prevent the intermediate replicas from
-intermediate replicas from over-relaxing.
+over-relaxing.
 
 After converging a NEB calculation using an *estyle* of
 *last/efirst/middle*, you should check that all intermediate replicas
@@ -237,9 +236,10 @@ target energy.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global or per-atom quantities are stored
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-by this fix for access by various :doc:`output commands <Howto_output>`.
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 

doc/src/fix_nonaffine_displacement.rst

@@ -44,7 +44,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 This fix computes different metrics of the nonaffine displacement of
 particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`
@@ -86,8 +86,8 @@ Both of these methods require defining a reference state. With the *fixed* refer
 style, the user picks a specific timestep *nstep* at which particle positions are saved.
 If peratom data is accessed from this compute prior to this timestep, it will simply be
 zeroed. The *update* reference style implies the reference state will be updated every
-*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
+*nstep* timesteps. The *offset* reference will update the reference state *nstep*
-update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
+timesteps before a multiple of *nevery* timesteps.
 
 
 ----------

doc/src/fix_property_atom.rst

@@ -22,6 +22,8 @@ Syntax
        *mol* = molecule IDs
        *q* = charge
        *rmass* = per-atom mass
+       *temperature* = internal temperature of atom
+       *heatflow* = internal heat flow of atom
        i_name = new integer vector referenced by name
        d_name = new floating-point vector referenced by name
        i2_name = new integer array referenced by name
@@ -59,14 +61,18 @@ these properties for each atom in the system when a data file is read.
 This fix augments the set of per-atom properties with new custom
 ones. This can be useful in several scenarios.
 
-If the atom style does not define molecule IDs, per-atom charge, or
+If the atom style does not define molecule IDs, per-atom charge,
-per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
+per-atom mass, internal temperature, or internal heat flow, they can
+be added using the *mol*\ , *q*, *rmass*, *temperature*, or *heatflow*
 keywords.  This could be useful to define "molecules" to use as rigid
 bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
 around an extra flag with atoms (stored as a molecule ID) that can be
 used by various commands like :doc:`compute chunk/atom
 <compute_chunk_atom>` to group atoms without having to use the group
 command (which is limited to a total of 32 groups including *all*\ ).
+For finite-size particles, an internal temperature and heat flow can
+be used to model heat conduction as in the
+:doc:`GRANULAR package <Howto_granular>`.
 
 Another application is to use the *rmass* flag in order to have
 per-atom masses instead of per-type masses.  This could be used to
@@ -85,9 +91,10 @@ properties that are not needed such as bond lists, which incurs some
 overhead when there are no bonds.
 
 In the future, we may add additional existing per-atom properties to
-fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
+fix property/atom, similar to *mol*\ , *q*, *rmass*\ , *temperature*\ ,
-"turn-on" specific properties defined by some atom styles, so they can
+or *heatflow* which "turn-on" specific properties defined by some atom
-be easily used by atom styles that do not define them.
+styles, so they can be easily used by atom styles that do not define
+them.
 
 More generally, the *i_name* and *d_name* options allow one or more
 new custom per-atom vectors to be defined.  Likewise the *i2_name* and

doc/src/fix_sgcmc.rst

@@ -155,6 +155,9 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 At present the fix provides optimized subroutines for EAM type
 potentials (see above) that calculate potential energy changes due to
 *local* atom type swaps very efficiently.  Other potentials are

doc/src/fix_ttm.rst

@@ -96,11 +96,11 @@ each processor, which is acceptable when the overall grid is reasonably
 small.  For larger grids you should use fix *ttm/grid* instead.
 
 Fix *ttm/mod* adds options to account for external heat sources (e.g. at
-a surface) and for specifying parameters that allow the electronic
+a surface) and for specifying parameters that allow the electronic heat
-heat capacity to depend strongly on electronic temperature.  It is
+capacity to depend strongly on electronic temperature.  It is more
-more expensive computationally than fix *ttm* because it treats the
+expensive computationally than fix *ttm* because it treats the thermal
-thermal diffusion equation as non-linear.  More details on fix *ttm/mod*
+diffusion equation as non-linear.  More details on fix *ttm/mod* are
-are given below.
+given below.
 
 Heat transfer between the electronic and atomic subsystems is carried
 out via an inhomogeneous Langevin thermostat.  Only atoms in the fix
@@ -303,15 +303,15 @@ The current fix ttm/mod implementation allows TTM simulations with a
 vacuum. The vacuum region is defined as the grid cells with zero
 electronic temperature. The numerical scheme does not allow energy
 exchange with such cells. Since the material can expand to previously
-unoccupied region in some simulations, the vacuum border can be
+unoccupied region in some simulations, the vacuum border can be allowed
-allowed to move. It is controlled by the *surface_movement* parameter
+to move. It is controlled by the *surface_movement* parameter in the
-in the *init_file*. If it is set to 1, then "vacuum" cells can be
+*init_file*. If it is set to 1, then "vacuum" cells can be changed to
-changed to "electron-filled" cells with the temperature *T_e_min* if
+"electron-filled" cells with the temperature *T_e_min* if atoms move
-atoms move into them (currently only implemented for the case of
+into them (currently only implemented for the case of 1-dimensional
-1-dimensional motion of flat surface normal to the X axis). The
+motion of a flat surface normal to the X axis). The initial locations of
-initial borders of vacuum can be set in the *init_file* via *lsurface*
+the interfaces of the electron density to the vacuum can be set in the
-and *rsurface* parameters. In this case, electronic pressure gradient
+*init_file* via *lsurface* and *rsurface* parameters. In this case,
-is calculated as
+electronic pressure gradient is calculated as
 
 .. math::
 

doc/src/fix_wall_flow.rst

@@ -0,0 +1,175 @@
+.. index:: fix wall/flow
+.. index:: fix wall/flow/kk
+
+fix wall/flow command
+=====================
+
+Accelerator Variants: *wall/flow/kk*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID wall/flow axis vflow T seed N coords ... keyword value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* wall/flow = style name of this fix command
+* axis = flow axis (*x*, *y*, or *z*)
+* vflow = generated flow velocity in *axis* direction (velocity units)
+* T = flow temperature (temperature units)
+* seed = random seed for stochasticity (positive integer)
+* N = number of walls
+* coords = list of N wall positions along the *axis* direction in ascending order (distance units)
+* zero or more keyword/value pairs may be appended
+* keyword = *units*
+
+  .. parsed-literal::
+
+       *units* value = *lattice* or *box*
+         *lattice* = wall positions are defined in lattice units
+         *box* = the wall positions are defined in simulation box units
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all wall/flow x 0.4 1.5 593894 4 2.0 4.0 6.0 8.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix implements flow boundary conditions (FBC) introduced in
+:ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
+The goal is to generate a stationary flow with a shifted Maxwell
+velocity distribution:
+
+.. math::
+
+   f_a(v_a) \propto \exp{\left(-\frac{m (v_a-v_{\text{flow}})^2}{2 kB T}\right)}
+
+where :math:`v_a` is the component of velocity along the specified
+*axis* argument (a = x,y,z), :math:`v_{\text{flow}}` is the flow
+velocity specified as the *vflow* argument, *T* is the specified flow
+temperature, *m* is the particle mass, and *kB* is the Boltzmann
+constant.
+
+This is achieved by defining a series of *N* transparent walls along
+the flow *axis* direction.  Each wall is at the specified position
+listed in the *coords* argument.  Note that an additional transparent
+wall is defined by the code at the boundary of the (periodic)
+simulation domain in the *axis* direction.  So there are effectively
+N+1 walls.
+
+Each time a particle in the specified group passes through one of the
+transparent walls, its velocity is re-assigned.  Particles not in the
+group do not interact with the wall. This can be used, for example, to
+add obstacles composed of atoms, or to simulate a solution of complex
+molecules in a one-atom liquid (note that the fix has been tested for
+one-atom systems only).
+
+Conceptually, the velocity re-assignment represents creation of a new
+particle within the system with simultaneous removal of the particle
+which passed through the wall.  The velocity components in directions
+parallel to the wall are re-assigned according to the standard Maxwell
+velocity distribution for the specified temperature *T*.  The velocity
+component perpendicular to the wall is re-assigned according to the
+shifted Maxwell distribution defined above:
+
+.. math::
+
+   f_{\text{a generated}}(v_a) \propto v_a f_a(v_a)
+
+It can be shown that for an ideal-gas scenario this procedure makes
+the velocity distribution of particles between walls exactly as
+desired.
+
+Since in most cases simulated systems are not an ideal gas, multiple
+walls can be defined, since a single wall may not be sufficient for
+maintaining a stationary flow without "congestion" which can manifest
+itself as regions in the flow with increased particle density located
+upstream from static obstacles.
+
+For the same reason, the actual temperature and velocity of the
+generated flow may differ from what is requested.  The degree of
+discrepancy is determined by how different from an ideal gas the
+simulated system is.  Therefore, a calibration procedure may be
+required for such a system as described in :ref:`(Pavlov)
+<fbc-Pavlov2>`.
+
+Note that the interactions between particles on different sides of a
+transparent wall are not disabled or neglected.  Likewise particle
+positions are not altered by the velocity reassignment.  This removes
+the need to modify the force field to work correctly in cases when a
+particle is close to a wall.
+
+For example, if particle positions were uniformly redistributed across
+the surface of a wall, two particles could end up too close to each
+other, potentially causing the simulation to explode.  However due to
+this compromise, some collective phenomena such as regions with
+increased/decreased density or collective movements are not fully
+removed when particles cross a wall.  This unwanted consequence can
+also be potentially mitigated by using more multiple walls.
+
+.. note::
+
+  When the specified flow has a high velocity, a lost atoms error can
+  occur (see :doc:`error messages <Errors_messages>`).  If this
+  happens, you should ensure the checks for neighbor list rebuilds,
+  set via the :doc:`neigh_modify <neigh_modify>` command, are as
+  conservative as possible (every timestep if needed).  Those are the
+  default settings.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to
+this fix.
+
+No global or per-atom quantities are stored by this fix for access by
+various :doc:`output commands <Howto_output>`.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+Fix *wall_flow* is part of the EXTRA-FIX package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Flow boundary conditions should not be used with rigid bodies such as
+those defined by a "fix rigid" command.
+
+This fix can only be used with periodic boundary conditions along the
+flow axis. The size of the box in this direction must not change. Also,
+the fix is designed to work only in an orthogonal simulation box.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix wall/reflect <fix_wall>` command
+
+Default
+"""""""
+
+The default for the units keyword is lattice.
+
+----------
+
+.. _fbc-Pavlov1:
+
+**(Pavlov1)** Pavlov, Kolotinskii, Stegailov, "GPU-Based Molecular Dynamics of Turbulent Liquid Flows with OpenMM", Proceedings of PPAM-2022, LNCS (Springer), vol. 13826, pp. 346-358 (2023)
+
+.. _fbc-Pavlov2:
+
+**(Pavlov2)** Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)

doc/src/fix_widom.rst

@@ -195,8 +195,11 @@ doc page for more info.
 Do not set "neigh_modify once yes" or else this fix will never be
 called.  Reneighboring is **required**.
 
-Can be run in parallel, but aspects of the GCMC part will not scale well
+This fix style requires an :doc:`atom style <atom_style>` with per atom
-in parallel. Only usable for 3D simulations.
+type masses.
+
+Can be run in parallel, but some aspects of the insertion procedure
+will not scale well in parallel. Only usable for 3D simulations.
 
 
 Related commands

doc/src/info.rst

@@ -10,7 +10,7 @@ Syntax
 
    info args
 
-* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, or *configuration*
+* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, *fft* or *configuration*
 * *out* values = *screen*, *log*, *append* filename, *overwrite* filename
 * *styles* values = *all*, *angle*, *atom*, *bond*, *compute*, *command*, *dump*, *dihedral*, *fix*, *improper*, *integrate*, *kspace*, *minimize*, *pair*, *region*
 
@@ -92,6 +92,13 @@ The *accelerator* category prints out information about compile time
 settings of included accelerator support for the GPU, KOKKOS, INTEL,
 and OPENMP packages.
 
+.. versionadded:: 7Feb2024
+
+The *fft* category prints out information about the included 3d-FFT
+support.  This lists the 3d-FFT engine, FFT precision, FFT library
+used by the FFT engine. If the KOKKOS package is included, the settings
+used for the KOKKOS package are displayed as well.
+
 The *styles* category prints the list of styles available in the
 current LAMMPS binary. It supports one of the following options
 to control which category of styles is printed out:

doc/src/kspace_style.rst

@@ -450,7 +450,10 @@ relative RMS error.
   For the KOKKOS package, the *pppm/kk* style performs charge
   assignment and force interpolation calculations, along with the FFTs
   themselves, on the GPU or (optionally) threaded on the CPU when
-  using OpenMP and FFTW3.
+  using OpenMP and FFTW3. The specific FFT library is selected using
+  the FFT_KOKKOS CMake parameter. See the
+  :doc:`Build settings <Build_settings>` doc page for how to select a
+  3rd-party FFT library.
 
 ----------
 

doc/src/molecule.rst

@@ -126,14 +126,50 @@ molecule (header keyword = inertia).
 Format of a molecule file
 """""""""""""""""""""""""
 
-The format of an individual molecule file is similar but
+The format of an individual molecule file looks similar but is
-(not identical) to the data file read by the :doc:`read_data <read_data>`
+different than that of a data file read by the :doc:`read_data <read_data>`
-commands, and is as follows.
+commands.  Here is a simple example for a TIP3P water molecule:
+
+.. code-block::
+
+   # Water molecule. TIP3P geometry
+   # header section:
+   3 atoms
+   2 bonds
+   1 angles
+
+   # body section:
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+
+   Charges
+
+   1       -0.834
+   2        0.417
+   3        0.417
+
+   Bonds
+
+   1   1      1      2
+   2   1      1      3
+
+   Angles
+
+   1   1      2      1      3
 
 A molecule file has a header and a body.  The header appears first.  The
-first line of the header and thus of the molecule file is *always* skipped;
+first line of the header and thus of the molecule file is *always*
-it typically contains a description of the file or a comment from the software
+skipped; it typically contains a description of the file or a comment
-that created the file.
+from the software that created the file.
 
 Then lines are read one line at a time.  Lines can have a trailing
 comment starting with '#' that is ignored.  There *must* be at least one
@@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
 defining a *body* particle, which requires setting the number of
 *atoms* to 1, and setting the *inertia* in a specific section (see below).
 
-* N *atoms* = # of atoms N in molecule, default = 0
+   .. list-table::
-* Nb *bonds* = # of bonds Nb in molecule, default = 0
+      :header-rows: 1
-* Na *angles* = # of angles Na in molecule, default = 0
+      :widths: auto
-* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
-* Ni *impropers* = # of impropers Ni in molecule, default = 0
-* Nf *fragments* = # of fragments Nf in molecule, default = 0
-* Ninteger Ndouble *body* = # of integer and floating-point values
-  in body particle, default = 0
-* Mtotal *mass* = total mass of molecule
-* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
-* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
 
-For *mass*, *com*, and *inertia*, the default is for LAMMPS to
+      * - Number(s)
-calculate this quantity itself if needed, assuming the molecules
+        - Keyword
-consist of a set of point particles or finite-size particles (with a
+        - Meaning
-non-zero diameter) that do not overlap.  If finite-size particles in
+        - Default Value
-the molecule do overlap, LAMMPS will not account for the overlap
+      * - N
-effects when calculating any of these 3 quantities, so you should
+        - atoms
-pre-compute them yourself and list the values in the file.
+        - # of atoms N in molecule
+        - 0
+      * - Nb
+        - bonds
+        - # of bonds Nb in molecule
+        - 0
+      * - Na
+        - angles
+        - # of angles Na in molecule
+        - 0
+      * - Nd
+        - dihedrals
+        - # of dihedrals Nd in molecule
+        - 0
+      * - Ni
+        - impropers
+        - # of impropers Ni in molecule
+        - 0
+      * - Nf
+        - fragments
+        - # of fragments Nf in molecule
+        - 0
+      * - Ninteger Ndouble
+        - body
+        - # of integer and floating-point values in body particle
+        - 0
+      * - Mtotal
+        - mass
+        - total mass of molecule
+        - computed
+      * - Xc Yc Zc
+        - com
+        - coordinates of center-of-mass of molecule
+        - computed
+      * - Ixx Iyy Izz Ixy Ixz Iyz
+        - inertia
+        - 6 components of inertia tensor of molecule
+        - computed
+
+For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
+this quantity itself if needed, assuming the molecules consist of a set
+of point particles or finite-size particles (with a non-zero diameter)
+that do **not** overlap.  If finite-size particles in the molecule
+**do** overlap, LAMMPS will not account for the overlap effects when
+calculating any of these 3 quantities, so you should pre-compute them
+yourself and list the values in the file.
 
 The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@@ -188,7 +261,7 @@ internally.
 
 These are the allowed section keywords for the body of the file.
 
-* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
+* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
 * *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
 * *Special Bond Counts, Special Bonds* = special neighbor info
 * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
 
 ----------
 
+.. versionadded:: 7Feb2024
+
+*Dipoles* section:
+
+* one line per atom
+* line syntax: ID mux muy muz
+* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
+
+This section is only allowed for :doc:`atom styles <atom_style>` that
+support particles with point dipoles, e.g. atom_style dipole.  If not
+listed, the default dipole component of each atom in the molecule is set
+to 0.0.
+
+----------
+
 *Masses* section:
 
 * one line per atom

doc/src/neb.rst

@@ -10,7 +10,7 @@ Syntax
 
    neb etol ftol N1 N2 Nevery file-style arg keyword values
 
-* etol = stopping tolerance for energy (energy units)
+* etol = stopping tolerance for energy (dimensionless)
 * ftol = stopping tolerance for force (force units)
 * N1 = max # of iterations (timesteps) to run initial NEB
 * N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@@ -89,10 +89,11 @@ potentials, and the starting configuration when the neb command is
 issued should be the same for every replica.
 
 In a NEB calculation each replica is connected to other replicas by
-inter-replica nudging forces.  These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
+inter-replica nudging forces.  These forces are imposed by the
-neb command.  The group used to define the fix neb command defines the
+:doc:`fix neb <fix_neb>` command, which must be used in conjunction
-NEB atoms which are the only ones that inter-replica springs are
+with the neb command.  The group used to define the fix neb command
-applied to.  If the group does not include all atoms, then non-NEB
+defines the NEB atoms which are the only ones that inter-replica springs
+are applied to.  If the group does not include all atoms, then non-NEB
 atoms have no inter-replica springs and the forces they feel and their
 motion is computed in the usual way due only to other atoms within
 their replica.  Conceptually, the non-NEB atoms provide a background
@@ -445,7 +446,7 @@ Related commands
 """"""""""""""""
 
 :doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
-:doc:`fix viscous <fix_viscous>`
+:doc:`fix viscous <fix_viscous>`, :doc:`fix neb <fix_neb>`
 
 Default
 """""""

doc/src/package.rst

@@ -74,7 +74,7 @@ Syntax
            *no_affinity* values = none
        *kokkos* args = keyword value ...
          zero or more keyword/value pairs may be appended
-         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *gpu/aware* or *pair/only*
+         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *atom/map* or *gpu/aware* or *pair/only*
            *neigh* value = *full* or *half*
              full = full neighbor list
              half = half neighbor list built in thread-safe manner
@@ -108,6 +108,9 @@ Syntax
            *sort* value = *no* or *device*
              *no* = perform atom sorting in non-KOKKOS mode
              *device* = perform atom sorting on device (e.g. on GPU)
+           *atom/map* value = *no* or *device*
+             *no* = build atom map in non-KOKKOS mode
+             *device* = build atom map on device (e.g. on GPU)
            *gpu/aware* = *off* or *on*
              *off* = do not use GPU-aware MPI
              *on* = use GPU-aware MPI (default)
@@ -566,15 +569,19 @@ performing the exchange pack/unpack on the host CPU can give speedup
 since it reduces the number of CUDA kernel launches.
 
 The *sort* keyword determines whether the host or device performs atom
-sorting, see the :doc:`atom_modify sort <atom_modify>` command.  The
+sorting, see the :doc:`atom_modify sort <atom_modify>` command.  The value
-value options for the *sort* keyword are *no* or *device* similar to the
+options for the *sort* keyword are *no* or *device* similar to the *comm*
-*comm* keywords above. If a value of *host* is used it will be
+keywords above. If a value of *host* is used it will be automatically be
-automatically be changed to *no* since the *sort* keyword does not
+changed to *no* since the *sort* keyword does not support *host* mode. Not
-support *host* mode. The value of *no* will also always be used when
+all fix styles with extra atom data support *device* mode and in that case
-running on the CPU, i.e. setting the value to *device* will have no
+a warning will be given and atom sorting will run in *no* mode instead.
-effect if the simulation is running on the CPU. Not all fix styles with
+
-extra atom data support *device* mode and in that case a warning will be
+.. versionadded:: TBD
-given and atom sorting will run in *no* mode instead.
+
+The *atom/map* keyword determines whether the host or device builds the
+atom_map, see the :doc:`atom_modify map <atom_modify>` command.  The
+value options for the *atom/map* keyword are identical to the *sort*
+keyword above.
 
 The *gpu/aware* keyword chooses whether GPU-aware MPI will be used. When
 this keyword is set to *on*, buffers in GPU memory are passed directly
@@ -593,12 +600,13 @@ for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
 Spectrum MPI when the "-gpu" flag is used.
 
 The *pair/only* keyword can change how the KOKKOS suffix "kk" is applied
-when using an accelerator device.  By default device acceleration is
+when using an accelerator device.  By default device acceleration is always
-always used for all available styles.  With *pair/only* set to *on* the
+used for all available styles.  With *pair/only* set to *on* the suffix
-suffix setting will choose device acceleration only for pair styles and
+setting will choose device acceleration only for pair styles and run all
-run all other force computations on the host CPU.
+other force computations on the host CPU.  The *comm* flags, along with the
-The *comm* flags will also automatically be changed to *no*\ . This can
+*sort* and *atom/map* keywords will also automatically be changed to *no*\ .
-result in better performance for certain configurations and system sizes.
+This can result in better performance for certain configurations and
+system sizes.
 
 ----------
 
@@ -684,18 +692,18 @@ Restrictions
 This command cannot be used after the simulation box is defined by a
 :doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.
 
-The gpu style of this command can only be invoked if LAMMPS was built
+The *gpu* style of this command can only be invoked if LAMMPS was built
 with the GPU package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
-The intel style of this command can only be invoked if LAMMPS was
+The *intel* style of this command can only be invoked if LAMMPS was
 built with the INTEL package.  See the :doc:`Build package <Build_package>` page for more info.
 
-The kk style of this command can only be invoked if LAMMPS was built
+The *kokkos* style of this command can only be invoked if LAMMPS was built
 with the KOKKOS package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
-The omp style of this command can only be invoked if LAMMPS was built
+The *omp* style of this command can only be invoked if LAMMPS was built
 with the OPENMP package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
@@ -704,19 +712,27 @@ Related commands
 
 :doc:`suffix <suffix>`, :doc:`-pk command-line switch <Run_options>`
 
-Default
+Defaults
-"""""""
+""""""""
 
-For the GPU package, the default is Ngpu = 0 and the option defaults are neigh
+For the GPU package, the default parameters and settings are:
-= yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1,
-omp = 0, and platform=-1.  These settings are made automatically if the "-sf
-gpu" :doc:`command-line switch <Run_options>` is used.  If it is not used, you
-must invoke the package gpu command in your input script or via the "-pk gpu"
-:doc:`command-line switch <Run_options>`.
 
-For the INTEL package, the default is Nphi = 1 and the option defaults are omp
+.. parsed-literal::
-= 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table =
+
-yes.  The default ghost option is determined by the pair style being used.
+   Ngpu = 0, neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1, omp = 0, platform=-1.
+
+These settings are made automatically if the "-sf gpu"
+:doc:`command-line switch <Run_options>` is used.  If it is not used,
+you must invoke the package gpu command in your input script or via the
+"-pk gpu" :doc:`command-line switch <Run_options>`.
+
+For the INTEL package, the default parameters and settings are:
+
+.. parsed-literal::
+
+   Nphi = 1, omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table = yes
+
+The default ghost option is determined by the pair style being used.
 This value is output to the screen in the offload report at the end of each
 run.  Note that all of these settings, except "omp" and "mode", are ignored if
 LAMMPS was not built with Xeon Phi co-processor support.  These settings are
@@ -724,20 +740,35 @@ made automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
 is used.  If it is not used, you must invoke the package intel command in your
 input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
 
-For the KOKKOS package, the option defaults for GPUs are neigh = full,
+For the KOKKOS package when using GPUs, the option defaults are:
-neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default value,
-comm = device, sort = device, neigh/transpose = off, gpu/aware = on. When
-LAMMPS can safely detect that GPU-aware MPI is not available, the default value
-of gpu/aware becomes "off". For CPUs or Xeon Phis, the option defaults are
-neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, and sort
-= no. For GPUs, option neigh/thread = on when there are 16k atoms or less on an MPI
-rank, otherwise it is "off". These settings are made automatically by the
-required "-k on" :doc:`command-line switch <Run_options>`. You can change them
-by using the package kokkos command in your input script or via the :doc:`-pk
-kokkos command-line switch <Run_options>`.
 
-For the OMP package, the default is Nthreads = 0 and the option defaults are
+.. parsed-literal::
-neigh = yes.  These settings are made automatically if the "-sf omp"
+
-:doc:`command-line switch <Run_options>` is used.  If it is not used, you must
+   neigh = full, neigh/qeq = full, newton = off, binsize = 2x LAMMPS default value, comm = device, sort = device, atom/map = device, neigh/transpose = off, gpu/aware = on
-invoke the package omp command in your input script or via the "-pk omp"
+
-:doc:`command-line switch <Run_options>`.
+For GPUs, option neigh/thread = on when there are 16k atoms or less on
+an MPI rank, otherwise it is "off". When LAMMPS can safely detect that
+GPU-aware MPI is not available, the default value of gpu/aware becomes
+"off".
+
+For the KOKKOS package when using CPUs or Xeon Phis, the option defaults are:
+
+.. parsed-literal::
+
+   neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, sort = no, atom/map = no
+
+These settings are made automatically by
+the required "-k on" :doc:`command-line switch <Run_options>`.  You can
+change them by using the package kokkos command in your input script or
+via the :doc:`-pk kokkos command-line switch <Run_options>`.
+
+For the OMP package, the defaults are
+
+.. parsed-literal::
+
+   Nthreads = 0, neigh = yes
+
+These settings are made automatically if the "-sf omp"
+:doc:`command-line switch <Run_options>` is used.  If it is not used,
+you must invoke the package omp command in your input script or via the
+"-pk omp" :doc:`command-line switch <Run_options>`.

doc/src/pair_airebo.rst

@@ -156,7 +156,7 @@ pair_coeff command:
 The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
 The first three C arguments map LAMMPS atom types 1,2,3 to the C
 element in the AIREBO file.  The final H argument maps LAMMPS atom
-type 4 to the H element in the SW file.  If a mapping value is
+type 4 to the H element in the AIREBO file.  If a mapping value is
 specified as NULL, the mapping is not performed.  This can be used
 when a *airebo* potential is used as part of the *hybrid* pair style.
 The NULL values are placeholders for atom types that will be used with
@@ -222,12 +222,12 @@ enabled if LAMMPS was built with that package.  See the :doc:`Build package <Bui
 These pair potentials require the :doc:`newton <newton>` setting to be
 "on" for pair interactions.
 
-The CH.airebo and CH.airebo-m potential files provided with LAMMPS
+The CH.airebo and CH.airebo-m potential files provided with LAMMPS (see
-(see the potentials directory) are parameterized for metal :doc:`units <units>`.
+the potentials directory) are parameterized for metal :doc:`units
-You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
+<units>`.  You can use the pair styles with *any* LAMMPS units, but you
-but you would need to create your own AIREBO or AIREBO-M potential file
+would need to create your own AIREBO or AIREBO-M potential file with
-with coefficients listed in the appropriate units, if your simulation
+coefficients listed in the appropriate units, if your simulation does
-does not use "metal" units.
+not use "metal" units.
 
 The pair styles provided here **only** support potential files parameterized
 for the elements carbon and hydrogen (designated with "C" and "H" in the

doc/src/pair_charmm.rst

@@ -16,6 +16,7 @@
 .. index:: pair_style lj/charmm/coul/msm/omp
 .. index:: pair_style lj/charmmfsw/coul/charmmfsh
 .. index:: pair_style lj/charmmfsw/coul/long
+.. index:: pair_style lj/charmmfsw/coul/long/kk
 
 pair_style lj/charmm/coul/charmm command
 ========================================
@@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
 pair_style lj/charmmfsw/coul/long command
 =========================================
 
+Accelerator Variants: *lj/charmmfsw/coul/long/kk*
+
 Syntax
 """"""
 
@@ -281,7 +284,9 @@ page for more info.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
+:doc:`dihedral_style charmm <dihedral_charmm>`,
+:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

doc/src/pair_dsmc.rst

@@ -138,8 +138,12 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This style is part of the MC package.  It is only enabled if LAMMPS
+This pair style is part of the MC package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires an :doc:`atom style <atom_style>` with per
+atom type masses.
 
 Related commands
 """"""""""""""""

doc/src/pair_lepton.rst

@@ -72,7 +72,7 @@ interactions between particles which depend on the distance and have a
 cutoff.  The potential function must be provided as an expression string
 using "r" as the distance variable.  With pair style *lepton/coul* one
 may additionally reference the charges of the two atoms of the pair with
-"qi" and "qj", respectively.  With pair style *lepton/coul* one may
+"qi" and "qj", respectively.  With pair style *lepton/sphere* one may
 instead reference the radii of the two atoms of the pair with "radi" and
 "radj", respectively; this is half of the diameter that can be set in
 :doc:`data files <read_data>` or the :doc:`set command <set>`.
@@ -166,8 +166,8 @@ mixing.  Thus, expressions for *all* I,J pairs must be specified
 explicitly.
 
 Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
-option for shifting the energy of the pair interaction so that it is
+option for shifting the potential energy of the pair interaction so that
-0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
+it is 0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
 
 The :doc:`pair_modify table <pair_modify>` options are not relevant for
 the these pair styles.

doc/src/pair_meam.rst

@@ -427,8 +427,8 @@ package. They are only enabled if LAMMPS was built with that package.
 See the :doc:`Build package <Build_package>` page for more info.
 
 The maximum number of elements, that can be read from the MEAM library
-file, is determined at compile time. The default is 5.  If you need
+file, is determined at compile time. The default is 8.  If you need
-support for more elements, you have to change the the constant 'maxelt'
+support for more elements, you have to change the the constant 'MAXELT'
 at the beginning of the file ``src/MEAM/meam.h`` and update/recompile
 LAMMPS.  There is no limit on the number of atoms types.
 

doc/src/pair_rebomos.rst

@@ -0,0 +1,150 @@
+.. index:: pair_style rebomos
+.. index:: pair_style rebomos/omp
+
+pair_style rebomos command
+==========================
+
+Accelerator Variants: *rebomos/omp*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rebomos
+
+* rebomos = name of this pair style
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rebomos
+   pair_coeff * * ../potentials/MoS.rebomos Mo S
+
+Example input scripts available: examples/threebody/
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *rebomos* pair style computes the interactions between molybdenum
+and sulfur atoms :ref:`(Stewart) <Stewart>` utilizing an adaptive
+interatomic reactive empirical bond order potential that is similar in
+form to the AIREBO potential :ref:`(Stuart) <Stuart2>`.  The potential
+is based on an earlier parameterizations for :math:`\text{MoS}_2`
+developed by :ref:`(Liang) <Liang>`.
+
+The REBOMoS potential consists of two terms:
+
+.. math::
+
+   E & = \frac{1}{2} \sum_i \sum_{j \neq i}
+   \left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij}  \right] \\
+
+The :math:`E^{\text{REBO}}` term describes the covalently bonded
+interactions between Mo and S atoms while the :math:`E^{\text{LJ}}` term
+describes longer range dispersion forces between layers.  A cubic spline
+function is applied to smoothly switch between covalent bonding at short
+distances to dispersion interactions at longer distances. This allows
+the model to capture bond formation and breaking events which may occur
+between adjacent MoS2 layers, edges, defects, and more.
+
+----------
+
+Only a single pair_coeff command is used with the *rebomos* pair style
+which specifies an REBOMoS potential file with parameters for Mo and S.
+These are mapped to LAMMPS atom types by specifying N additional
+arguments after the filename in the pair_coeff command, where N is the
+number of LAMMPS atom types:
+
+* filename
+* :math:`N` element names = mapping of REBOMoS elements to atom types
+
+See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
+to specify the path for the potential file.
+
+As an example, if your LAMMPS simulation has three atom types and you want
+the first two to be Mo, and the third to be S, you would use the following
+pair_coeff command:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * MoS.rebomos Mo Mo S
+
+The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The first two Mo arguments map LAMMPS atom types 1 and 2 to the Mo
+element in the REBOMoS file.  The final S argument maps LAMMPS atom type
+3 to the S element in the REBOMoS file.  If a mapping value is specified
+as NULL, the mapping is not performed.  This can be used when a
+*rebomos* potential is used as part of the *hybrid* pair style.  The
+NULL values are placeholders for atom types that will be used with other
+potentials.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+mix, shift, table, and tail options.
+
+This pair style does not write their information to :doc:`binary restart
+files <restart>`, since it is stored in potential files.  Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+This pair styles can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+Restrictions
+""""""""""""
+
+This pair style is part of the MANYBODY package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+These pair potentials require the :doc:`newton <newton>` setting to be
+"on" for pair interactions.
+
+The MoS.rebomos potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal :doc:`units <units>`.  You can use
+the *rebomos* pair style with any LAMMPS units setting, but you would
+need to create your own REBOMoS potential file with coefficients listed
+in the appropriate units.
+
+The pair style provided here **only** supports potential files parameterized
+for the elements molybdenum and sulfur (designated with "Mo" and "S" in the
+*pair_coeff* command.  Using potential files for other elements will trigger
+an error.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair style rebo <pair_airebo>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Stewart:
+
+**(Steward)**  Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
+
+.. _Stuart2:
+
+**(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486, (2000).
+
+.. _Liang:
+
+**(Liang)**  Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)

doc/src/pair_style.rst

@@ -333,6 +333,7 @@ accelerated styles exist.
 * :doc:`rann <pair_rann>` -
 * :doc:`reaxff <pair_reaxff>` - ReaxFF potential
 * :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
+* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
 * :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions

doc/src/processors.rst

@@ -25,6 +25,8 @@ Syntax
            *numa* params = none
            *custom* params = infile
              infile = file containing grid layout
+       *numa_nodes* arg = Nn
+             Nn = number of numa domains per node
        *map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
           cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
           cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
@@ -159,24 +161,28 @@ surface-to-volume ratio of each processor's subdomain.
 
 The *numa* style operates similar to the *twolevel* keyword except
 that it auto-detects which cores are running on which nodes.
-Currently, it does this in only 2 levels, but it may be extended in
+It will also subdivide the cores into numa domains. Currently, the
-the future to account for socket topology and other non-uniform memory
+number of numa domains is not autodetected and must be specified using
-access (NUMA) costs.  It also uses a different algorithm than the
+the *numa_nodes* keyword; otherwise, the default value is used. The
-*twolevel* keyword for doing the two-level factorization of the
+*numa* style uses a different algorithm than the *twolevel* keyword for
-simulation box into a 3d processor grid to minimize off-node
+doing the two-level factorization of the simulation box into a 3d
-communication, and it does its own MPI-based mapping of nodes and
+processor grid to minimize off-node communication and communication
+across numa domains. It does its own MPI-based mapping of nodes and
 cores to the regular 3d grid.  Thus it may produce a different layout
 of the processors than the *twolevel* options.
 
 The *numa* style will give an error if the number of MPI processes is
 not divisible by the number of cores used per node, or any of the Px
-or Py of Pz values is greater than 1.
+or Py or Pz values is greater than 1.
 
 .. note::
 
    Unlike the *twolevel* style, the *numa* style does not require
-   any particular ordering of MPI ranks i norder to work correctly.  This
+   any particular ordering of MPI ranks in order to work correctly. This
    is because it auto-detects which processes are running on which nodes.
+   However, it assumes that the lowest ranks are in the first numa
+   domain, and so forth. MPI rank orderings that do not preserve this
+   property might result in more intranode communication between CPUs.
 
 The *custom* style uses the file *infile* to define both the 3d
 factorization and the mapping of processors to the grid.
@@ -207,6 +213,14 @@ any order, but no processor ID should appear more than once.
 
 ----------
 
+The *numa_nodes* keyword is used to specifiy the number of numa domains
+per node. It is currently only used by the *numa* style for two-level
+factorization to reduce the amount of MPI communications between CPUs.
+A good setting for this will typically be equal to the number of CPU
+sockets per node.
+
+----------
+
 The *map* keyword affects how the P processor IDs (from 0 to P-1) are
 mapped to the 3d grid of processors.  It is only used by the
 *onelevel* and *twolevel* grid settings.
@@ -356,5 +370,5 @@ Related commands
 Default
 """""""
 
-The option defaults are Px Py Pz = \* \* \*, grid = onelevel, and map =
+The option defaults are Px Py Pz = \* \* \*, grid = onelevel, map =
-cart.
+cart, and numa_nodes = 2.

doc/src/variable.rst

@@ -706,7 +706,7 @@ library.  Ceil() is the smallest integer not less than its argument.
 Floor() if the largest integer not greater than its argument.  Round()
 is the nearest integer to its argument.
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 The ternary(x,y,z) function is the equivalent of the ternary operator
 (? and :) in C or C++.  It takes 3 arguments.  The first argument is a
@@ -1155,7 +1155,7 @@ variable by using the :doc:`compute property/atom
 Custom atom properties
 ----------------------
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Custom atom properties refer to per-atom integer and floating point
 vectors or arrays that have been added via the :doc:`fix property/atom

doc/utils/sphinx-config/false_positives.txt

@@ -125,6 +125,7 @@ antisymmetry
 anton
 Antonelli
 api
+apolar
 Apoorva
 Appl
 Appshaw
@@ -799,6 +800,7 @@ dlabel
 dlambda
 DLAMMPS
 dll
+dlm
 dlopen
 dm
 dmax
@@ -1016,6 +1018,7 @@ Ercolessi
 Erdmann
 erf
 erfc
+erforce
 Erhart
 erorate
 erose
@@ -1767,6 +1770,7 @@ Kolafa
 Kollman
 kolmogorov
 Kolmogorov
+Kolotinskii
 Kondor
 konglt
 Koning
@@ -2236,8 +2240,10 @@ Mohd
 Mohles
 mol
 Mol
+molatom
 molfile
 Molfile
+molindex
 MolPairStyle
 moltemplate
 momb
@@ -2261,6 +2267,7 @@ morris
 Morriss
 morse
 Morteza
+MoS
 Mosayebi
 Moseler
 Moskalev
@@ -2570,6 +2577,7 @@ ns
 Ns
 Nsample
 Nskip
+nspecial
 Nspecies
 nsq
 Nstart
@@ -2768,6 +2776,7 @@ PEigenDense
 Peng
 peptide
 peratom
+Perf
 Pergamon
 pergrid
 peri
@@ -3064,6 +3073,7 @@ reaxff
 ReaxFF
 REAXFF
 rebo
+rebomos
 recurse
 recursing
 Ree
@@ -3591,6 +3601,7 @@ tesselation
 tesselations
 Tetot
 tex
+textrm
 tfac
 tfmc
 tfMC
@@ -3791,6 +3802,7 @@ unimodal
 uninstall
 unitarg
 unitless
+unittest
 Universite
 unix
 unmaintained
@@ -3877,7 +3889,10 @@ Verlet
 versa
 Verstraelen
 ves
+vf
 vflag
+vflow
+vfrac
 vhi
 vibrational
 Vij

examples/ASPHERE/dimer/in.dimer

@@ -1,104 +1,104 @@
 # SRD diffusion demo - dimer particles
 
-units		lj
+units           lj
-atom_style	sphere
+atom_style      sphere
-atom_modify	map array first big
+atom_modify     map array first big
-dimension	2
+dimension       2
 
 # read in clusters of rigid bodies
 
-fix             molprop all property/atom mol
+fix             molprop all property/atom mol ghost yes
-read_data	data.dimer fix molprop NULL Molecules
+read_data       data.dimer fix molprop NULL Molecules
+
+set             type 1 mass 1.0
+group           big type 1
+velocity        big create 1.44 87287 loop geom
 
-set		type 1 mass 1.0
-group		big type 1
-velocity	big create 1.44 87287 loop geom
-	
 # equilibrate big particles
 
-pair_style	soft 1.12
+pair_style      soft 1.12
-pair_coeff	1 1 0.0 
+pair_coeff      1 1 0.0 
-pair_coeff	2 2 0.0 0.0
+pair_coeff      2 2 0.0 0.0
-pair_coeff	1 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
 
 variable        prefactor equal ramp(0,60)
 fix             soft all adapt 1 pair soft a * * v_prefactor
 
-fix		1 big rigid molecule
+fix             1 big rigid molecule
-fix		2 all enforce2d
+fix             2 all enforce2d
 
-#dump		1 all atom 10 dump.dimer.equil
+#dump           1 all atom 10 dump.dimer.equil
 
-thermo		100
+thermo          100
-run		1000
+run             1000
 
-#undump		1
+#undump         1
 unfix           soft
-unfix		1
+unfix           1
-unfix		2
+unfix           2
 
 # add small particles as hi density lattice
 
-region		plane block INF INF INF INF -0.001 0.001 units box
+region          plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 85.0
+lattice         sq 85.0
-create_atoms	2 region plane
+create_atoms    2 region plane
 
-set		type 2 mass 0.1
+set             type 2 mass 0.1
-group		small type 2
+group           small type 2
-velocity	small create 1.0 593849 loop geom
+velocity        small create 1.0 593849 loop geom
 
 # delete overlaps
 # must set 1-2 cutoff to non-zero value
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
+pair_coeff      1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff      2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.5
+pair_coeff      1 2 0.0 1.0 0.5
 
-delete_atoms	overlap 0.5 small big
+delete_atoms    overlap 0.5 small big
 
 # SRD run
 
-reset_timestep	0
+reset_timestep  0
 
-neighbor	0.3 multi
+neighbor        0.3 multi
-neigh_modify	delay 0 every 1 check yes
+neigh_modify    delay 0 every 1 check yes
 
-comm_modify	mode multi group big vel yes
+comm_modify     mode multi group big vel yes
-neigh_modify	include big
+neigh_modify    include big
 
 # no pairwise interactions with small particles
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
+pair_coeff      1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff      2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
 
 # use fix SRD to push small particles out from inside big ones
 # if comment out, big particles won't see SRD particles
 
-timestep	0.001
+timestep        0.001
 
-fix		1 big rigid molecule
+fix             1 big rigid molecule
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
-		  search 0.2 collision slip inside ignore overlap yes
+                  search 0.2 collision slip inside ignore overlap yes
-fix		3 all enforce2d
+fix             3 all enforce2d
 
 # diagnostics
 
-compute		tbig big temp/sphere
+compute         tbig big temp/sphere
-variable	pebig equal pe*atoms/count(big)
+variable        pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp f_2[8] etotal v_pebig v_ebig press &
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press &
-		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
+                f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
-		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+                f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
 
-thermo_modify	temp tbig
+thermo_modify   temp tbig
-thermo		1000
+thermo          1000
 
-#dump		1 all atom 1000 dump.dimer
+#dump           1 all atom 1000 dump.dimer
 
-#dump		1 all image 1000 image.*.jpg type type zoom 1.6
+#dump           1 all image 1000 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
 
-run		100000
+run             10000

examples/ASPHERE/dimer/in.dimer.mp

@@ -1,105 +1,105 @@
 # SRD viscosity demo - dimer particles
 
-units		lj
+units           lj
-atom_style	sphere
+atom_style      sphere
-atom_modify	map array first big
+atom_modify     map array first big
-dimension	2
+dimension       2
 
 # read in clusters of rigid bodies
 
-fix             molprop all property/atom mol
+fix             molprop all property/atom mol ghost yes
-read_data	data.dimer fix molprop NULL Molecules
+read_data       data.dimer fix molprop NULL Molecules
 
-set		type 1 mass 1.0
+set             type 1 mass 1.0
-group		big type 1
+group           big type 1
-velocity	big create 1.44 87287 loop geom
+velocity        big create 1.44 87287 loop geom
 
 # equilibrate big particles
 
-pair_style	soft 1.12
+pair_style      soft 1.12
-pair_coeff	1 1 0.0 
+pair_coeff      1 1 0.0 
-pair_coeff	2 2 0.0 0.0
+pair_coeff      2 2 0.0 0.0
-pair_coeff	1 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
 
 variable        prefactor equal ramp(0,60)
 fix             soft all adapt 1 pair soft a * * v_prefactor
 
-fix		1 big rigid molecule
+fix             1 big rigid molecule
-fix		2 all enforce2d
+fix             2 all enforce2d
 
-#dump		1 all atom 10 dump.dimer.equil
+#dump           1 all atom 10 dump.dimer.equil
 
-thermo		100
+thermo          100
-run		1000
+run             1000
 
-#undump		1
+#undump         1
 unfix           soft
-unfix		1
+unfix           1
-unfix		2
+unfix           2
 
 # add small particles as hi density lattice
 
-region		plane block INF INF INF INF -0.001 0.001 units box
+region          plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 85.0
+lattice         sq 85.0
-create_atoms	2 region plane
+create_atoms    2 region plane
 
-set		type 2 mass 0.1
+set             type 2 mass 0.1
-group		small type 2
+group           small type 2
-velocity	small create 1.0 593849 loop geom
+velocity        small create 1.0 593849 loop geom
 
 # delete overlaps
 # must set 1-2 cutoff to non-zero value
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
+pair_coeff      1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff      2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.5
+pair_coeff      1 2 0.0 1.0 0.5
 
-delete_atoms	overlap 0.5 small big
+delete_atoms    overlap 0.5 small big
 
 # SRD run
 
-reset_timestep	0
+reset_timestep  0
 
-neighbor	0.3 multi
+neighbor        0.3 multi
-neigh_modify	delay 0 every 1 check yes
+neigh_modify    delay 0 every 1 check yes
 
-comm_modify	mode multi group big vel yes
+comm_modify     mode multi group big vel yes
-neigh_modify	include big
+neigh_modify    include big
 
 # no pairwise interactions with small particles
 
-pair_style	lj/cut 2.5
+pair_style      lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
+pair_coeff      1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff      2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
 
 # use fix SRD to push small particles out from inside big ones
 # if comment out, big particles won't see SRD particles
 
-timestep	0.001
+timestep        0.001
 
-fix		1 big rigid molecule
+fix             1 big rigid molecule
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
-		  search 0.2 collision slip inside ignore overlap yes
+                  search 0.2 collision slip inside ignore overlap yes
-fix		3 small viscosity 10 x y 50
+fix             3 small viscosity 10 x y 50
-fix		4 all enforce2d
+fix             4 all enforce2d
 
 # diagnostics
 
-compute		tbig big temp/sphere
+compute         tbig big temp/sphere
-variable	pebig equal pe*atoms/count(big)
+variable        pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp f_2[8] etotal v_pebig v_ebig press &
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press &
-		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
+                f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
-		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+                f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
 
-thermo_modify	temp tbig
+thermo_modify   temp tbig
-thermo		1000
+thermo          1000
 
-#dump		1 all atom 500 dump.dimer.mp
+#dump           1 all atom 500 dump.dimer.mp
 
-#dump		1 all image 500 image.*.jpg type type zoom 1.6
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
 
-run		50000
+run             25000

examples/ASPHERE/dimer/log.1Feb14.dimer.g++.8

@@ -1,286 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD diffusion demo - dimer particles
-
-units		lj
-atom_style	sphere
-atom_modify	map array first big
-dimension	2
-
-# read in clusters of rigid bodies
-
-fix             molprop all property/atom mol
-read_data	data.dimer fix molprop NULL Molecules
-  orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  200 atoms
-
-set		type 1 mass 1.0
-  200 settings made for mass
-group		big type 1
-200 atoms in group big
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles
-
-pair_style	soft 1.12
-pair_coeff	1 1 0.0
-pair_coeff	2 2 0.0 0.0
-pair_coeff	1 2 0.0 0.0
-
-variable        prefactor equal ramp(0,60)
-fix             soft all adapt 1 pair soft a * * v_prefactor
-
-fix		1 big rigid molecule
-100 rigid bodies with 200 atoms
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.dimer.equil
-
-thermo		100
-run		1000
-Memory usage per processor = 3.1029 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0    3.4028231            0            0   0.83369167  -0.55065517 
-     100    9.5167872     2.392105            0    4.7237178    2.8319556 
-     200    13.564465    3.0352634            0    6.3585572    3.6388732 
-     300    13.133051    4.3835112            0    7.6011086     4.060051 
-     400    14.584346    5.5141254            0    9.0872901    4.4231056 
-     500    15.331515    6.6554832            0    10.411704     4.847642 
-     600    16.953755    7.4794317            0    11.633102    5.2020696 
-     700    16.503256    8.8572339            0    12.900532    5.6694613 
-     800    17.006131     9.877343            0    14.043845    5.5483363 
-     900    17.305927    11.081594            0    15.321546    6.2908201 
-    1000    18.122491    12.126462            0    16.566472    5.7536055 
-Loop time of 0.185949 on 8 procs for 1000 steps with 200 atoms
-
-Pair  time (%) = 0.00187448 (1.00806)
-Neigh time (%) = 0.000561714 (0.30208)
-Comm  time (%) = 0.0652371 (35.0833)
-Outpt time (%) = 0.00209856 (1.12857)
-Other time (%) = 0.116177 (62.4779)
-
-Nlocal:    25 ave 30 max 20 min
-Histogram: 1 0 1 1 0 0 3 1 0 1
-Nghost:    28.375 ave 36 max 22 min
-Histogram: 1 0 1 2 1 0 2 0 0 1
-Neighs:    33.125 ave 45 max 22 min
-Histogram: 1 0 2 1 0 1 1 0 1 1
-
-Total # of neighbors = 265
-Ave neighs/atom = 1.325
-Neighbor list builds = 99
-Dangerous builds = 96
-
-#undump		1
-unfix           soft
-unfix		1
-unfix		2
-
-# add small particles as hi density lattice
-
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 85.0
-Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
-create_atoms	2 region plane
-Created 29929 atoms
-
-set		type 2 mass 0.1
-  29929 settings made for mass
-group		small type 2
-29929 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.5
-
-delete_atoms	overlap 0.5 small big
-Deleted 12759 atoms, new total = 17370
-
-# SRD run
-
-reset_timestep	0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.0
-
-# use fix SRD to push small particles out from inside big ones
-# if comment out, big particles won't see SRD particles
-
-timestep	0.001
-
-fix		1 big rigid molecule
-100 rigid bodies with 200 atoms
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 		  search 0.2 collision slip inside ignore overlap yes
-fix		3 all enforce2d
-
-# diagnostics
-
-compute		tbig big temp/sphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp f_2[8] etotal v_pebig v_ebig press 		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
-
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-thermo		1000
-
-#dump		1 all atom 1000 dump.dimer
-
-#dump		1 all image 1000 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
-
-run		100000
-SRD info:
-  SRD/big particles = 17170 200
-  big particle diameter max/min = 1 1
-  SRD temperature & lamda = 1 0.0632456
-  SRD max distance & max velocity = 0.252982 12.6491
-  SRD grid counts: 75 75 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
-  SRD per actual grid cell = 5.5499
-  SRD viscosity = 0.235551
-  big/SRD mass density ratio = 0.142367
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.20347 7.72323
-  ave/max big velocity = 2.64047 6.60911
-Memory usage per processor = 7.0395 Mbytes
-Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] 
-       0    6.9744766            0   0.30175295    21.011259    26.207244    2.7219331            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000    1.1941672         3369   0.24718395    20.578272    21.467926    9.8944086        13658           56           56            2          664        40320         5625         3369    1.1358997            0            4            0 
-    2000    1.3247909         3390   0.24717547     20.48022    21.467189    6.5341926        13389           48           48            3         1988        40320         5625         3390    1.1814916            0          144            0 
-    3000     1.386904         3355   0.24769415    20.478993    21.512237    6.1207029        13507           45           45            0         2871        40320         5625         3355    1.1657697            0          144            0 
-    4000    1.1567347         3376   0.24573733     20.48052    21.342287    3.5540965        13475           46           46            0         3731        40320         5625         3376    1.1485984            0          144            0 
-    5000    1.2565155         3376   0.24620928    20.447172    21.383276    2.5808161        13267           55           55            0         4559        40320         5625         3376    1.1778096            0          144            0 
-    6000    1.1489985         3375   0.24520477    20.440031    21.296035    7.8204262        13362           59           59            0         5354        40320         5625         3375    1.1530517            0          144            0 
-    7000    1.1608248         3399   0.24587989    20.489854    21.354669    7.9622779        13333           59           59            2         6254        40320         5625         3399    1.1809325            0          144            0 
-    8000    1.1749441         3374   0.24700359    20.576929    21.452262    6.7498405        13495           64           64            0         7134        40320         5625         3374    1.1445035            0          144            0 
-    9000    1.1285085         3405   0.24536183    20.468936    21.309675    5.8959937        13333           60           60            0         8008        40320         5625         3405     1.162836            0          144            0 
-   10000    1.1462675         3425   0.24564758    20.480523    21.334492    7.0047543        13487           45           45            0         8967        40320         5625         3425    1.1881074            0          144            0 
-   11000    1.2854766         3388     0.246088    20.415062    21.372742    7.8508136        13491           60           60            1         9833        40320         5625         3388    1.1698514            0          144            0 
-   12000    1.2926536         3360   0.24602616    20.404345    21.367372    7.9286141        13142           64           64            1        11029        40320         5625         3360    1.1658039            0          161            0 
-   13000    1.2289767         3412   0.24595657     20.44574    21.361328    2.2809592        13162           56           56            1        12018        40320         5625         3412    1.1665531            0          161            0 
-   14000    1.3518235         3380   0.24629055    20.383226    21.390334    8.0062608        13310           59           59            7        13146        40320         5625         3380    1.1733296            0          161            0 
-   15000    1.2971143         3355   0.24671134     20.46053     21.42688    9.7871945        12967           60           60            3        14084        40320         5625         3355    1.1703643            0          161            0 
-   16000    1.4160948         3384    0.2478594    20.471598    21.526589    7.3141215        13123           56           56            1        14929        40320         5625         3384    1.1666782            0          161            0 
-   17000    1.3172038         3391     0.247377    20.503375    21.484692    6.1541908        12957           54           54            0        15778        40320         5625         3391    1.1639931            0          161            0 
-   18000   0.98748293         3369    0.2443499    20.486114    21.221789    4.0981146        13355           50           50            1        17031        40320         5625         3369    1.2083414            0          192            0 
-   19000    1.4619261         3367   0.24867817    20.508564    21.597699     11.68547        13519           58           58            0        18334        40320         5625         3367    1.1667505            0          192            0 
-   20000      1.44087         3391   0.24747923    20.420123    21.493571    4.0409936        13594           67           67            0        19303        40320         5625         3391    1.1869387            0          192            0 
-   21000    1.1155365         3377   0.24474418    20.424957    21.256032    8.4985692        13423           52           52            0        20245        40320         5625         3377    1.1726608            0          192            0 
-   22000    1.2045785         3382   0.24466159    20.351448    21.248859    7.0518674        13271           62           62            0        21128        40320         5625         3382    1.1658557            0          192            0 
-   23000    1.2634616         3378   0.24571326    20.398918    21.340197    6.8382109        13246           61           61            1        22067        40320         5625         3378     1.170196            0          192            0 
-   24000     1.365723         3375   0.24749053    20.477089    21.494552    5.9584152        13017           46           46            1        23017        40320         5625         3375    1.1841192            0          192            0 
-   25000    1.1421045         3367   0.24497142      20.4249    21.275768    10.381661        13049           66           66            1        23907        40320         5625         3367    1.1856767            0          192            0 
-   26000    1.4008939         3340   0.24678624    20.389719    21.433385    7.3799658        12971           53           53            5        24850        40320         5625         3340    1.1713233            0          192            0 
-   27000    1.1835022         3379   0.24522732    20.416284    21.297993    7.2251705        12717           46           46            1        25723        40320         5625         3379    1.1798333            0          192            0 
-   28000    1.0496668         3398   0.24461816    20.463086    21.245087    6.5485338        13385           60           60            0        26990        40320         5625         3398    1.1765205            0          192            0 
-   29000    1.1779927         3453   0.24501083    20.401586     21.27919    4.8540048        13157           77           77            2        28023        40320         5625         3453    1.1741595            0          192            0 
-   30000    1.2277637         3375   0.24554215    20.410652    21.325336    10.087705        12939           72           72            1        28855        40320         5625         3375    1.1627414            0          192            0 
-   31000    1.1575066         3397   0.24504213    20.419566    21.281909    6.4849648        12977           66           66            0        29745        40320         5625         3397    1.1575018            0          192            0 
-   32000    1.1752733         3381    0.2451073     20.41199    21.287569    7.2784509        12971           48           48            0        30561        40320         5625         3381    1.1790395            0          192            0 
-   33000    1.1743895         3370   0.24485514    20.390748    21.265669     9.084299        12810           64           64            0        31342        40320         5625         3370    1.1429061            0          192            0 
-   34000    1.2975876         3377   0.24608262    20.405573    21.372276    10.624304        12610           60           60            1        32140        40320         5625         3377    1.1685718            0          192            0 
-   35000    1.7701252         3356    0.2497356    20.370794    21.689537     7.107766        12983           45           45            8        33862        40320         5625         3356    1.1720964            0          242            0 
-   36000    1.2711521         3393   0.24675748    20.483878    21.430887    8.7087273        13175           60           60            0        34920        40320         5625         3393    1.1796212            0          242            0 
-   37000    1.1140649         3373   0.24450996    20.405711     21.23569    8.0025138        12964           50           50            1        35770        40320         5625         3373    1.1772234            0          242            0 
-   38000    1.3128798         3379   0.24583813    20.372946    21.351041    5.0554655        12939           56           56            1        36679        40320         5625         3379    1.1702949            0          242            0 
-   39000    1.2093703         3365   0.24536578    20.409037    21.310018    5.6243735        12873           62           62            3        37511        40320         5625         3365    1.1751064            0          242            0 
-   40000    1.2095402         3365   0.24485106    20.364207    21.265315    3.9565189        12876           54           54            1        38503        40320         5625         3365    1.1637516            0          242            0 
-   41000    1.1146238         3350   0.24476111    20.427107    21.257502    6.5033046        12656           53           53            0        39313        40320         5625         3350    1.1553197            0          242            0 
-   42000    1.2302245         3370   0.24452048    20.320087    21.236604      10.7363        12676           52           52            1        40108        40320         5625         3370    1.1492163            0          242            0 
-   43000    1.2749689         3404   0.24511103    20.338041    21.287893      9.18604        13057           72           72            1        41014        40320         5625         3404    1.1572511            0          242            0 
-   44000    1.1989211         3385   0.24450633    20.342179    21.235375    7.6714085        13086           52           53            1        41840        40320         5625         3385    1.1530041            0          242            0 
-   45000    1.6465972         3370     0.249994    20.485264    21.711979    7.4908607        12894           58           58            7        43545        40320         5625         3370    1.1978571            0          361            0 
-   46000    1.3082316         3412   0.24665637    20.447473    21.422106    8.9900563        13136           53           53            4        44510        40320         5625         3412    1.1686573            0          361            0 
-   47000    1.2163258         3355   0.24493724    20.366636    21.272799    6.9309438        13020           56           56            0        45414        40320         5625         3355    1.1620943            0          361            0 
-   48000     1.349966         3362   0.24683156    20.431596    21.437321    8.8527164        13044           64           64            1        46260        40320         5625         3362    1.1683452            0          361            0 
-   49000    1.3903769         3347   0.24726403    20.439051    21.474881    5.9250552        13103           58           59            2        49229        40320         5625         3347    1.1924538            0          578            0 
-   50000    1.2737918         3349   0.24563843    20.384723    21.333698    7.2419874        12892           41           41            1        50225        40320         5625         3349    1.1803233            0          578            0 
-   51000    1.2229799         3355   0.24504936    20.371417    21.282537    8.5556146        12912           63           63            0        51096        40320         5625         3355    1.1333843            0          578            0 
-   52000    1.2326547         3386   0.24596384    20.443632    21.361959    6.1757404        12790           66           66            1        52114        40320         5625         3386    1.1685608            0          578            0 
-   53000    1.3695441         3389   0.24696147    20.428294    21.448604    8.7464732        12997           60           60            1        53115        40320         5625         3389    1.1631228            0          578            0 
-   54000    1.0711204         3400   0.24322154    20.325806     21.12379    8.7228921        13005           56           56            0        53913        40320         5625         3400    1.1250986            0          578            0 
-   55000    1.3412565         3360   0.24617922    20.381429    21.380665    6.9489559        12960           46           46            0        55249        40320         5625         3360     1.176467            0          578            0 
-   56000    1.3910761         3355    0.2467942    20.397725    21.434077    6.6762734        12966           65           65            2        56653        40320         5625         3355    1.1715559            0          578            0 
-   57000    1.1177307         3388   0.24424738    20.380176    21.212885    5.5073089        13153           62           62            1        57550        40320         5625         3388    1.1576307            0          578            0 
-   58000    1.3136279         3365   0.24661231    20.439627    21.418279    9.1390284        12799           52           52            1        58366        40320         5625         3365     1.159026            0          578            0 
-   59000    1.2667621         3374   0.24556104    20.383238    21.326976    3.4246418        13127           54           54            1        59170        40320         5625         3374    1.1461442            0          578            0 
-   60000    1.1903121         3326   0.24492127    20.384629    21.271412    6.9439977        13078           47           47            2        60105        40320         5625         3326    1.1665886            0          578            0 
-   61000     1.209313         3362    0.2455341    20.423699    21.324637    9.1212002        13225           61           61            4        61358        40320         5625         3362    1.1725894            0          578            0 
-   62000    1.1720074         3366   0.24476301    20.384522    21.257667    7.7592884        13187           53           54            2        62257        40320         5625         3366    1.1599665            0          578            0 
-   63000    1.2155508         3386   0.24486685    20.361101    21.266686    5.7864126        13090           42           42            0        63137        40320         5625         3386    1.1724234            0          578            0 
-   64000    1.1967326         3379    0.2451834    20.402613    21.294179    4.8815049        13033           48           48            4        64152        40320         5625         3379    1.1818756            0          578            0 
-   65000    1.1732378         3386   0.24500733    20.404824    21.278887    11.381026        12998           59           59            0        65071        40320         5625         3386    1.1625543            0          578            0 
-   66000    1.1960739         3385   0.24407516    20.306852    21.197927     12.17249        12994           61           61            0        65941        40320         5625         3385    1.1826516            0          578            0 
-   67000    1.3468331         3366   0.24657491     20.41164    21.415031    7.8115623        12894           62           62            1        66788        40320         5625         3366    1.1750424            0          578            0 
-   68000    1.0742924         3369   0.24347736    20.345661    21.146009    9.5240252        13065           68           68            2        67665        40320         5625         3369    1.1561575            0          578            0 
-   69000    1.1411254         3380    0.2450544    20.432836    21.282975    8.0392218        13134           49           49            1        68471        40320         5625         3380    1.1405485            0          578            0 
-   70000    1.1585312         3388   0.24435206    20.358871    21.221977    7.5303626        13113           59           59            0        69320        40320         5625         3388    1.1726416            0          578            0 
-   71000    1.3418857         3382   0.24598802    20.364355     21.36406    9.2840877        13265           68           68            0        70522        40320         5625         3382    1.1696767            0          578            0 
-   72000    1.1547857         3388   0.24328952     20.26938    21.129695    7.9643121        13270           50           50            1        71384        40320         5625         3388    1.1647353            0          578            0 
-   73000    1.1114283         3385   0.24397276     20.36102    21.189034    13.168935        13110           62           62            0        72335        40320         5625         3385    1.1625358            0          578            0 
-   74000    1.6120075         3370   0.25009739    20.520013    21.720959    12.065782        12902           51           51            9        73743        40320         5625         3370    1.1873738            0          578            0 
-   75000    1.3271087         3353   0.24600453    20.376798    21.365493    7.5902315        13076           51           51            1        74746        40320         5625         3353    1.1706259            0          578            0 
-   76000    1.1908626         3386    0.2451628    20.405197    21.292389    6.8084086        13124           58           58            1        75702        40320         5625         3386    1.1765809            0          578            0 
-   77000     1.042536         3391   0.24320847    20.345966    21.122655    6.4883579        12846           57           57            0        76930        40320         5625         3391    1.1769829            0          578            0 
-   78000    1.3791243         3355   0.24628683    20.362563    21.390011    9.2397346        12897           56           56           12        78068        40320         5625         3355    1.1905167            0          578            0 
-   79000    1.2058397         3391    0.2453076    20.406614    21.304965    9.7949819        13020           51           51            1        79065        40320         5625         3391    1.1777257            0          578            0 
-   80000    1.0634737         3383   0.24440921    20.434652     21.22694    7.5296946        12973           61           61            2        80029        40320         5625         3383    1.1648017            0          578            0 
-   81000    1.3768966         3373   0.24730623    20.452758    21.478546    7.1508584        13297           56           56            1        81172        40320         5625         3373    1.1740603            0          578            0 
-   82000    1.3348382         3375   0.24680945    20.440946      21.4354    9.3251946        12822           56           56            2        82447        40320         5625         3375    1.1573749            0          578            0 
-   83000    1.2042501         3393   0.24484972    20.368032    21.265198    7.5283729        12990           51           51            0        83344        40320         5625         3393    1.1833162            0          578            0 
-   84000    1.1985223         3405   0.24537841    20.418216    21.311115     7.848856        13189           60           60            0        84147        40320         5625         3405     1.173911            0          578            0 
-   85000    1.1811593         3391   0.24418657     20.32764    21.207604    8.3169438        13303           51           51            0        85022        40320         5625         3391    1.1586027            0          578            0 
-   86000    1.2595689         3385   0.24556774    20.389179    21.327558    8.3808674        12966           56           56            1        85962        40320         5625         3385    1.1617838            0          578            0 
-   87000    1.1419322         3356   0.24399697    20.340397    21.191137    6.8911116        13166           63           63            0        86753        40320         5625         3356    1.1729274            0          578            0 
-   88000     1.275219         3380   0.24586129    20.403015    21.353053     6.838563        12963           56           56            0        87729        40320         5625         3380    1.1511968            0          578            0 
-   89000    1.2794858         3366   0.24507826     20.33183    21.285047    9.3370019        12889           64           64            1        88575        40320         5625         3366    1.1660311            0          578            0 
-   90000    1.0549593         3402   0.24289618    20.309589    21.095533    4.9944605        13076           59           59            1        89560        40320         5625         3402    1.1744335            0          578            0 
-   91000     1.214812         3402   0.24442304    20.323106    21.228141    7.5681019        13229           44           44            1        90440        40320         5625         3402    1.1696689            0          578            0 
-   92000    1.2019714         3374   0.24469176    20.356011     21.25148    7.6728432        13331           64           64            2        91243        40320         5625         3374    1.1678246            0          578            0 
-   93000    1.0964004         3364   0.24364709    20.343931     21.16075    5.9650235        13086           55           55            0        92088        40320         5625         3364    1.1570838            0          578            0 
-   94000    1.1722133         3393   0.24332541    20.259513    21.132812    7.1743779        13206           66           66            0        92858        40320         5625         3393     1.154328            0          578            0 
-   95000    1.2413711         3373   0.24549874    20.396744    21.321566     8.131371        12967           61           61            1        93789        40320         5625         3373    1.1635681            0          578            0 
-   96000    1.1702409         3363   0.24528289    20.430989    21.302819    11.399295        12776           63           63            0        94571        40320         5625         3363    1.1367365            0          578            0 
-   97000    1.0696537         3368     0.242673    20.279258     21.07615     8.537175        13054           55           55            0        95403        40320         5625         3368    1.1648141            0          578            0 
-   98000    1.1635952         3369   0.24486659    20.399785    21.266664    8.6714443        12750           70           70            0        96296        40320         5625         3369    1.1686272            0          578            0 
-   99000    1.1286255         3397   0.24343772     20.30174    21.142566    6.7153212        12810           44           45            1        97021        40320         5625         3397     1.137818            0          578            0 
-  100000    1.2847818         3367   0.24509282    20.329149    21.286312    8.7486629        13260           64           64            0        97855        40320         5625         3367    1.1597138            0          578            0 
-Loop time of 20.8136 on 8 procs for 100000 steps with 17370 atoms
-
-Pair  time (%) = 0.322913 (1.55145)
-Neigh time (%) = 1.11753 (5.36921)
-Comm  time (%) = 1.72335 (8.27991)
-Outpt time (%) = 0.00594518 (0.0285638)
-Other time (%) = 17.6439 (84.7709)
-
-Nlocal:    2171.25 ave 2428 max 1747 min
-Histogram: 1 0 0 0 1 1 2 1 0 2
-Nghost:    61.25 ave 69 max 54 min
-Histogram: 1 1 0 1 1 1 0 2 0 1
-Neighs:    175.625 ave 225 max 132 min
-Histogram: 1 1 1 1 1 0 1 0 0 2
-
-Total # of neighbors = 1405
-Ave neighs/atom = 0.0808866
-Neighbor list builds = 5156
-Dangerous builds = 1
-
-Please see the log.cite file for references relevant to this simulation
-

examples/ASPHERE/dimer/log.1Feb14.dimer.mp.g++.8

@@ -1,237 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD viscosity demo - dimer particles
-
-units		lj
-atom_style	sphere
-atom_modify	map array first big
-dimension	2
-
-# read in clusters of rigid bodies
-
-fix             molprop all property/atom mol
-read_data	data.dimer fix molprop NULL Molecules
-  orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  200 atoms
-
-set		type 1 mass 1.0
-  200 settings made for mass
-group		big type 1
-200 atoms in group big
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles
-
-pair_style	soft 1.12
-pair_coeff	1 1 0.0
-pair_coeff	2 2 0.0 0.0
-pair_coeff	1 2 0.0 0.0
-
-variable        prefactor equal ramp(0,60)
-fix             soft all adapt 1 pair soft a * * v_prefactor
-
-fix		1 big rigid molecule
-100 rigid bodies with 200 atoms
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.dimer.equil
-
-thermo		100
-run		1000
-Memory usage per processor = 3.1029 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0    3.4028231            0            0   0.83369167  -0.55065517 
-     100    9.5167872     2.392105            0    4.7237178    2.8319556 
-     200    13.564465    3.0352634            0    6.3585572    3.6388732 
-     300    13.133051    4.3835112            0    7.6011086     4.060051 
-     400    14.584346    5.5141254            0    9.0872901    4.4231056 
-     500    15.331515    6.6554832            0    10.411704     4.847642 
-     600    16.953755    7.4794317            0    11.633102    5.2020696 
-     700    16.503256    8.8572339            0    12.900532    5.6694613 
-     800    17.006131     9.877343            0    14.043845    5.5483363 
-     900    17.305927    11.081594            0    15.321546    6.2908201 
-    1000    18.122491    12.126462            0    16.566472    5.7536055 
-Loop time of 0.0603173 on 8 procs for 1000 steps with 200 atoms
-
-Pair  time (%) = 0.00182396 (3.02395)
-Neigh time (%) = 0.000557959 (0.92504)
-Comm  time (%) = 0.0127766 (21.1823)
-Outpt time (%) = 0.000280827 (0.465583)
-Other time (%) = 0.0448779 (74.4031)
-
-Nlocal:    25 ave 30 max 20 min
-Histogram: 1 0 1 1 0 0 3 1 0 1
-Nghost:    28.375 ave 36 max 22 min
-Histogram: 1 0 1 2 1 0 2 0 0 1
-Neighs:    33.125 ave 45 max 22 min
-Histogram: 1 0 2 1 0 1 1 0 1 1
-
-Total # of neighbors = 265
-Ave neighs/atom = 1.325
-Neighbor list builds = 99
-Dangerous builds = 96
-
-#undump		1
-unfix           soft
-unfix		1
-unfix		2
-
-# add small particles as hi density lattice
-
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 85.0
-Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
-create_atoms	2 region plane
-Created 29929 atoms
-
-set		type 2 mass 0.1
-  29929 settings made for mass
-group		small type 2
-29929 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.5
-
-delete_atoms	overlap 0.5 small big
-Deleted 12759 atoms, new total = 17370
-
-# SRD run
-
-reset_timestep	0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.0
-
-# use fix SRD to push small particles out from inside big ones
-# if comment out, big particles won't see SRD particles
-
-timestep	0.001
-
-fix		1 big rigid molecule
-100 rigid bodies with 200 atoms
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 		  search 0.2 collision slip inside ignore overlap yes
-fix		3 small viscosity 10 x y 50
-fix		4 all enforce2d
-
-# diagnostics
-
-compute		tbig big temp/sphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp f_2[8] etotal v_pebig v_ebig press 		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
-
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-thermo		1000
-
-#dump		1 all atom 500 dump.dimer.mp
-
-#dump		1 all image 500 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
-
-run		50000
-SRD info:
-  SRD/big particles = 17170 200
-  big particle diameter max/min = 1 1
-  SRD temperature & lamda = 1 0.0632456
-  SRD max distance & max velocity = 0.252982 12.6491
-  SRD grid counts: 75 75 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
-  SRD per actual grid cell = 5.5499
-  SRD viscosity = 0.235551
-  big/SRD mass density ratio = 0.142367
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.20347 7.72323
-  ave/max big velocity = 2.64047 6.60911
-Memory usage per processor = 7.0395 Mbytes
-Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] 
-       0    6.9744766            0   0.30175295    21.011259    26.207244    2.7219331            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000     1.906187         3319   0.25279446     20.53509    21.955199    9.3471734        14560           77           77            9         6051        40320         5625         3319    1.2073941            0         1062            0 
-    2000    1.6009081         3420   0.25060769    20.572601    21.765278    12.835365        13521           63           63            1         7515        40320         5625         3420    1.1621445            0         1062            0 
-    3000    1.8288965         3342   0.25195284    20.519576    21.882104    7.1720562        13550           62           62            1         8561        40320         5625         3342    1.1411375            0         1062            0 
-    4000    1.8940522         3383   0.25185767    20.462769    21.873838    7.3011842        13210           55           55            0         9536        40320         5625         3383    1.1541274            0         1062            0 
-    5000    1.7848964         3377   0.25063675    20.438054    21.767801    5.7235852        13258           60           60            1        10628        40320         5625         3377    1.1401366            0         1062            0 
-    6000    2.0436442         3393    0.2528503    20.437534    21.960048    4.3266887        13369           65           65            1        11693        40320         5625         3393    1.1363335            0         1062            0 
-    7000    2.0248598         3377   0.25304247    20.468218    21.976738    9.1535003        13126           69           69            2        12819        40320         5625         3377    1.1556137            0         1062            0 
-    8000    1.9627172         3397   0.25201977    20.425693    21.887917    7.9563872        13216           58           58            3        14113        40320         5625         3397     1.144738            0         1062            0 
-    9000    2.4805409         3385   0.25688024    20.462046    22.310049    6.0178529        13031           42           42            1        15329        40320         5625         3385    1.1667813            0         1062            0 
-   10000     2.534712         3377   0.25802283    20.520922    22.409283    5.8494568        12804           49           50            1        16835        40320         5625         3377    1.1559636            0         1062            0 
-   11000    2.4295377         3368   0.25671703    20.485869    22.295874    7.0797587        13097           56           56            2        18180        40320         5625         3368    1.1634145            0         1062            0 
-   12000    2.5699389         3377   0.25784825    20.479516     22.39412    10.440503        13263           63           63            5        19848        40320         5625         3377    1.1714081            0         1062            0 
-   13000    2.5416625         3359   0.25893582    20.595038    22.488576     6.823793        12926           57           57            1        21307        40320         5625         3359    1.1478982            0         1062            0 
-   14000    2.9400702         3353   0.26140738    20.512878    22.703231    10.592709        12848           67           67            0        22782        40320         5625         3353    1.1642018            0         1062            0 
-   15000    2.7315042         3364   0.26050572    20.589951    22.624922    7.6633608        12640           49           49            0        24273        40320         5625         3364    1.1532394            0         1062            0 
-   16000    2.7176527         3389   0.25840703       20.418    22.442651    8.0150175        13019           59           59            1        25970        40320         5625         3389    1.1555937            0         1062            0 
-   17000     2.883266         3355   0.26040537    20.468173    22.616206     6.053208        12916           54           54            1        27532        40320         5625         3355    1.1363169            0         1062            0 
-   18000    2.8072496         3369   0.26013039    20.500924    22.592325    5.7179969        12989           45           45            0        29011        40320         5625         3369    1.1341799            0         1062            0 
-   19000    2.8007066         3372    0.2602809     20.51887    22.605396    8.9063895        12817           59           59            1        30504        40320         5625         3372    1.1253001            0         1062            0 
-   20000    3.0147455         3352   0.26233709    20.537991    22.783977     10.01786        13099           63           63            2        32100        40320         5625         3352    1.1263738            0         1062            0 
-   21000    2.5502874         3354   0.25762968    20.475174    22.375138    7.4525361        12917           55           55            3        33904        40320         5625         3354    1.1432482            0         1062            0 
-   22000    2.5643661         3357   0.25754499     20.45733    22.367782    9.5567227        12893           58           58            0        35500        40320         5625         3357    1.1309581            0         1062            0 
-   23000    2.8451307         3387   0.26090715    20.540164    22.659786    7.8308779        12735           65           65            2        37080        40320         5625         3387    1.1666359            0         1062            0 
-   24000    2.6241046         3341   0.25916876    20.553849    22.508807    9.7905794        12815           54           54            1        38864        40320         5625         3341    1.1422596            0         1062            0 
-   25000    2.6054468         3374   0.25897446    20.550874    22.491932    9.4099539        13094           59           59            4        40505        40320         5625         3374    1.1887482            0         1062            0 
-   26000    3.1370949         3356   0.26301193     20.50545    22.842586     9.930938        12785           59           59            0        42126        40320         5625         3356    1.1539158            0         1062            0 
-   27000     2.757373         3361   0.26029623    20.552484    22.606727    7.4336931        12687           59           59            2        43728        40320         5625         3361    1.1408006            0         1062            0 
-   28000    2.9939441         3393   0.26250984    20.568491     22.79898     9.201853        12802           66           66            0        45174        40320         5625         3393    1.1429688            0         1062            0 
-   29000    3.1611971         3376   0.26252235    20.444974    22.800066    8.2146139        13042           48           48            0        46696        40320         5625         3376    1.1370708            0         1062            0 
-   30000    2.2624796         3374   0.25475303    20.439753    22.125301    9.3304907        13249           53           53            1        48164        40320         5625         3374    1.1062325            0         1062            0 
-   31000    2.6864602         3393    0.2607928    20.648442    22.649855    7.6108593        13028           58           58            0        49556        40320         5625         3393    1.1154125            0         1062            0 
-   32000    2.8404087         3377   0.26037369    20.497351    22.613455    6.9017135        13055           63           63            1        51004        40320         5625         3377    1.1320087            0         1062            0 
-   33000    2.8467378         3365   0.26095982    20.543541    22.664361     7.194747        13306           58           58            0        52481        40320         5625         3365    1.1312548            0         1062            0 
-   34000    3.0833296         3382   0.26259198    20.509033    22.806114      7.44833        12988           59           60            1        54049        40320         5625         3382    1.1447344            0         1062            0 
-   35000    3.1068536         3382   0.26441995    20.650266    22.964872    9.3804156        13139           54           54            0        55749        40320         5625         3382    1.1272861            0         1062            0 
-   36000    2.6998442         3369   0.25864735    20.452138    22.463522    6.3327985        13317           52           52            0        57348        40320         5625         3369    1.1312386            0         1062            0 
-   37000     2.600171         3376   0.25882039    20.541424    22.478551    9.3909788        12841           57           57            0        58880        40320         5625         3376    1.1319429            0         1062            0 
-   38000    2.3962821         3367   0.25728672    20.560122    22.345352    7.4364329        13039           66           66            0        60627        40320         5625         3367    1.1468141            0         1062            0 
-   39000    2.8548804         3422   0.26044489    20.492753    22.619638    6.0832552        13249           50           50            0        62327        40320         5625         3422    1.1442726            0         1062            0 
-   40000    2.7721124         3375   0.25927374    20.452701    22.517924    10.368128        13197           55           55            1        63903        40320         5625         3375     1.140807            0         1062            0 
-   41000    3.0463159         3378   0.26123216    20.418508    22.688013    10.179554        13030           64           64            0        65629        40320         5625         3378    1.1277894            0         1062            0 
-   42000    2.9625288         3388   0.26205988    20.552817    22.759901    8.8326646        12958           64           64            0        67242        40320         5625         3388     1.159201            0         1062            0 
-   43000    2.7524867         3347    0.2592403    20.464417     22.51502     10.30221        12815           65           65            2        68734        40320         5625         3347    1.1444123            0         1062            0 
-   44000    2.8779981         3354   0.26009923     20.44551    22.589618    12.127509        12743           67           67            3        70309        40320         5625         3354    1.1467915            0         1062            0 
-   45000    2.7833999         3365   0.25968205    20.479753    22.553386    8.6942365        12909           46           47            0        71846        40320         5625         3365    1.1480348            0         1062            0 
-   46000    2.6564678         3370   0.25935897    20.546258    22.525327    9.2618375        12923           61           61            1        73491        40320         5625         3370    1.1528284            0         1062            0 
-   47000     2.821625         3414   0.25999655     20.47859      22.5807    7.5359036        12861           55           55            2        75201        40320         5625         3414    1.1395745            0         1062            0 
-   48000    2.9301623         3351   0.26139433    20.519127    22.702098    9.5177842        13037           49           49            2        76819        40320         5625         3351    1.1472505            0         1062            0 
-   49000     2.528824         3390   0.25834586    20.553364    22.437338     8.953785        13127           49           49            0        78450        40320         5625         3390    1.1495903            0         1062            0 
-   50000    3.0054471         3375     0.261046    20.432787    22.671845    7.9749959        13089           56           56            2        80717        40320         5625         3375    1.1574724            0         1062            0 
-Loop time of 10.5055 on 8 procs for 50000 steps with 17370 atoms
-
-Pair  time (%) = 0.156617 (1.49081)
-Neigh time (%) = 0.556925 (5.30126)
-Comm  time (%) = 0.902042 (8.58637)
-Outpt time (%) = 0.00305247 (0.0290559)
-Other time (%) = 8.88688 (84.5925)
-
-Nlocal:    2171.25 ave 2567 max 1849 min
-Histogram: 2 0 0 1 1 2 1 0 0 1
-Nghost:    62.625 ave 71 max 57 min
-Histogram: 2 0 1 0 2 2 0 0 0 1
-Neighs:    168.25 ave 232 max 120 min
-Histogram: 1 0 1 2 2 1 0 0 0 1
-
-Total # of neighbors = 1346
-Ave neighs/atom = 0.0774899
-Neighbor list builds = 2599
-Dangerous builds = 17
-
-Please see the log.cite file for references relevant to this simulation
-

examples/ASPHERE/dimer/log.1Feb24.dimer.g++.1

@@ -0,0 +1,312 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD diffusion demo - dimer particles
+
+units           lj
+atom_style      sphere
+atom_modify     map array first big
+dimension       2
+
+# read in clusters of rigid bodies
+
+fix             molprop all property/atom mol ghost yes
+read_data       data.dimer fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  200 settings made for mass
+group           big type 1
+200 atoms in group big
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      soft 1.12
+pair_coeff      1 1 0.0
+pair_coeff      2 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
+
+variable        prefactor equal ramp(0,60)
+fix             soft all adapt 1 pair soft a * * v_prefactor
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.dimer.equil
+
+thermo          100
+run             1000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42
+  ghost atom cutoff = 1.42
+  binsize = 0.71, bins = 27 27 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   3.4028231      0              0              0.83369167    -0.55065517   
+       100   9.5167872      2.392105       0              4.7237178      2.8319556    
+       200   13.564465      3.0352634      0              6.3585572      3.6388732    
+       300   13.133051      4.3835112      0              7.6011086      4.060051     
+       400   14.576837      5.5141059      0              9.0854309      4.422762     
+       500   15.227825      6.6472106      0              10.378028      4.8598912    
+       600   16.93219       7.454865       0              11.603251      5.2908894    
+       700   16.573769      8.7323442      0              12.792918      5.3544684    
+       800   17.482599      9.7221047      0              14.005341      5.6200973    
+       900   18.548144      10.739353      0              15.283649      4.7817995    
+      1000   18.068079      12.058417      0              16.485096      6.5773091    
+Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0095507  | 0.0095507  | 0.0095507  |   0.0 | 18.69
+Neigh   | 0.0042239  | 0.0042239  | 0.0042239  |   0.0 |  8.26
+Comm    | 0.002203   | 0.002203   | 0.002203   |   0.0 |  4.31
+Output  | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 |   0.0 |  0.17
+Modify  | 0.03336    | 0.03336    | 0.03336    |   0.0 | 65.27
+Other   |            | 0.001685   |            |       |  3.30
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             64 ave          64 max          64 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            275 ave         275 max         275 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 275
+Ave neighs/atom = 1.375
+Neighbor list builds = 193
+Dangerous builds = 0
+
+#undump         1
+unfix           soft
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 85.0
+Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
+create_atoms    2 region plane
+Created 29929 atoms
+  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  create_atoms CPU = 0.007 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  29929 settings made for mass
+group           small type 2
+29929 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.5
+
+delete_atoms    overlap 0.5 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 14 14 1
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 12776 atoms, new total = 17353
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
+fix             3 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/sphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all atom 1000 dump.dimer
+
+#dump           1 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 17153 200
+  big particle diameter max/min = 1 1
+  SRD temperature & lamda = 1 0.063245553
+  SRD max distance & max velocity = 0.25298221 12.649111
+  SRD grid counts: 75 75 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
+  SRD per actual grid cell = 5.544404
+  SRD viscosity = 0.23553122
+  big/SRD mass density ratio = 0.14250828
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.191188 7.6900178
+  ave/max big velocity = 2.6813242 7.1846104
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 18.683304, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
+   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555741      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.2285566      3375           0.24673495     20.492683      21.407958      5.237464       13477          54             54             1              652            16900          5625           3375           1.1653557      0              15             0            
+      2000   1.3561011      3395           0.24763991     20.476182      21.486477      9.2878509      13435          67             67             0              1504           16900          5625           3395           1.1651182      0              15             0            
+      3000   1.2445369      3352           0.24713723     20.515681      21.442861      8.0289529      13186          62             63             2              2379           16900          5625           3352           1.1746721      0              15             0            
+      4000   1.1058201      3389           0.24596239     20.51709       21.340926      10.003266      13466          66             66             0              3264           16900          5625           3389           1.1671415      0              15             0            
+      5000   1.0584198      3407           0.24539623     20.503281      21.291804      9.1119405      13254          64             64             0              4189           16900          5625           3407           1.1687685      0              15             0            
+      6000   1.3335611      3360           0.24737788     20.470239      21.463742      8.6885126      13281          62             62             1              5031           16900          5625           3360           1.1568996      0              15             0            
+      7000   1.1384759      3401           0.24570869     20.47075       21.318914      9.1801119      13059          47             47             1              5878           16900          5625           3401           1.182474       0              15             0            
+      8000   1.2982334      3397           0.24667224     20.435333      21.402517      6.5904007      13405          56             56             0              6729           16900          5625           3397           1.169017       0              24             0            
+      9000   1.0456752      3381           0.24504517     20.482316      21.261344      10.497413      13205          81             81             2              7706           16900          5625           3381           1.1694675      0              24             0            
+     10000   1.2222547      3394           0.24653264     20.479825      21.390405      8.7495888      13296          68             68             1              8581           16900          5625           3394           1.1613437      0              24             0            
+Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms
+
+Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 Matom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14497    | 0.14497    | 0.14497    |   0.0 |  2.02
+Neigh   | 0.031835   | 0.031835   | 0.031835   |   0.0 |  0.44
+Comm    | 0.094201   | 0.094201   | 0.094201   |   0.0 |  1.31
+Output  | 0.00082765 | 0.00082765 | 0.00082765 |   0.0 |  0.01
+Modify  | 6.8507     | 6.8507     | 6.8507     |   0.0 | 95.35
+Other   |            | 0.06259    |            |       |  0.87
+
+Nlocal:          17353 ave       17353 max       17353 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            128 ave         128 max         128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1334 ave        1334 max        1334 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1334
+Ave neighs/atom = 0.076874316
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/ASPHERE/dimer/log.1Feb24.dimer.g++.4

@@ -0,0 +1,312 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD diffusion demo - dimer particles
+
+units           lj
+atom_style      sphere
+atom_modify     map array first big
+dimension       2
+
+# read in clusters of rigid bodies
+
+fix             molprop all property/atom mol ghost yes
+read_data       data.dimer fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  200 settings made for mass
+group           big type 1
+200 atoms in group big
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      soft 1.12
+pair_coeff      1 1 0.0
+pair_coeff      2 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
+
+variable        prefactor equal ramp(0,60)
+fix             soft all adapt 1 pair soft a * * v_prefactor
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.dimer.equil
+
+thermo          100
+run             1000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42
+  ghost atom cutoff = 1.42
+  binsize = 0.71, bins = 27 27 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   3.4028231      0              0              0.83369167    -0.55065517   
+       100   9.5167872      2.392105       0              4.7237178      2.8319556    
+       200   13.564465      3.0352634      0              6.3585572      3.6388732    
+       300   13.133051      4.3835112      0              7.6011086      4.060051     
+       400   14.576837      5.5141059      0              9.0854309      4.422762     
+       500   15.227825      6.6472106      0              10.378028      4.8598912    
+       600   16.93219       7.454865       0              11.603251      5.2908894    
+       700   16.573769      8.7323442      0              12.792918      5.3544684    
+       800   17.482599      9.7221047      0              14.005341      5.6200973    
+       900   18.548144      10.739353      0              15.283649      4.7817995    
+      1000   18.068079      12.058417      0              16.485096      6.5773093    
+Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms
+
+Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s
+98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0022758  | 0.0023448  | 0.002442   |   0.1 |  5.52
+Neigh   | 0.0011082  | 0.0011236  | 0.0011582  |   0.1 |  2.64
+Comm    | 0.0099484  | 0.010092   | 0.010247   |   0.1 | 23.76
+Output  | 9.551e-05  | 0.00010604 | 0.00013381 |   0.0 |  0.25
+Modify  | 0.026025   | 0.026222   | 0.026405   |   0.1 | 61.73
+Other   |            | 0.00259    |            |       |  6.10
+
+Nlocal:             50 ave          55 max          47 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:          33.75 ave          38 max          32 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:          68.75 ave          77 max          64 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 275
+Ave neighs/atom = 1.375
+Neighbor list builds = 193
+Dangerous builds = 0
+
+#undump         1
+unfix           soft
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 85.0
+Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
+create_atoms    2 region plane
+Created 29929 atoms
+  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  create_atoms CPU = 0.002 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  29929 settings made for mass
+group           small type 2
+29929 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.5
+
+delete_atoms    overlap 0.5 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 14 14 1
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 12776 atoms, new total = 17353
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
+fix             3 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/sphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all atom 1000 dump.dimer
+
+#dump           1 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 17153 200
+  big particle diameter max/min = 1 1
+  SRD temperature & lamda = 1 0.063245553
+  SRD max distance & max velocity = 0.25298221 12.649111
+  SRD grid counts: 75 75 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
+  SRD per actual grid cell = 5.544404
+  SRD viscosity = 0.23553122
+  big/SRD mass density ratio = 0.14250828
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.191188 7.6900178
+  ave/max big velocity = 2.6813242 7.1846103
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 18.683304, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
+   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555746      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.1648085      3389           0.24643931     20.514525      21.382307      5.5927686      13390          59             59             0              1015           28224          5625           3389           1.1513276      0              111            0            
+      2000   1.1870311      3385           0.24701637     20.548037      21.432375      5.9269821      13271          57             57             2              1878           28224          5625           3385           1.1619099      0              111            0            
+      3000   1.1362839      3365           0.24577276     20.477942      21.324474      5.1621045      13244          59             60             1              2778           28224          5625           3365           1.1807679      0              111            0            
+      4000   1.3023748      3390           0.24679509     20.442907      21.413176      5.6127077      13413          65             65             1              3705           28224          5625           3390           1.1726946      0              111            0            
+      5000   1.195496       3387           0.2458055      20.43667       21.327314      6.1843476      13248          51             51             1              4638           28224          5625           3387           1.1730279      0              111            0            
+      6000   1.2389419      3387           0.24546635     20.374876      21.297888      5.5909826      13184          54             54             1              5494           28224          5625           3387           1.1859134      0              111            0            
+      7000   1.2068912      3378           0.24564722     20.414447      21.313581      8.5604547      13188          57             57             1              6428           28224          5625           3378           1.1499181      0              111            0            
+      8000   1.1014154      3374           0.24514746     20.449665      21.270219      7.3483529      13179          63             63             0              7591           28224          5625           3374           1.1769322      0              121            0            
+      9000   1.356464       3388           0.24749513     20.463349      21.473915      7.6809833      13138          50             50             2              8485           28224          5625           3388           1.1448659      0              121            0            
+     10000   1.1632951      3402           0.24560819     20.44354       21.310195      9.5738599      13323          64             67             0              9304           28224          5625           3402           1.1550136      0              121            0            
+Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms
+
+Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.037524   | 0.039903   | 0.042215   |   1.1 |  1.61
+Neigh   | 0.01053    | 0.010805   | 0.011068   |   0.2 |  0.44
+Comm    | 0.14536    | 0.14822    | 0.15102    |   0.6 |  6.00
+Output  | 0.00051847 | 0.00054674 | 0.0006272  |   0.0 |  0.02
+Modify  | 2.2276     | 2.2334     | 2.2381     |   0.3 | 90.35
+Other   |            | 0.03895    |            |       |  1.58
+
+Nlocal:        4338.25 ave        4488 max        4277 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost:          76.75 ave          85 max          69 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:         331.25 ave         355 max         306 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 1325
+Ave neighs/atom = 0.076355673
+Neighbor list builds = 507
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.1

@@ -0,0 +1,328 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD viscosity demo - dimer particles
+
+units           lj
+atom_style      sphere
+atom_modify     map array first big
+dimension       2
+
+# read in clusters of rigid bodies
+
+fix             molprop all property/atom mol ghost yes
+read_data       data.dimer fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  200 settings made for mass
+group           big type 1
+200 atoms in group big
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      soft 1.12
+pair_coeff      1 1 0.0
+pair_coeff      2 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
+
+variable        prefactor equal ramp(0,60)
+fix             soft all adapt 1 pair soft a * * v_prefactor
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.dimer.equil
+
+thermo          100
+run             1000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42
+  ghost atom cutoff = 1.42
+  binsize = 0.71, bins = 27 27 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   3.4028231      0              0              0.83369167    -0.55065517   
+       100   9.5167872      2.392105       0              4.7237178      2.8319556    
+       200   13.564465      3.0352634      0              6.3585572      3.6388732    
+       300   13.133051      4.3835112      0              7.6011086      4.060051     
+       400   14.576837      5.5141059      0              9.0854309      4.422762     
+       500   15.227825      6.6472106      0              10.378028      4.8598912    
+       600   16.93219       7.454865       0              11.603251      5.2908894    
+       700   16.573769      8.7323442      0              12.792918      5.3544684    
+       800   17.482599      9.7221047      0              14.005341      5.6200973    
+       900   18.548144      10.739353      0              15.283649      4.7817995    
+      1000   18.068079      12.058417      0              16.485096      6.5773091    
+Loop time of 0.0502552 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 8596132.389 tau/day, 19898.455 timesteps/s, 3.980 Matom-step/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0095071  | 0.0095071  | 0.0095071  |   0.0 | 18.92
+Neigh   | 0.0042809  | 0.0042809  | 0.0042809  |   0.0 |  8.52
+Comm    | 0.0022049  | 0.0022049  | 0.0022049  |   0.0 |  4.39
+Output  | 0.0001259  | 0.0001259  | 0.0001259  |   0.0 |  0.25
+Modify  | 0.032467   | 0.032467   | 0.032467   |   0.0 | 64.60
+Other   |            | 0.00167    |            |       |  3.32
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             64 ave          64 max          64 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            275 ave         275 max         275 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 275
+Ave neighs/atom = 1.375
+Neighbor list builds = 193
+Dangerous builds = 0
+
+#undump         1
+unfix           soft
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 85.0
+Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
+create_atoms    2 region plane
+Created 29929 atoms
+  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  create_atoms CPU = 0.006 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  29929 settings made for mass
+group           small type 2
+29929 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.5
+
+delete_atoms    overlap 0.5 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 14 14 1
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 12776 atoms, new total = 17353
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
+fix             3 small viscosity 10 x y 50
+fix             4 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/sphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all atom 500 dump.dimer.mp
+
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
+
+run             25000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 17153 200
+  big particle diameter max/min = 1 1
+  SRD temperature & lamda = 1 0.063245553
+  SRD max distance & max velocity = 0.25298221 12.649111
+  SRD grid counts: 75 75 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
+  SRD per actual grid cell = 5.544404
+  SRD viscosity = 0.23553122
+  big/SRD mass density ratio = 0.14250828
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.191188 7.6900178
+  ave/max big velocity = 2.6813242 7.1846104
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 18.683304, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
+   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555741      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.3421139      3394           0.24797209     20.515424      21.515299      5.9986227      13474          52             52             1              704            16900          5625           3394           1.1328453      0              14             0            
+      2000   1.3372296      3366           0.24694513     20.429958      21.426194      9.640193       13302          74             74             0              1516           16900          5625           3366           1.1634167      0              14             0            
+      3000   1.4022742      3360           0.24799552     20.472637      21.517331      5.9446731      13483          47             47             0              2989           16900          5625           3360           1.1774442      0              217            0            
+      4000   1.6325677      3376           0.25066282     20.532497      21.74876       6.9698781      13206          61             61             2              4198           16900          5625           3376           1.1749717      0              217            0            
+      5000   2.0992887      3391           0.25484065     20.547279      22.111249      10.648531      13414          62             69             1              6389           16900          5625           3391           1.1862903      0              412            0            
+      6000   1.7584548      3388           0.25126127     20.490636      21.800684      8.68036        13456          58             58             0              7672           16900          5625           3388           1.1553986      0              412            0            
+      7000   2.2384486      3343           0.25650382     20.58791       22.255554      12.008146      13187          59             59             0              8879           16900          5625           3343           1.1728994      0              412            0            
+      8000   2.4981644      3380           0.25734806     20.467672      22.328804      6.7156077      13383          51             51             0              10085          16900          5625           3380           1.156205       0              412            0            
+      9000   2.4321991      3384           0.25838085     20.606426      22.418415      9.9820399      12847          55             55             0              11445          16900          5625           3384           1.156145       0              412            0            
+     10000   2.2560205      3387           0.25541566     20.480404      22.161139      10.87418       13022          66             66             0              12863          16900          5625           3387           1.1559136      0              412            0            
+     11000   2.2321955      3378           0.25533735     20.491359      22.154345      8.510825       13175          70             70             1              14273          16900          5625           3378           1.1470284      0              412            0            
+     12000   2.2715125      3377           0.25469529     20.40636       22.098637      9.0604601      13146          68             68             0              15742          16900          5625           3377           1.171755       0              412            0            
+     13000   2.3766974      3364           0.25667348     20.499635      22.270275      10.766786      12829          60             60             1              17214          16900          5625           3364           1.130354       0              412            0            
+     14000   2.5659704      3347           0.25802994     20.47632       22.387967      8.2568074      13090          66             66             1              18767          16900          5625           3347           1.1609852      0              412            0            
+     15000   2.3235671      3400           0.25603152     20.483517      22.214574      5.4785711      13389          50             50             0              20173          16900          5625           3400           1.149754       0              412            0            
+     16000   2.6335413      3373           0.25956137     20.558854      22.520843      4.7121947      13027          58             58             1              21668          16900          5625           3373           1.1308267      0              412            0            
+     17000   2.5603168      3410           0.25744829     20.430065      22.337501      6.1898616      13218          51             51             1              23170          16900          5625           3410           1.1285699      0              412            0            
+     18000   2.7801428      3362           0.26002524     20.489884      22.56109       8.9919312      13002          57             57             3              24829          16900          5625           3362           1.1610153      0              412            0            
+     19000   2.7869738      3364           0.26033026     20.51126       22.587555      9.6539159      13085          46             46             0              26476          16900          5625           3364           1.1431913      0              412            0            
+     20000   2.678182       3383           0.2586317      20.444934      22.44018       7.3468277      12939          42             42             0              27992          16900          5625           3383           1.143534       0              412            0            
+     21000   2.8094503      3375           0.26088069     20.542272      22.635313      8.2257869      13449          52             52             0              29570          16900          5625           3375           1.1375499      0              412            0            
+     22000   3.2220363      3377           0.26464914     20.561866      22.962283      6.6329375      13178          65             65             6              31203          16900          5625           3377           1.1683184      0              412            0            
+     23000   3.2268368      3339           0.26414495     20.514543      22.918536      4.6879815      12589          51             51             0              32929          16900          5625           3339           1.1378613      0              412            0            
+     24000   2.6062461      3380           0.25967238     20.588821      22.530474      10.036449      12745          53             54             0              34460          16900          5625           3380           1.1396017      0              412            0            
+     25000   3.2519674      3373           0.26376614     20.462953      22.885669      7.7592712      12856          52             52             1              36172          16900          5625           3373           1.1858891      0              412            0            
+Loop time of 20.7208 on 1 procs for 25000 steps with 17353 atoms
+
+Performance: 104243.242 tau/day, 1206.519 timesteps/s, 20.937 Matom-step/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.39343    | 0.39343    | 0.39343    |   0.0 |  1.90
+Neigh   | 0.09039    | 0.09039    | 0.09039    |   0.0 |  0.44
+Comm    | 0.26483    | 0.26483    | 0.26483    |   0.0 |  1.28
+Output  | 0.0021023  | 0.0021023  | 0.0021023  |   0.0 |  0.01
+Modify  | 19.785     | 19.785     | 19.785     |   0.0 | 95.49
+Other   |            | 0.1847     |            |       |  0.89
+
+Nlocal:          17353 ave       17353 max       17353 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            146 ave         146 max         146 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1326 ave        1326 max        1326 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1326
+Ave neighs/atom = 0.0764133
+Neighbor list builds = 1290
+Dangerous builds = 0
+Total wall time: 0:00:21

examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.4

@@ -0,0 +1,328 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD viscosity demo - dimer particles
+
+units           lj
+atom_style      sphere
+atom_modify     map array first big
+dimension       2
+
+# read in clusters of rigid bodies
+
+fix             molprop all property/atom mol ghost yes
+read_data       data.dimer fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  200 settings made for mass
+group           big type 1
+200 atoms in group big
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      soft 1.12
+pair_coeff      1 1 0.0
+pair_coeff      2 2 0.0 0.0
+pair_coeff      1 2 0.0 0.0
+
+variable        prefactor equal ramp(0,60)
+fix             soft all adapt 1 pair soft a * * v_prefactor
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.dimer.equil
+
+thermo          100
+run             1000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42
+  ghost atom cutoff = 1.42
+  binsize = 0.71, bins = 27 27 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   3.4028231      0              0              0.83369167    -0.55065517   
+       100   9.5167872      2.392105       0              4.7237178      2.8319556    
+       200   13.564465      3.0352634      0              6.3585572      3.6388732    
+       300   13.133051      4.3835112      0              7.6011086      4.060051     
+       400   14.576837      5.5141059      0              9.0854309      4.422762     
+       500   15.227825      6.6472106      0              10.378028      4.8598912    
+       600   16.93219       7.454865       0              11.603251      5.2908894    
+       700   16.573769      8.7323442      0              12.792918      5.3544684    
+       800   17.482599      9.7221047      0              14.005341      5.6200973    
+       900   18.548144      10.739353      0              15.283649      4.7817995    
+      1000   18.068079      12.058417      0              16.485096      6.5773093    
+Loop time of 0.0421376 on 4 procs for 1000 steps with 200 atoms
+
+Performance: 10252121.014 tau/day, 23731.762 timesteps/s, 4.746 Matom-step/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.002222   | 0.0023177  | 0.0024199  |   0.2 |  5.50
+Neigh   | 0.0010943  | 0.0011428  | 0.001174   |   0.1 |  2.71
+Comm    | 0.0097533  | 0.009878   | 0.010001   |   0.1 | 23.44
+Output  | 9.4323e-05 | 0.0001028  | 0.00012783 |   0.0 |  0.24
+Modify  | 0.02557    | 0.026225   | 0.026638   |   0.3 | 62.24
+Other   |            | 0.002471   |            |       |  5.86
+
+Nlocal:             50 ave          55 max          47 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:          33.75 ave          38 max          32 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:          68.75 ave          77 max          64 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 275
+Ave neighs/atom = 1.375
+Neighbor list builds = 193
+Dangerous builds = 0
+
+#undump         1
+unfix           soft
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 85.0
+Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
+create_atoms    2 region plane
+Created 29929 atoms
+  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
+  create_atoms CPU = 0.002 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  29929 settings made for mass
+group           small type 2
+29929 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.5
+
+delete_atoms    overlap 0.5 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 14 14 1
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 12776 atoms, new total = 17353
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 200 atoms
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
+fix             3 small viscosity 10 x y 50
+fix             4 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/sphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all atom 500 dump.dimer.mp
+
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
+
+run             25000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 17153 200
+  big particle diameter max/min = 1 1
+  SRD temperature & lamda = 1 0.063245553
+  SRD max distance & max velocity = 0.25298221 12.649111
+  SRD grid counts: 75 75 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
+  SRD per actual grid cell = 5.544404
+  SRD viscosity = 0.23553122
+  big/SRD mass density ratio = 0.14250828
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.191188 7.6900178
+  ave/max big velocity = 2.6813242 7.1846103
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 18.683304, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
+   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555746      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.2739082      3360           0.24704957     20.486195      21.435256      3.6693454      13497          46             46             2              816            28224          5625           3360           1.1564821      0              54             0            
+      2000   1.3843858      3380           0.24759985     20.451634      21.483001      5.2299666      13363          70             70             0              1671           28224          5625           3380           1.170199       0              54             0            
+      3000   1.3942166      3373           0.24823326     20.499268      21.537959      7.7943821      13214          59             59             2              2600           28224          5625           3373           1.1539593      0              54             0            
+      4000   1.6387342      3366           0.24966206     20.441071      21.661928      4.3859226      13280          49             49             2              3568           28224          5625           3366           1.176006       0              54             0            
+      5000   1.8677297      3388           0.25278915     20.541792      21.933251      5.9053775      13238          68             68             2              4553           28224          5625           3388           1.1728833      0              54             0            
+      6000   1.8884914      3372           0.25216944     20.472555      21.879481      7.5864922      13142          62             62             1              5645           28224          5625           3372           1.1733967      0              54             0            
+      7000   2.0575519      3387           0.25374609     20.483403      22.016279      6.9842803      13101          41             41             0              6805           28224          5625           3387           1.1503024      0              54             0            
+      8000   1.9800593      3373           0.252975       20.474232      21.949376      8.3493951      13176          63             64             1              8166           28224          5625           3373           1.1621339      0              67             0            
+      9000   2.2288114      3403           0.25526729     20.487802      22.148267      6.7676677      12866          61             61             1              9360           28224          5625           3403           1.1446891      0              67             0            
+     10000   2.4854456      3339           0.25713924     20.45903       22.310687      9.3781009      12692          65             65             1              10680          28224          5625           3339           1.1417733      0              67             0            
+     11000   2.5850677      3335           0.25820147     20.476975      22.402851      9.9421534      12954          70             70             2              11964          28224          5625           3335           1.1497985      0              67             0            
+     12000   2.5087529      3358           0.25746572     20.469992      22.339013      9.9566718      12959          58             58             0              13462          28224          5625           3358           1.1365643      0              98             0            
+     13000   2.5480838      3371           0.25761214     20.453395      22.351717      8.6628089      13142          54             54             3              14985          28224          5625           3371           1.1510123      0              98             0            
+     14000   2.946645       3384           0.26176446     20.516743      22.711994      8.5668798      12579          53             53             0              16336          28224          5625           3384           1.1546089      0              98             0            
+     15000   4.025292       3338           0.27188564     20.591315      23.590157      9.8722859      12824          50             50             15             18115          28224          5625           3338           1.164518       0              122            0            
+     16000   2.2744945      3376           0.25598709     20.516221      22.21072       9.1890215      13020          52             52             0              19689          28224          5625           3376           1.1439385      0              122            0            
+     17000   2.3857021      3353           0.25662954     20.489114      22.266462      10.24809       12776          51             51             0              21158          28224          5625           3353           1.1435041      0              122            0            
+     18000   2.9678193      3330           0.26255063     20.56918       22.780206      8.6799225      12810          49             49             2              23066          28224          5625           3330           1.1567395      0              133            0            
+     19000   2.7464034      3368           0.2613984      20.634162      22.680232      9.5420188      12746          47             47             3              24675          28224          5625           3368           1.1426658      0              133            0            
+     20000   2.8228684      3367           0.26137363     20.575046      22.678083      8.0865322      12886          51             51             0              26119          28224          5625           3367           1.1484398      0              133            0            
+     21000   2.8903033      3389           0.26173565     20.556218      22.709494      11.038294      13152          41             41             1              27685          28224          5625           3389           1.1398936      0              133            0            
+     22000   2.8279828      3331           0.26058759     20.503035      22.609882      8.3647396      12895          57             57             1              29333          28224          5625           3331           1.1551348      0              133            0            
+     23000   2.9320035      3376           0.26178899     20.529779      22.714121      7.1841698      13077          54             54             1              30908          28224          5625           3376           1.1453809      0              133            0            
+     24000   2.8508425      3366           0.26104722     20.525884      22.649762      10.680819      13019          58             58             4              32831          28224          5625           3366           1.1391852      0              154            0            
+     25000   2.7878254      3333           0.25961        20.448132      22.525062      11.149479      12960          57             57             1              34494          28224          5625           3333           1.172964       0              154            0            
+Loop time of 6.5335 on 4 procs for 25000 steps with 17353 atoms
+
+Performance: 330603.792 tau/day, 3826.433 timesteps/s, 66.400 Matom-step/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.097519   | 0.10401    | 0.10744    |   1.2 |  1.59
+Neigh   | 0.027038   | 0.028067   | 0.028678   |   0.4 |  0.43
+Comm    | 0.39354    | 0.39697    | 0.40246    |   0.6 |  6.08
+Output  | 0.0013442  | 0.0014045  | 0.0015827  |   0.3 |  0.02
+Modify  | 5.8667     | 5.8905     | 5.9143     |   0.8 | 90.16
+Other   |            | 0.1126     |            |       |  1.72
+
+Nlocal:        4338.25 ave        4476 max        4199 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:           78.5 ave          83 max          75 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs:            328 ave         352 max         309 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+
+Total # of neighbors = 1312
+Ave neighs/atom = 0.075606523
+Neighbor list builds = 1274
+Dangerous builds = 0
+Total wall time: 0:00:06

examples/ASPHERE/ellipsoid/in.ellipsoid

@@ -116,4 +116,4 @@ thermo          1000
 #dump           2 all image 1000 image.*.jpg type type zoom 1.6
 #dump_modify    2 pad 6 adiam 1 1 adiam 2 0.2
 
-run             100000
+run             10000

examples/ASPHERE/ellipsoid/in.ellipsoid.mp

@@ -117,4 +117,4 @@ thermo          1000
 #dump           1 all image 500 image.*.jpg type type zoom 1.6
 #dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
 
-run             50000
+run             10000

examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.g++.8

@@ -1,190 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD diffusion demo - ellipsoids
-
-units		lj
-atom_style	ellipsoid
-atom_modify	first big
-dimension	2
-
-# create big ellipsoidal particles
-
-lattice		sq 0.14
-Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
-region		box block 0 10 0 10 -0.5 0.5
-create_box	2 box
-Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
-  4 by 2 by 1 MPI processor grid
-create_atoms	1 region box
-Created 100 atoms
-
-set		type 1 mass 1.0
-  100 settings made for mass
-set		type 1 shape 3.0 1.0 1.0
-  100 settings made for shape
-group		big type 1
-100 atoms in group big
-set		group big quat/random 29898
-  100 settings made for quat/random
-
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles
-
-pair_style      gayberne 1.0 3.0 1.0 4.0
-pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
-pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
-pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big nve/asphere
-fix		2 all enforce2d
-
-compute		rot big temp/asphere
-
-#dump		1 all custom 10 dump.ellipsoid.equil id type x y z #		  quatw quati quatj quatk
-
-thermo_style	custom step temp c_rot epair etotal press
-thermo		100
-
-run		1000
-Memory usage per processor = 3.31932 Mbytes
-Step Temp rot E_pair TotEng Press 
-       0         1.44   0.95677852    2.7038078    4.1294078    10.518912 
-     100    2.5524145     2.801098  -0.37027046    2.1566199   0.84703874 
-     200    2.6266386    2.7938164  -0.35322565    2.2471465     1.004886 
-     300    2.9987557    2.9499545  -0.58917376    2.3795944   0.73081788 
-     400    2.8557446    2.8208128  -0.39904801    2.4281391   0.91808964 
-     500    2.4399047    2.8255746  -0.40056447    2.0149412    1.0538908 
-     600     2.854258    2.9166789  -0.53424483    2.2914706    0.8117508 
-     700    2.9593679    2.8231211  -0.40051714    2.5292571    1.1630889 
-     800    2.7632971    2.9060854  -0.52075339    2.2149107   0.77106814 
-     900    2.9905601    2.8869672  -0.49099457    2.4696599   0.69616725 
-    1000    2.8470146    2.9004954  -0.51281252     2.305732   0.68820531 
-Loop time of 0.0485955 on 8 procs for 1000 steps with 100 atoms
-
-Pair  time (%) = 0.0201517 (41.4682)
-Neigh time (%) = 0.000492364 (1.01319)
-Comm  time (%) = 0.0191883 (39.4858)
-Outpt time (%) = 0.000273198 (0.562188)
-Other time (%) = 0.00848994 (17.4706)
-
-Nlocal:    12.5 ave 16 max 8 min
-Histogram: 1 1 0 0 0 3 0 0 1 2
-Nghost:    34.125 ave 42 max 28 min
-Histogram: 1 0 2 2 0 1 0 1 0 1
-Neighs:    46.125 ave 65 max 20 min
-Histogram: 1 0 1 0 1 2 0 0 1 2
-
-Total # of neighbors = 369
-Ave neighs/atom = 3.69
-Neighbor list builds = 174
-Dangerous builds = 0
-
-#undump		1
-unfix		1
-unfix		2
-
-# add small particles as hi density lattice
-
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 120.0
-Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
-create_atoms	2 region plane
-Created 85849 atoms
-
-set		type 2 mass 0.01
-  85849 settings made for mass
-group		small type 2
-85849 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 2.0
-
-neigh_modify	one 10000
-
-delete_atoms	overlap 1.6 small big
-Deleted 71060 atoms, new total = 14889
-
-# SRD run
-
-reset_timestep	0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style      gayberne 1.0 3.0 1.0 4.0
-pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
-pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
-pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
-
-# use fix SRD to push small particles out from inside big ones
-# if comment out, big particles won't see SRD particles
-
-timestep	0.0005
-
-fix		1 big nve/asphere
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 		  collision noslip search 0.2 inside ignore exact no bounce 50
-fix		3 all enforce2d
-
-# diagnostics
-
-compute		tbig big temp/asphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
-
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-thermo		1000
-
-#dump		1 all custom 1000 dump.ellipsoid id type x y z #                quatw quati quatj quatk
-
-#dump		1 all image 1000 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
-
-run		100000
-SRD info:
-  SRD/big particles = 14789 100
-  big particle diameter max/min = 3 1
-  SRD temperature & lamda = 1 0.1
-  SRD max distance & max velocity = 0.4 40
-  SRD grid counts: 107 107 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
-  SRD per actual grid cell = 1.92757
-  SRD viscosity = 0.688101
-  big/SRD mass density ratio = 1.37367
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 13.3093 24.3359
-  ave/max big velocity = 2.08028 5.05671
-Memory usage per processor = 10.9077 Mbytes
-Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] 
-       0    2.9004954    2.9004954            0  0.025582146  -0.51281252    3.8089257   0.89865242            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000    3.3106106    3.3106106    1.0635866  0.029956176  -0.47263474    4.4601751    1.8111247        14000           35          160            0       224946        98040        11449         4182    1.0635866         1047           50            0 
-    2000    2.2814487    2.2814487    1.2237286  0.017972589  -0.72341981    2.6759388    1.3454977        15318           47          276            0       528340        98040        11449         4136    1.2237286         2383           50            0 
-    3000    4.2476485    4.2476485    1.2992612  0.038526442  -0.59279435    5.7362019    1.6896403        16506           63          410            0       830594        98040        11449         4172    1.2992612         3834           50            0 
-    4000    2.4798681    2.4798681    1.3453264  0.022837826  -0.29467953    3.4003239    2.0765724        17201           51          403            0      1185573        98040        11449         4233    1.3453264         5456           50            0 
-    5000    3.0852629    3.0852629    1.3915904   0.02760985  -0.48621111    4.1108305    1.2676357        17540           61          591            0      1594856        98040        11449         4306    1.3915904         7419           50            0 
-    6000    6.7201122    6.7201122    1.3649223  0.064627842  -0.39052776    9.6224394    2.5524159        17997           59          564            0      2010250        98040        11449         4213    1.3649223         9280           50            0 
-    7000     2.720343     2.720343    1.3909677  0.024282471  -0.43789405    3.6154171    1.5288376        17922           64          342            0      2392388        98040        11449         4228    1.3909677        10947           50            0 
-    8000    1.9181626    1.9181626    1.3514483  0.014305579  -0.72810462    2.1299577   0.89423917        18188           42          260            0      2751626        98040        11449         4236    1.3514483        12556           50            0 
-    9000    2.9090186    2.9090186    1.3688847   0.02558926  -0.52445278    3.8099849    1.1756318        18536           63          440            0      3112508        98040        11449         4227    1.3688847        14164           50            0 
-   10000    1.9647403    1.9647403    1.3979066  0.015375037  -0.63827389    2.2891892   0.65597214        18817           60          466            0      3501352        98040        11449         4257    1.3979066        16016           50            0 
-   11000    1.9989051    1.9989051    1.3872043  0.016191243  -0.56765443    2.4107142   0.80582429        18756           58          767            0      3856028        98040        11449         4254    1.3872043        17611           50            0 
-   12000    1.7538755    1.7538755    1.4594883  0.013930543  -0.53915598    2.0741185    1.0563875        18602           58          335            0      4248666        98040        11449         4251    1.4594883        19350           50            0 
-   13000    13.730871    13.730871    1.4864545   0.13447802  -0.43656501    20.022433    3.6701166        19144           74          681            0      4708523        98040        11449         4104    1.4864545        21589           50            0 
-   14000    5.1078782    5.1078782    1.3637807  0.049721182  -0.20775172    7.4029868     2.559935        18494           65          713            0      5139143        98040        11449         4167    1.3637807        23555           50            0 
-   15000    2.5843962    2.5843962    1.3450247  0.022294373  -0.53134114    3.3194092    1.1069147        18489           52          260            0      5489252        98040        11449         4262    1.3450247        25209           50            0 
-ERROR: Lost atoms: original 14889 current 14819 (../thermo.cpp:392)

examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.mp.g++.8

@@ -1,247 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD viscosity demo - ellipsoids
-
-units		lj
-atom_style	ellipsoid
-atom_modify	first big
-dimension	2
-
-# create big ellipsoidal particles
-
-lattice		sq 0.14
-Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
-region		box block 0 10 0 10 -0.5 0.5
-create_box	2 box
-Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
-  4 by 2 by 1 MPI processor grid
-create_atoms	1 region box
-Created 100 atoms
-
-set		type 1 mass 1.0
-  100 settings made for mass
-set		type 1 shape 3.0 1.0 1.0
-  100 settings made for shape
-group		big type 1
-100 atoms in group big
-set		group big quat/random 29898
-  100 settings made for quat/random
-
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles
-
-pair_style      gayberne 1.0 3.0 1.0 4.0
-pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
-pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
-pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big nve/asphere
-fix		2 all enforce2d
-
-compute		rot big temp/asphere
-
-#dump		1 all custom 10 dump.ellipsoid.equil id type x y z #		  quatw quati quatj quatk
-
-thermo_style	custom step temp c_rot epair etotal press
-thermo		100
-
-run		1000
-Memory usage per processor = 3.31932 Mbytes
-Step Temp rot E_pair TotEng Press 
-       0         1.44   0.95677852    2.7038078    4.1294078    10.518912 
-     100    2.5524145     2.801098  -0.37027046    2.1566199   0.84703874 
-     200    2.6266386    2.7938164  -0.35322565    2.2471465     1.004886 
-     300    2.9987557    2.9499545  -0.58917376    2.3795944   0.73081788 
-     400    2.8557446    2.8208128  -0.39904801    2.4281391   0.91808964 
-     500    2.4399047    2.8255746  -0.40056447    2.0149412    1.0538908 
-     600     2.854258    2.9166789  -0.53424483    2.2914706    0.8117508 
-     700    2.9593679    2.8231211  -0.40051714    2.5292571    1.1630889 
-     800    2.7632971    2.9060854  -0.52075339    2.2149107   0.77106814 
-     900    2.9905601    2.8869672  -0.49099457    2.4696599   0.69616725 
-    1000    2.8470146    2.9004954  -0.51281252     2.305732   0.68820531 
-Loop time of 0.0581853 on 8 procs for 1000 steps with 100 atoms
-
-Pair  time (%) = 0.0202803 (34.8546)
-Neigh time (%) = 0.000480682 (0.826122)
-Comm  time (%) = 0.0264942 (45.5342)
-Outpt time (%) = 0.000326395 (0.560958)
-Other time (%) = 0.0106037 (18.2241)
-
-Nlocal:    12.5 ave 16 max 8 min
-Histogram: 1 1 0 0 0 3 0 0 1 2
-Nghost:    34.125 ave 42 max 28 min
-Histogram: 1 0 2 2 0 1 0 1 0 1
-Neighs:    46.125 ave 65 max 20 min
-Histogram: 1 0 1 0 1 2 0 0 1 2
-
-Total # of neighbors = 369
-Ave neighs/atom = 3.69
-Neighbor list builds = 174
-Dangerous builds = 0
-
-#undump		1
-unfix		1
-unfix		2
-
-# add small particles as hi density lattice
-
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 120.0
-Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
-create_atoms	2 region plane
-Created 85849 atoms
-
-set		type 2 mass 0.01
-  85849 settings made for mass
-group		small type 2
-85849 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 2.0
-
-neigh_modify	one 10000
-
-delete_atoms	overlap 1.6 small big
-Deleted 71060 atoms, new total = 14889
-
-# SRD run
-
-reset_timestep	0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style      gayberne 1.0 3.0 1.0 4.0
-pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
-pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
-pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
-
-# use fix SRD to push small particles out from inside big ones
-# if comment out, big particles won't see SRD particles
-
-timestep	0.0005
-
-fix		1 big nve/asphere
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   collision noslip search 0.2 inside ignore exact no bounce 50
-fix		3 small viscosity 20 x y 50
-fix		4 all enforce2d
-
-# diagnostics
-
-compute		tbig big temp/asphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
-
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-thermo		1000
-
-#dump		1 all custom 500 dump.ellipsoid.mp id type x y z #                quatw quati quatj quatk
-
-#dump		1 all image 500 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
-
-run		50000
-SRD info:
-  SRD/big particles = 14789 100
-  big particle diameter max/min = 3 1
-  SRD temperature & lamda = 1 0.1
-  SRD max distance & max velocity = 0.4 40
-  SRD grid counts: 107 107 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
-  SRD per actual grid cell = 1.92757
-  SRD viscosity = 0.688101
-  big/SRD mass density ratio = 1.37367
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 13.3093 24.3359
-  ave/max big velocity = 2.08028 5.05671
-Memory usage per processor = 10.9077 Mbytes
-Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] 
-       0    2.9004954    2.9004954            0  0.025582146  -0.51281252    3.8089257   0.89865242            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000    3.1663129    3.1663129    1.0612788  0.028825811  -0.42593131     4.291875    1.8917479        14347           45          319            0       247730        98040        11449         4128    1.0612788         1160           50            0 
-    2000    2.3854865    2.3854865    1.2711805  0.019550917   -0.6434388     2.910936    1.4342405        15199           41          151            0       526468        98040        11449         4191    1.2711805         2321           50            0 
-    3000    2.6796789    2.6796789    1.2494843  0.023573743  -0.48282696    3.5098946    1.6090734        16441           52          230            0       827117        98040        11449         4203    1.2494843         3659           50            0 
-    4000    2.7945661    2.7945661    1.3021617  0.024256529   -0.5523488    3.6115547    1.2702377        16935           52          474            0      1127934        98040        11449         4215    1.3021617         4966           50            0 
-    5000    2.7061959    2.7061959     1.338483  0.023736966    -0.498035    3.5341969    1.2801942        17578           49          277            0      1435089        98040        11449         4261     1.338483         6351           50            0 
-    6000    3.2698703    3.2698703    1.3285507  0.029840303  -0.42918398    4.4429227    1.4528039        17882           63          228            0      1776449        98040        11449         4252    1.3285507         7935           50            0 
-    7000    3.9340641    3.9340641    1.3823898  0.035368008  -0.59581277    5.2659427    1.1321242        18069           49          462            0      2090062        98040        11449         4265    1.3823898         9343           50            0 
-    8000    3.6037728    3.6037728    1.4150583  0.032400676  -0.54548483    4.8241367    1.2091317        18275           56          369            0      2486575        98040        11449         4229    1.4150583        11121           50            0 
-    9000    105.15275    105.15275    1.3630934    1.0504642  -0.27397996    156.40361    23.278069        18139          107          732            0      2861341        98040        11449         4217    1.3630934        12781           50            0 
-   10000    3.5224307    3.5224307    1.3897056    0.0324883   -0.4112387     4.837183    1.6093705        19100           61          347            0      3248400        98040        11449         4204    1.3897056        14424           50            0 
-   11000    4.1949959    4.1949959     1.421272   0.03853305  -0.51335814    5.7371858    1.3586332        18670           52          590            0      3722041        98040        11449         4263     1.421272        16373           50            0 
-   12000    3.1692742    3.1692742    1.3999982  0.028463927  -0.48422456     4.237994    1.1713046        18787           61          323            0      4117517        98040        11449         4202    1.3999982        18125           50            0 
-   13000    3.5868757    3.5868757    1.3193021  0.032298734  -0.53548629    4.8089585    1.0664078        18572           67          224            0      4417636        98040        11449         4277    1.3193021        19546           50            0 
-   14000     3.708681     3.708681     1.317797  0.033355183  -0.55968141    4.9662533    1.3959088        18284           67          207            0      4675359        98040        11449         4253     1.317797        20631           50            0 
-   15000    3.7410393    3.7410393    1.4017441  0.033377852  -0.60452027    4.9696283    1.2506767        18385           51          189            0      4956150        98040        11449         4275    1.4017441        21763           50            0 
-   16000    5.3298522    5.3298522    1.3456075  0.049673767  -0.54555257    7.3959272     1.841432        18693           63          549            0      5301393        98040        11449         4196    1.3456075        23216           50            0 
-   17000    3.7425275    3.7425275     1.321554  0.036608704  -0.12569607    5.4506699    2.3767421        18377           68          526            0      5637038        98040        11449         4261     1.321554        24829           50            0 
-   18000    6.1904009    6.1904009    1.3905006   0.05857936  -0.50181651    8.7218809    1.7936734        18422           63          522            0      6049781        98040        11449         4280    1.3905006        26646           50            0 
-   19000    3.1770374    3.1770374    1.3694174  0.028096405  -0.55051202    4.1832737   0.98036773        18342           54          343            0      6383253        98040        11449         4239    1.3694174        28038           50            0 
-   20000    3.5793112    3.5793112    1.3160294  0.031413769  -0.65597761     4.677196    1.0713128        18739           60          272            0      6692090        98040        11449         4262    1.3160294        29389           50            0 
-   21000    3.2300481    3.2300481    1.3407923  0.027955254  -0.65051393    4.1622578   0.89783071        18582           55          456            0      6999361        98040        11449         4237    1.3407923        30653           50            0 
-   22000    3.5879886    3.5879886    1.3790201  0.031692391   -0.6274228    4.7186802   0.97752405        18768           63          552            0      7350833        98040        11449         4308    1.3790201        32120           50            0 
-   23000    3.5666316    3.5666316    1.4123826  0.031275136   -0.6577261     4.656555   0.99950405        18864           49          231            0      7741276        98040        11449         4265    1.4123826        33939           50            0 
-   24000    3.7306353    3.7306353    1.3854831  0.032426295   -0.7306956     4.827951   0.93575015        18488           63          552            0      8096740        98040        11449         4238    1.3854831        35503           50            0 
-   25000    4.2971901    4.2971901    1.4207289  0.038358698  -0.69158669    5.7112265    1.0308127        18922           58          430            0      8518804        98040        11449         4254    1.4207289        37429           50            0 
-   26000     9.514164     9.514164    1.4209186   0.09200552  -0.47740255    13.698702    2.4102159        18934           63          570            0      8931705        98040        11449         4233    1.4209186        39132           50            0 
-   27000    3.9153535    3.9153535    1.3814961  0.036650525  -0.37698007    5.4568967    1.4531475        19153           65          553            0      9277922        98040        11449         4299    1.3814961        40660           50            0 
-   28000    3.6560048    3.6560048    1.3520603  0.033100525  -0.51910991    4.9283372    1.3474705        19529           59          447            0      9642607        98040        11449         4278    1.3520603        42335           50            0 
-   29000    14.835118    14.835118    1.3981622   0.14535835   -0.4619207    21.642405    3.6917556        19265           52          102            0      9937354        98040        11449         4224    1.3981622        43664           50            0 
-   30000    5.3595251    5.3595251    1.3636194  0.050893845  -0.40810785    7.5775845    1.7023989        19065           43          131            0     10261222        98040        11449         4170    1.3636194        45193           50            0 
-   31000    5.1821698    5.1821698    1.3180039  0.049074014  -0.41480304      7.30663    1.6943582        19142           58          282            0     10584027        98040        11449         4228    1.3180039        46636           50            0 
-   32000    4.3056534    4.3056534    1.3508467  0.040670309  -0.36002116    6.0554024    1.7875405        19065           36          284            0     10933981        98040        11449         4286    1.3508467        48240           50            0 
-   33000    3.8277999    3.8277999    1.3770405  0.034411971  -0.57982354    5.1235984    1.1046562        18838           71          729            0     11329901        98040        11449         4257    1.3770405        50046           50            0 
-   34000    4.6562056    4.6562056    1.3938501  0.043777831  -0.41966518    6.5180812    1.3815841        18914           61          269            0     11758952        98040        11449         4221    1.3938501        51773           50            0 
-   35000    3.4251492    3.4251492    1.3813031  0.031876928  -0.35731644    4.7461558    1.4152845        18838           60          283            0     12159425        98040        11449         4238    1.3813031        53477           50            0 
-   36000    4.2565688    4.2565688    1.3474871  0.039214915   -0.5035788    5.8387088    1.1222014        18765           56          240            0     12568711        98040        11449         4249    1.3474871        55170           50            0 
-   37000    5.3745505    5.3745505    1.4215553  0.053606226  -0.02664916     7.981431    2.8011643        19103           58          504            0     12941065        98040        11449         4270    1.4215553        56743           50            0 
-   38000    4.0346121    4.0346121    1.4354472  0.036753623  -0.53932498     5.472247    1.1475792        18829           62          623            0     13351480        98040        11449         4226    1.4354472        58443           50            0 
-   39000    4.0471971    4.0471971     1.417888  0.037884509   -0.3896991    5.6406246    1.3824278        19047           70          579            0     13752101        98040        11449         4219     1.417888        60208           50            0 
-   40000    4.1611575    4.1611575    1.3712048  0.039505792  -0.31810741    5.8820173    1.6615204        18811           65          378            0     14143802        98040        11449         4313    1.3712048        61793           50            0 
-   41000     4.852673     4.852673    1.3719985  0.044831688   -0.5554927      6.67499    1.2744313        18899           53          414            0     14505662        98040        11449         4274    1.3719985        63358           50            0 
-   42000    4.8338875    4.8338875    1.3595624  0.045465888  -0.43307636    6.7694161    1.6297026        18708           46          360            0     14839866        98040        11449         4224    1.3595624        64895           50            0 
-   43000    5.0243115    5.0243115    1.4371431  0.047111836  -0.47174292    7.0144813    1.5899963        18704           55          291            0     15195383        98040        11449         4209    1.4371431        66440           50            0 
-   44000    7.2748224    7.2748224    1.3693754  0.069498669  -0.49182853    10.347657    1.9007074        18751           73          423            0     15572639        98040        11449         4253    1.3693754        68148           50            0 
-   45000    5.4888002    5.4888002    1.3501677  0.050885254  -0.60200685    7.5763055    1.2841374        18662           51          314            0     15972088        98040        11449         4227    1.3501677        69998           50            0 
-   46000    3.2144774    3.2144774    1.3342547  0.028194354  -0.59171403    4.1978573    0.9459541        18948           50          534            0     16308430        98040        11449         4253    1.3342547        71549           50            0 
-   47000    4.0640905    4.0640905    1.3473081  0.036715084  -0.58898597    5.4665088    1.2043249        19188           57          236            0     16670321        98040        11449         4239    1.3473081        73216           50            0 
-   48000    3.7843815    3.7843815    1.3413467  0.034360184  -0.52284075    5.1158877    1.1195984        19477           57          283            0     17000588        98040        11449         4307    1.3413467        74662           50            0 
-   49000    4.3042567    4.3042567     1.354248  0.039635615  -0.51199566    5.9013468     1.410884        19628           68          456            0     17319627        98040        11449         4277     1.354248        75983           50            0 
-   50000     4.015575     4.015575    1.3058373  0.036258162  -0.58472888    5.3984778   0.84500807        19257           63          416            0     17675269        98040        11449         4254    1.3058373        77468           50            0 
-Loop time of 11.9502 on 8 procs for 50000 steps with 14889 atoms
-
-Pair  time (%) = 1.09132 (9.13222)
-Neigh time (%) = 0.959464 (8.02883)
-Comm  time (%) = 1.19057 (9.96277)
-Outpt time (%) = 0.00310364 (0.0259714)
-Other time (%) = 8.70577 (72.8502)
-
-Nlocal:    1861.12 ave 1979 max 1606 min
-Histogram: 1 0 0 0 1 1 1 0 0 4
-Nghost:    35 ave 39 max 32 min
-Histogram: 1 0 2 0 3 1 0 0 0 1
-Neighs:    46 ave 61 max 31 min
-Histogram: 1 1 0 1 1 0 2 0 1 1
-
-Total # of neighbors = 368
-Ave neighs/atom = 0.0247162
-Neighbor list builds = 2624
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.1

@@ -0,0 +1,346 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD diffusion demo - ellipsoids
+
+units           lj
+atom_style      ellipsoid
+atom_modify     first big
+dimension       2
+
+# create big ellipsoidal particles
+
+lattice         sq 0.14
+Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
+region          box block 0 10 0 10 -0.5 0.5
+create_box      2 box
+Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.000 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+set             type 1 shape 3.0 1.0 1.0
+Setting atom values ...
+  100 settings made for shape
+group           big type 1
+100 atoms in group big
+set             group big quat/random 29898
+Setting atom values ...
+  100 settings made for quat/random
+
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve/asphere
+fix             2 all enforce2d
+
+compute         rot big temp/asphere
+compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
+
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+thermo_style    custom step temp c_rot epair etotal press
+thermo          100
+
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair gayberne command: doi:10.1063/1.3058435
+
+@Article{Brown09,
+ author =  {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
+ title =   {Liquid Crystal Nanodroplets in Solution},
+ journal = {J.~Chem.\ Phys.},
+ year =    2009,
+ volume =  130,
+ number =  4,
+ pages =   {044901}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 13 13 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
+   Step          Temp          c_rot          E_pair         TotEng         Press     
+         0   1.44           0.95677852     2.7038078      4.1294078      10.518912    
+       100   2.5524145      2.801098      -0.37027046     2.1566199      0.84703874   
+       200   2.6266386      2.7938164     -0.35322565     2.2471465      1.004886     
+       300   2.9987557      2.9499545     -0.58917376     2.3795944      0.73081788   
+       400   2.8557446      2.8208128     -0.39904801     2.4281391      0.91808964   
+       500   2.4399047      2.8255746     -0.40056447     2.0149412      1.0538908    
+       600   2.854258       2.9166789     -0.53424483     2.2914706      0.8117508    
+       700   2.9593679      2.8231211     -0.40051715     2.5292571      1.1630889    
+       800   2.7632972      2.9060854     -0.52075351     2.2149107      0.7710678    
+       900   2.9905597      2.8869667     -0.49099378     2.4696603      0.69616841   
+      1000   2.8470138      2.9005012     -0.51282088     2.3057228      0.68817567   
+Loop time of 0.192737 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 2241395.423 tau/day, 5188.415 timesteps/s, 518.842 katom-step/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.17225    | 0.17225    | 0.17225    |   0.0 | 89.37
+Neigh   | 0.0025287  | 0.0025287  | 0.0025287  |   0.0 |  1.31
+Comm    | 0.0023396  | 0.0023396  | 0.0023396  |   0.0 |  1.21
+Output  | 0.00025405 | 0.00025405 | 0.00025405 |   0.0 |  0.13
+Modify  | 0.013955   | 0.013955   | 0.013955   |   0.0 |  7.24
+Other   |            | 0.001413   |            |       |  0.73
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             77 ave          77 max          77 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            369 ave         369 max         369 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 369
+Ave neighs/atom = 3.69
+Neighbor list builds = 174
+Dangerous builds = 0
+
+#undump         1
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 120.0
+Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
+create_atoms    2 region plane
+Created 85849 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.015 seconds
+
+set             type 2 mass 0.01
+Setting atom values ...
+  85849 settings made for mass
+group           small type 2
+85849 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 2.0
+
+neigh_modify    one 10000
+
+delete_atoms    overlap 1.6 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 20 20 2
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 71060 atoms, new total = 14889
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0005
+
+fix             1 big nve/asphere
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   collision noslip search 0.2 inside ignore exact no bounce 50
+fix             3 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/asphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+#dump           2 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    2 pad 6 adiam 1 1 adiam 2 0.2
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14789 100
+  big particle diameter max/min = 3 1
+  SRD temperature & lamda = 1 0.1
+  SRD max distance & max velocity = 0.4 40
+  SRD grid counts: 107 107 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
+  SRD per actual grid cell = 1.9275711
+  SRD viscosity = 0.68810145
+  big/SRD mass density ratio = 1.3736715
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 13.30933 24.335888
+  ave/max big velocity = 2.0802836 5.05672
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 26.726124, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
+   Step          Temp          c_rot          f_2[9]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   2.9005012      2.9005012      0              0.025582147   -0.51282088     3.8089259      0.8986241      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   2.1884096      2.1884096      0.81792923     0.016786763   -0.7613492      2.4993811      1.1765894      13834          35             35             0              241            38416          11449          4172           0.81792923     16             50             0            
+      2000   1.2708697      1.2708697      0.90821156     0.0069438942  -0.8597194      1.0338764      0.9801188      14658          35             35             0              372            38416          11449          4281           0.90821156     16             50             0            
+      3000   1.1130928      1.1130928      0.9590586      0.0052557024  -0.8759868      0.78252152     0.70461705     15267          28             28             0              519            38416          11449          4292           0.9590586      16             50             0            
+      4000   0.8649005      0.8649005      0.9947477      0.0026217985  -0.89834217     0.39035958     0.77420962     15681          36             36             0              698            38416          11449          4339           0.9947477      16             50             0            
+      5000   1.1743692      1.1743692      0.98116608     0.0069116456  -0.72073526     1.0290749      0.8829165      15974          37             37             0              881            38416          11449          4328           0.98116608     16             50             0            
+      6000   1.0190814      1.0190814      1.0138428      0.0048088112  -0.80244733     0.7159839      0.79743882     16092          36             36             0              1090           38416          11449          4319           1.0138428      16             50             0            
+      7000   1.0824823      1.0824823      1.0415165      0.0049127988  -0.88143205     0.73146661     0.48157537     16178          46             46             0              1328           38416          11449          4370           1.0415165      23             50             0            
+      8000   1.0482457      1.0482457      1.0336952      0.0051802902  -0.79059275     0.7712934      0.75744414     16622          33             33             0              1579           38416          11449          4340           1.0336952      24             50             0            
+      9000   0.98889815     0.98889815     1.0126005      0.00397567    -0.88152073     0.59193751     0.52056685     16877          41             41             0              1811           38416          11449          4370           1.0126005      27             50             0            
+     10000   0.96559538     0.96559538     1.0234124      0.0045683795  -0.7585511      0.68018602     0.70666049     16833          32             32             0              2038           38416          11449          4330           1.0234124      27             50             0            
+Loop time of 9.04639 on 1 procs for 10000 steps with 14889 atoms
+
+Performance: 47753.873 tau/day, 1105.414 timesteps/s, 16.459 Matom-step/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.862      | 1.862      | 1.862      |   0.0 | 20.58
+Neigh   | 0.018395   | 0.018395   | 0.018395   |   0.0 |  0.20
+Comm    | 0.060502   | 0.060502   | 0.060502   |   0.0 |  0.67
+Output  | 0.00092704 | 0.00092704 | 0.00092704 |   0.0 |  0.01
+Modify  | 7.0482     | 7.0482     | 7.0482     |   0.0 | 77.91
+Other   |            | 0.05636    |            |       |  0.62
+
+Nlocal:          14889 ave       14889 max       14889 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             79 ave          79 max          79 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            416 ave         416 max         416 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 416
+Ave neighs/atom = 0.02794009
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:11

examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.4

@@ -0,0 +1,346 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD diffusion demo - ellipsoids
+
+units           lj
+atom_style      ellipsoid
+atom_modify     first big
+dimension       2
+
+# create big ellipsoidal particles
+
+lattice         sq 0.14
+Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
+region          box block 0 10 0 10 -0.5 0.5
+create_box      2 box
+Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  2 by 2 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+set             type 1 shape 3.0 1.0 1.0
+Setting atom values ...
+  100 settings made for shape
+group           big type 1
+100 atoms in group big
+set             group big quat/random 29898
+Setting atom values ...
+  100 settings made for quat/random
+
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve/asphere
+fix             2 all enforce2d
+
+compute         rot big temp/asphere
+compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
+
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+thermo_style    custom step temp c_rot epair etotal press
+thermo          100
+
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair gayberne command: doi:10.1063/1.3058435
+
+@Article{Brown09,
+ author =  {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
+ title =   {Liquid Crystal Nanodroplets in Solution},
+ journal = {J.~Chem.\ Phys.},
+ year =    2009,
+ volume =  130,
+ number =  4,
+ pages =   {044901}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 13 13 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
+   Step          Temp          c_rot          E_pair         TotEng         Press     
+         0   1.44           0.95677852     2.7038078      4.1294078      10.518912    
+       100   2.5524145      2.801098      -0.37027046     2.1566199      0.84703874   
+       200   2.6266386      2.7938164     -0.35322565     2.2471465      1.004886     
+       300   2.9987557      2.9499545     -0.58917376     2.3795944      0.73081788   
+       400   2.8557446      2.8208128     -0.39904801     2.4281391      0.91808964   
+       500   2.4399047      2.8255746     -0.40056447     2.0149412      1.0538908    
+       600   2.854258       2.9166789     -0.53424483     2.2914706      0.8117508    
+       700   2.9593679      2.8231211     -0.40051715     2.5292571      1.1630889    
+       800   2.7632972      2.9060855     -0.52075354     2.2149107      0.77106773   
+       900   2.9905599      2.8869667     -0.49099386     2.4696604      0.69616823   
+      1000   2.8470131      2.9005016     -0.51282147     2.3057215      0.68817329   
+Loop time of 0.0666302 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 6483542.632 tau/day, 15008.201 timesteps/s, 1.501 Matom-step/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.039208   | 0.042833   | 0.045871   |   1.2 | 64.29
+Neigh   | 0.00065929 | 0.00071982 | 0.00076852 |   0.0 |  1.08
+Comm    | 0.013998   | 0.017169   | 0.02087    |   1.9 | 25.77
+Output  | 0.00018817 | 0.00020663 | 0.00025962 |   0.0 |  0.31
+Modify  | 0.0035046  | 0.0035933  | 0.003701   |   0.1 |  5.39
+Other   |            | 0.002109   |            |       |  3.16
+
+Nlocal:             25 ave          27 max          24 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:          42.25 ave          45 max          38 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+Neighs:          92.25 ave         104 max          85 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 369
+Ave neighs/atom = 3.69
+Neighbor list builds = 174
+Dangerous builds = 0
+
+#undump         1
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 120.0
+Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
+create_atoms    2 region plane
+Created 85849 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.004 seconds
+
+set             type 2 mass 0.01
+Setting atom values ...
+  85849 settings made for mass
+group           small type 2
+85849 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 2.0
+
+neigh_modify    one 10000
+
+delete_atoms    overlap 1.6 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 20 20 2
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 71060 atoms, new total = 14889
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0005
+
+fix             1 big nve/asphere
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   collision noslip search 0.2 inside ignore exact no bounce 50
+fix             3 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/asphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+#dump           2 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    2 pad 6 adiam 1 1 adiam 2 0.2
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14789 100
+  big particle diameter max/min = 3 1
+  SRD temperature & lamda = 1 0.1
+  SRD max distance & max velocity = 0.4 40
+  SRD grid counts: 107 107 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
+  SRD per actual grid cell = 1.9275711
+  SRD viscosity = 0.68810145
+  big/SRD mass density ratio = 1.3736715
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 13.30933 24.335888
+  ave/max big velocity = 2.080284 5.0567191
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 26.726124, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 16.89 | 16.9 | 16.91 Mbytes
+   Step          Temp          c_rot          f_2[9]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   2.9005016      2.9005016      0              0.025582147   -0.51282147     3.8089259      0.89862191     0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   2.7138279      2.7138279      0.82437872     0.023781703   -0.50274582     3.5408578      1.6816604      13758          32             34             0              274            66564          11449          4238           0.82437872     24             50             0            
+      2000   1.3183118      1.3183118      0.91362053     0.0077748292  -0.80669023     1.1575943      1.1678425      14118          23             23             0              414            66564          11449          4269           0.91362053     24             50             0            
+      3000   1.3117991      1.3117991      0.96889539     0.0065133847  -0.98480276     0.96977785     0.51801823     14675          35             36             0              588            66564          11449          4291           0.96889539     26             50             0            
+      4000   1.1034132      1.1034132      0.95899765     0.0042496304  -1.0113582      0.63272747     0.6382343      15146          38             38             0              776            66564          11449          4309           0.95899765     26             50             0            
+      5000   1.0814177      1.0814177      1.0037423      0.0047549676  -0.90334518     0.70796713     0.76138491     15275          40             40             0              973            66564          11449          4285           1.0037423      26             50             0            
+      6000   1.0515425      1.0515425      0.98728204     0.0041039749  -0.95575757     0.61104083     0.61253791     15685          34             34             0              1205           66564          11449          4328           0.98728204     26             50             0            
+      7000   0.96229389     0.96229389     1.0146054      0.0031968892  -0.95783307     0.47598483     0.4469161      15944          43             43             0              1412           66564          11449          4391           1.0146054      27             50             0            
+      8000   0.98798058     0.98798058     0.99692702     0.0037348841  -0.91600418     0.55608689     0.50558822     16250          43             43             0              1637           66564          11449          4330           0.99692702     27             50             0            
+      9000   1.0120554      1.0120554      1.0099521      0.0039518454  -0.91957229     0.58839026     0.4092229      16367          43             44             0              1899           66564          11449          4309           1.0099521      27             50             0            
+     10000   1.104152       1.104152       0.9993147      0.0053713858  -0.84544079     0.79974564     0.5119979      16331          50             50             0              2108           66564          11449          4353           0.9993147      27             50             0            
+Loop time of 2.95619 on 4 procs for 10000 steps with 14889 atoms
+
+Performance: 146134.205 tau/day, 3382.736 timesteps/s, 50.366 Matom-step/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.48773    | 0.52727    | 0.62879    |   8.1 | 17.84
+Neigh   | 0.0070094  | 0.0072204  | 0.0076255  |   0.3 |  0.24
+Comm    | 0.12898    | 0.22553    | 0.265      |  11.8 |  7.63
+Output  | 0.0005957  | 0.00064777 | 0.00075264 |   0.0 |  0.02
+Modify  | 2.1317     | 2.1512     | 2.166      |   0.9 | 72.77
+Other   |            | 0.04427    |            |       |  1.50
+
+Nlocal:        3722.25 ave        3968 max        3389 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost:          39.75 ave          44 max          35 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:            101 ave         125 max          86 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 404
+Ave neighs/atom = 0.027134126
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.1

@@ -0,0 +1,347 @@
+LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# SRD viscosity demo - ellipsoids
+
+units           lj
+atom_style      ellipsoid
+atom_modify     first big
+dimension       2
+
+# create big ellipsoidal particles
+
+lattice         sq 0.14
+Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
+region          box block 0 10 0 10 -0.5 0.5
+create_box      2 box
+Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.000 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+set             type 1 shape 3.0 1.0 1.0
+Setting atom values ...
+  100 settings made for shape
+group           big type 1
+100 atoms in group big
+set             group big quat/random 29898
+Setting atom values ...
+  100 settings made for quat/random
+
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve/asphere
+fix             2 all enforce2d
+
+compute         rot big temp/asphere
+compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
+
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+thermo_style    custom step temp c_rot epair etotal press
+thermo          100
+
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair gayberne command: doi:10.1063/1.3058435
+
+@Article{Brown09,
+ author =  {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
+ title =   {Liquid Crystal Nanodroplets in Solution},
+ journal = {J.~Chem.\ Phys.},
+ year =    2009,
+ volume =  130,
+ number =  4,
+ pages =   {044901}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 13 13 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
+   Step          Temp          c_rot          E_pair         TotEng         Press     
+         0   1.44           0.95677852     2.7038078      4.1294078      10.518912    
+       100   2.5524145      2.801098      -0.37027046     2.1566199      0.84703874   
+       200   2.6266386      2.7938164     -0.35322565     2.2471465      1.004886     
+       300   2.9987557      2.9499545     -0.58917376     2.3795944      0.73081788   
+       400   2.8557446      2.8208128     -0.39904801     2.4281391      0.91808964   
+       500   2.4399047      2.8255746     -0.40056447     2.0149412      1.0538908    
+       600   2.854258       2.9166789     -0.53424483     2.2914706      0.8117508    
+       700   2.9593679      2.8231211     -0.40051715     2.5292571      1.1630889    
+       800   2.7632972      2.9060854     -0.52075351     2.2149107      0.7710678    
+       900   2.9905597      2.8869667     -0.49099378     2.4696603      0.69616841   
+      1000   2.8470138      2.9005012     -0.51282088     2.3057228      0.68817567   
+Loop time of 0.192844 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 2240155.241 tau/day, 5185.545 timesteps/s, 518.554 katom-step/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.17225    | 0.17225    | 0.17225    |   0.0 | 89.32
+Neigh   | 0.0025614  | 0.0025614  | 0.0025614  |   0.0 |  1.33
+Comm    | 0.0024746  | 0.0024746  | 0.0024746  |   0.0 |  1.28
+Output  | 0.0001406  | 0.0001406  | 0.0001406  |   0.0 |  0.07
+Modify  | 0.014112   | 0.014112   | 0.014112   |   0.0 |  7.32
+Other   |            | 0.001306   |            |       |  0.68
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             77 ave          77 max          77 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            369 ave         369 max         369 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 369
+Ave neighs/atom = 3.69
+Neighbor list builds = 174
+Dangerous builds = 0
+
+#undump         1
+unfix           1
+unfix           2
+
+# add small particles as hi density lattice
+
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 120.0
+Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
+create_atoms    2 region plane
+Created 85849 atoms
+  using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
+  create_atoms CPU = 0.015 seconds
+
+set             type 2 mass 0.01
+Setting atom values ...
+  85849 settings made for mass
+group           small type 2
+85849 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 2.0
+
+neigh_modify    one 10000
+
+delete_atoms    overlap 1.6 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 20 20 2
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 71060 atoms, new total = 14889
+
+# SRD run
+
+reset_timestep  0
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      gayberne 1.0 3.0 1.0 4.0
+pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
+pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
+pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0005
+
+fix             1 big nve/asphere
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   collision noslip search 0.2 inside ignore exact no bounce 50
+fix             3 small viscosity 20 x y 50
+fix             4 all enforce2d
+
+# diagnostics
+
+compute         tbig big temp/asphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+thermo          1000
+
+#dump           1 all custom 500 dump.ellipsoid id type x y z c_0[*]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
+
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14789 100
+  big particle diameter max/min = 3 1
+  SRD temperature & lamda = 1 0.1
+  SRD max distance & max velocity = 0.4 40
+  SRD grid counts: 107 107 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
+  SRD per actual grid cell = 1.9275711
+  SRD viscosity = 0.68810145
+  big/SRD mass density ratio = 1.3736715
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 13.30933 24.335888
+  ave/max big velocity = 2.0802836 5.05672
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 26.726124, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gayberne, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/2d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
+   Step          Temp          c_rot          f_2[9]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
+         0   2.9005012      2.9005012      0              0.025582147   -0.51282088     3.8089259      0.8986241      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   2.3102693      2.3102693      0.82371999     0.019779507   -0.49733043     2.9449709      1.9807143      13954          30             30             0              277            38416          11449          4255           0.82371999     15             50             0            
+      2000   1.5312119      1.5312119      0.90846884     0.008532096   -1.011162       1.2703438      0.58038663     14523          37             37             0              439            38416          11449          4257           0.90846884     20             50             0            
+      3000   1.3603443      1.3603443      0.95241399     0.0085403252  -0.75534393     1.271569       1.2262133      14864          34             35             0              599            38416          11449          4287           0.95241399     20             50             0            
+      4000   2.2408861      2.2408861      0.99089404     0.016876315   -0.82620566     2.5127146      1.2664088      15457          35             35             0              809            38416          11449          4272           0.99089404     21             50             0            
+      5000   1.7110067      1.7110067      0.99729333     0.011146301   -0.88982716     1.6595728      0.97334407     15555          36             36             0              1026           38416          11449          4324           0.99729333     24             50             0            
+      6000   1.684666       1.684666       1.0235606      0.009751253   -1.0582882      1.4518641      0.62435255     15752          45             46             0              1256           38416          11449          4303           1.0235606      24             50             0            
+      7000   2.1142261      2.1142261      1.0160206      0.014786886   -0.94857757     2.2016194      0.7761903      16144          30             30             0              1492           38416          11449          4401           1.0160206      27             50             0            
+      8000   2.5622926      2.5622926      1.0125365      0.019933518   -0.84991443     2.9679015      0.93716383     16302          43             43             0              1720           38416          11449          4346           1.0125365      27             50             0            
+      9000   2.6593623      2.6593623      1.0110535      0.020725053   -0.87669675     3.0857531      0.97818336     16856          44             44             0              2000           38416          11449          4298           1.0110535      30             50             0            
+     10000   2.7567851      2.7567851      1.0379053      0.021598993   -0.8917358      3.2158741      0.74950846     16770          50             53             0              2284           38416          11449          4316           1.0379053      30             50             0            
+Loop time of 9.02679 on 1 procs for 10000 steps with 14889 atoms
+
+Performance: 47857.551 tau/day, 1107.814 timesteps/s, 16.494 Matom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8454     | 1.8454     | 1.8454     |   0.0 | 20.44
+Neigh   | 0.018708   | 0.018708   | 0.018708   |   0.0 |  0.21
+Comm    | 0.059853   | 0.059853   | 0.059853   |   0.0 |  0.66
+Output  | 0.00081453 | 0.00081453 | 0.00081453 |   0.0 |  0.01
+Modify  | 7.0469     | 7.0469     | 7.0469     |   0.0 | 78.07
+Other   |            | 0.05507    |            |       |  0.61
+
+Nlocal:          14889 ave       14889 max       14889 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             75 ave          75 max          75 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            382 ave         382 max         382 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 382
+Ave neighs/atom = 0.025656525
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:11