Merge branch 'develop' into electrode

.github/CODEOWNERS

@@ -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

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")
-    else()
-      message(STATUS "Using builtin distributed algorithms")
   endif()
   if(PKG_KOKKOS)
-      if(Kokkos_ENABLE_CUDA)
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
-        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/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

@@ -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/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/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_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

@@ -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/Fortran.rst

@@ -1402,7 +1402,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    Set the value of a string-style variable.
 
-   .. deprecated:: TBD
+   .. 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
@@ -1423,7 +1423,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    Set the value of a string-style variable.
 
-   .. versionadded:: TBD
+   .. 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
@@ -1439,7 +1439,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    Set the value of a internal-style variable.
 
-   .. versionadded:: TBD
+   .. 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

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/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
@@ -63,13 +80,13 @@ produce an executable compatible with a specific hardware.
    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::
 
@@ -420,11 +447,18 @@ Generally speaking, the following rules of thumb apply:
   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_lepton.rst

@@ -51,7 +51,7 @@ 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:: TBD
+.. 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

doc/src/bond_lepton.rst

@@ -50,7 +50,7 @@ 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:: TBD
+.. 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

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

@@ -23,6 +23,7 @@ Syntax
                              spx, spy, spz, sp, fmx, fmy, fmz,
                              nbonds,
                              radius, diameter, omegax, omegay, omegaz,
+                             temperature, heatflow,
                              angmomx, angmomy, angmomz,
                              shapex, shapey, shapez,
                              quatw, quati, quatj, quatk, tqx, tqy, tqz,
@@ -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_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/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_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_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_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}`

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_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

@@ -376,7 +376,7 @@ not listed, the default diameter of each atom in the molecule is 1.0.
 
 ----------
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 *Dipoles* section:
 

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_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_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/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

@@ -1770,6 +1770,7 @@ Kolafa
 Kollman
 kolmogorov
 Kolmogorov
+Kolotinskii
 Kondor
 konglt
 Koning
@@ -2266,6 +2267,7 @@ morris
 Morriss
 morse
 Morteza
+MoS
 Mosayebi
 Moseler
 Moskalev
@@ -2774,6 +2776,7 @@ PEigenDense
 Peng
 peptide
 peratom
+Perf
 Pergamon
 pergrid
 peri
@@ -3070,6 +3073,7 @@ reaxff
 ReaxFF
 REAXFF
 rebo
+rebomos
 recurse
 recursing
 Ree
@@ -3597,6 +3601,7 @@ tesselation
 tesselations
 Tetot
 tex
+textrm
 tfac
 tfmc
 tfMC
@@ -3797,6 +3802,7 @@ unimodal
 uninstall
 unitarg
 unitless
+unittest
 Universite
 unix
 unmaintained
@@ -3883,7 +3889,9 @@ Verlet
 versa
 Verstraelen
 ves
+vf
 vflag
+vflow
 vfrac
 vhi
 vibrational

examples/ASPHERE/dimer/in.dimer

@@ -7,7 +7,7 @@ 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
 
 set             type 1 mass 1.0
@@ -101,4 +101,4 @@ thermo		1000
 #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
+run             10000

examples/ASPHERE/dimer/in.dimer.mp

@@ -7,7 +7,7 @@ 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
 
 set             type 1 mass 1.0
@@ -102,4 +102,4 @@ 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             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

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

@@ -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)
+  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 0.0905036 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 4773291.472 tau/day, 11049.286 timesteps/s, 1.105 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    | 0.039039   | 0.053443   | 0.065528   |   5.0 | 59.05
+Neigh   | 0.00068257 | 0.00086692 | 0.0010442  |   0.0 |  0.96
+Comm    | 0.016567   | 0.028689   | 0.043189   |   6.8 | 31.70
+Output  | 0.00016989 | 0.00018594 | 0.0002316  |   0.0 |  0.21
+Modify  | 0.0035809  | 0.0043052  | 0.0050755  |   1.0 |  4.76
+Other   |            | 0.003013   |            |       |  3.33
+
+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 = 0.007 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 = 2.080284 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   2.5269102      2.5269102      0.8207596      0.022784455   -0.37271861     3.3923775      2.0963085      13925          34             34             0              322            66564          11449          4235           0.8207596      24             50             0            
+      2000   1.3685596      1.3685596      0.89115879     0.0089112146  -0.71236311     1.3267907      1.3970875      14444          25             25             0              454            66564          11449          4278           0.89115879     25             50             0            
+      3000   1.5234001      1.5234001      0.9828293      0.0090168318  -0.92735003     1.3425161      0.70104224     14946          37             37             0              608            66564          11449          4331           0.9828293      27             50             0            
+      4000   2.2536932      2.2536932      0.97648579     0.017005211   -0.82609701     2.5319058      1.190307       15428          43             43             0              827            66564          11449          4346           0.97648579     32             50             0            
+      5000   1.8106358      1.8106358      1.0143347      0.012032652   -0.90630586     1.7915415      0.83451531     15438          26             26             0              1039           66564          11449          4314           1.0143347      32             50             0            
+      6000   1.9880605      1.9880605      1.0142917      0.013767418   -0.91237924     2.0498309      0.87383026     15688          37             37             0              1279           66564          11449          4353           1.0142917      32             50             0            
+      7000   2.4772098      2.4772098      0.99457682     0.018062012   -1.0017896      2.689253       0.74369504     15723          38             38             0              1521           66564          11449          4293           0.99457682     32             50             0            
+      8000   2.5749419      2.5749419      1.0337514      0.019908918   -0.87242464     2.9642389      1.0460672      15932          33             34             0              1805           66564          11449          4320           1.0337514      32             50             0            
+      9000   2.4877578      2.4877578      1.0366259      0.019125113   -0.85922105     2.847538       0.95616808     16292          52             53             0              2099           66564          11449          4291           1.0366259      33             50             0            
+     10000   2.8498311      2.8498311      1.0117104      0.022669267   -0.87102125     3.3752271      0.98313087     16736          38             38             0              2415           66564          11449          4366           1.0117104      35             50             0            
+Loop time of 3.0339 on 4 procs for 10000 steps with 14889 atoms
+
+Performance: 142390.919 tau/day, 3296.086 timesteps/s, 49.075 Matom-step/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.46168    | 0.52303    | 0.69055    |  13.4 | 17.24
+Neigh   | 0.0068493  | 0.0072892  | 0.0081958  |   0.6 |  0.24
+Comm    | 0.12806    | 0.2911     | 0.34961    |  17.5 |  9.59
+Output  | 0.00055286 | 0.00057977 | 0.00065772 |   0.0 |  0.02
+Modify  | 2.1454     | 2.1674     | 2.1833     |   0.9 | 71.44
+Other   |            | 0.04447    |            |       |  1.47
+
+Nlocal:        3722.25 ave        4163 max        3210 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:          46.25 ave          49 max          43 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:          102.5 ave         143 max          79 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 410
+Ave neighs/atom = 0.027537108
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/ASPHERE/line/in.line

@@ -52,4 +52,4 @@ change_box      all triclinic
 
 fix             3 all deform 1 xy erate 0.01 units box
 
-run		100000
+run             10000

examples/ASPHERE/poly/in.poly

@@ -111,4 +111,4 @@ thermo		1000
 #dump           1 all image 1000 image.*.jpg type type zoom 1.6
 #dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
 
-run		100000
+run             10000

examples/ASPHERE/poly/in.poly.mp

@@ -112,4 +112,4 @@ thermo		1000
 #dump           1 all image 500 image.*.jpg type type zoom 1.6
 #dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
 
-run		50000
+run             10000

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

@@ -1,288 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD diffusion demo - poydisperse spheres
-
-units		lj
-atom_style	sphere
-atom_modify	first big
-dimension	2
-
-# create big particles with 3 different types and diameters
-
-lattice		sq 0.3
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region		box block 0 10 0 10 -0.5 0.5
-create_box	4 box
-Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
-  2 by 4 by 1 MPI processor grid
-create_atoms	1 region box
-Created 100 atoms
-
-group		big type 1
-100 atoms in group big
-set		group big type/fraction 2 0.33 394895
-  35 settings made for type/fraction
-set		group big type/fraction 3 0.5 989894
-  57 settings made for type/fraction
-group		big type 2 3
-100 atoms in group big
-
-set		type 1*3 mass 1.0
-  100 settings made for mass
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles, repulsive only to prevent aggregation
-
-pair_style	lj/cut 1.12
-pair_coeff	1 1 1.0 1.0 1.12
-pair_coeff	2 2 1.0 2.0 2.24
-pair_coeff	3 3 1.0 1.5 1.68
-pair_coeff	4 4 0.0 1.0 0.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big nve
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.poly.equil
-
-run		1000
-Memory usage per processor = 2.7472 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44  -0.16013916            0    1.2654608    1.1298975 
-    1000    1.3367862  -0.30816328            0    1.0152551    1.5440006 
-Loop time of 0.0221665 on 8 procs for 1000 steps with 100 atoms
-
-Pair  time (%) = 0.000323534 (1.45957)
-Neigh time (%) = 0.000274181 (1.23692)
-Comm  time (%) = 0.0146933 (66.2864)
-Outpt time (%) = 2.864e-05 (0.129204)
-Other time (%) = 0.00684676 (30.8879)
-
-Nlocal:    12.5 ave 18 max 10 min
-Histogram: 1 3 1 1 0 1 0 0 0 1
-Nghost:    27.75 ave 31 max 24 min
-Histogram: 1 0 1 0 2 2 0 0 0 2
-Neighs:    19 ave 30 max 16 min
-Histogram: 4 1 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 152
-Ave neighs/atom = 1.52
-Neighbor list builds = 115
-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 250.0
-Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
-create_atoms	4 region plane
-Created 83521 atoms
-
-set		type 4 mass 0.1
-  83521 settings made for mass
-group		small type 4
-83521 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set *-4 cutoffs to non-zero values
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 1.0 2.0
-pair_coeff	3 3 1.0 1.5
-pair_coeff	1 4 0.0 1.0 0.5
-pair_coeff	2 4 0.0 1.0 1.0
-pair_coeff	3 4 0.0 1.0 0.75
-
-delete_atoms	overlap 1.0 small big
-Deleted 63410 atoms, new total = 20211
-
-# 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 1.12
-pair_coeff	1 1 1.0 1.0 1.12
-pair_coeff	2 2 1.0 2.0 2.24
-pair_coeff	3 3 1.0 1.5 1.68
-pair_coeff	4 4 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 nve
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
-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]
-
-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.poly
-
-#dump		1 all image 1000 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
-
-run		100000
-SRD info:
-  SRD/big particles = 20111 100
-  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: 73 73 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
-  SRD per actual grid cell = 4.93717
-  SRD viscosity = 0.23322
-  big/SRD mass density ratio = 0.161311
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.19344 7.74495
-  ave/max big velocity = 1.43991 3.5724
-Memory usage per processor = 11.8633 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] 
-       0   0.88820023            0 0.0050232797  -0.30816328    1.0152551    1.5440006            0            0            0            0            0            0            0            0            0            0            0 
-    1000   0.84607633         3934 0.0065245151  0.058016014    1.3186697    4.2649214         7470           26           26            0          665        36480         5329         3934   0.95810956            0            2 
-    2000   0.86586785         3944 0.0045898954  -0.36247933   0.92766376    2.1563866         7786           30           30            0         1374        36480         5329         3944    1.0799777            0           49 
-    3000   0.78968677         4001   0.00417319  -0.33318986   0.84344343    1.9302042         7957           34           34            0         2129        36480         5329         4001    1.1247747            0           49 
-    4000    0.7110667         4005 0.0031642256  -0.41996775   0.63952164    1.9679689         8188           24           24            0         2925        36480         5329         4005    1.1345941            0           49 
-    5000   0.80379425         4052 0.0038912991  -0.41118297   0.78647047    1.6851034         8326           30           30            0         3794        36480         5329         4052    1.1310774            0           49 
-    6000   0.96927432         4048 0.0054656969  -0.33954674     1.104672    1.8976158         8380           23           23            0         4643        36480         5329         4048    1.1861264            0           49 
-    7000   0.75821666         4050 0.0036201309  -0.39807817   0.73166465    1.6087451         8450           51           51            0         5699        36480         5329         4050    1.1664119            0           49 
-    8000    0.8712338         4035 0.0047243103    -0.343308   0.95483036    1.4707918         8458           42           42            0         6974        36480         5329         4035    1.1947807            0           91 
-    9000   0.87995969         4048 0.0042778416  -0.44654537   0.86459457    1.5567027         8379           36           36            0         7965        36480         5329         4048    1.1675384            0           91 
-   10000   0.83009098         4053 0.0042178709  -0.38436167   0.85247389    1.9119485         8373           34           34            0         8952        36480         5329         4053    1.1933986            0           91 
-   11000   0.73595909         4015 0.0037439098  -0.33989742   0.75668162    1.6495307         8333           22           22            0         9983        36480         5329         4015    1.1959519            0           91 
-   12000   0.84043443         4034 0.0041823741  -0.40694768   0.84529962    1.5115578         8566           31           31            0        11023        36480         5329         4034    1.2064988            0           91 
-   13000   0.64253331         4044 0.0034868675  -0.25264383    0.7047308     1.739124         8528           31           31            0        12101        36480         5329         4044    1.1912336            0           91 
-   14000   0.99330171         4042 0.0055047339  -0.36745778    1.1125618    1.8215191         8548           36           36            0        13098        36480         5329         4042    1.1819124            0           91 
-   15000   0.90379859         4049 0.0049047446  -0.35536197   0.99129793    1.7159536         8459           37           37            0        14130        36480         5329         4049    1.1806762            0           91 
-   16000   0.87446498         4034 0.0053318245  -0.22533777    1.0776151    2.0239395         8690           33           33            0        15176        36480         5329         4034    1.1912858            0           91 
-   17000   0.95733995         4035 0.0053759665  -0.33989994    1.0865366    1.6243881         8518           27           27            0        16147        36480         5329         4035    1.2074487            0           91 
-   18000      1.03543         4032 0.0052946469  -0.47268961    1.0701011    1.5444562         8464           28           28            0        17230        36480         5329         4032    1.1959755            0           91 
-   19000   0.75997582         4051 0.0034371936  -0.43767278    0.6946912    1.4209137         8436           39           39            0        18276        36480         5329         4051     1.182461            0           91 
-   20000   0.89615234         4037 0.0048910458  -0.34673773   0.98852926    1.5843879         8433           28           28            0        19275        36480         5329         4037    1.1850673            0           91 
-   21000   0.85849578         4063 0.0044978314  -0.37010201    0.9090567    1.5445809         8504           40           40            0        20278        36480         5329         4063    1.1931031            0           91 
-   22000   0.79050471         4066 0.0038260812  -0.40456274   0.77328927    1.6214277         8463           44           44            0        21287        36480         5329         4066    1.1948824            0           91 
-   23000   0.89563532         4026 0.0051030186  -0.30312555    1.0313711    1.4848223         8548           35           35            0        22422        36480         5329         4026    1.1975081            0           91 
-   24000   0.83528717         4036 0.0043136275  -0.37275064   0.87182725    1.5504059         8527           34           34            0        23404        36480         5329         4036    1.1755463            0           91 
-   25000   0.64179358         4022 0.0035185741  -0.24513342   0.71113901    1.7238889         8452           47           47            0        24522        36480         5329         4022    1.2066339            0           91 
-   26000   0.86710098         4028 0.0046099591  -0.36026164   0.93171883    1.4255297         8734           33           33            0        25524        36480         5329         4028    1.2001233            0           91 
-   27000    0.8327003         4054 0.0045323379  -0.32469262   0.91603082    1.2654649         8468           34           34            0        26520        36480         5329         4054    1.1814901            0           91 
-   28000   0.84396759         4049 0.0042805934  -0.39236096   0.86515074    1.2929473         8536           37           37            0        27657        36480         5329         4049    1.1897647            0           91 
-   29000   0.77639299         4052 0.0038143413  -0.38590904   0.77091652    1.3627099         8637           36           36            0        28773        36480         5329         4052    1.1858017            0           91 
-   30000   0.69994805         4046 0.0034430868  -0.34704032   0.69588228    1.5351247         8704           46           46            0        29818        36480         5329         4046    1.1724555            0           91 
-   31000   0.73907898         4039  0.003034759  -0.48787254   0.61335514    1.2291035         8486           29           29            0        30848        36480         5329         4039    1.2063852            0           91 
-   32000   0.84649298         4052 0.0044326201  -0.36539769   0.89587685    1.4591662         8513           28           28            0        31917        36480         5329         4052    1.1917883            0           91 
-   33000    0.7188891         4031 0.0033440675  -0.39527528   0.67586949    1.2495703         8800           37           37            0        32938        36480         5329         4031     1.191087            0           91 
-   34000   0.93588921         4054 0.0054112843  -0.30080024    1.0936747    1.3650172         8585           33           33            0        33913        36480         5329         4054    1.1840415            0           91 
-   35000   0.86446961         4039 0.0053251497  -0.21179371     1.076266    1.3791947         8607           22           22            0        34865        36480         5329         4039    1.1916342            0           91 
-   36000   0.90510006         4011 0.0054168442   -0.2538007    1.0947984    1.5747653         8479           31           31            0        35842        36480         5329         4011    1.1760305            0           91 
-   37000   0.95332175         4058 0.0055020495  -0.30843018    1.1120192    1.4326924         8512           29           29            0        36751        36480         5329         4058     1.180738            0           91 
-   38000   0.71413841         4043 0.0038380378   -0.2883604   0.77570582    1.4283837         8611           39           39            0        37689        36480         5329         4043    1.1693806            0           91 
-   39000   0.81161335         4064 0.0044323475  -0.31348213   0.89582176    1.4378305         8697           28           28            0        38696        36480         5329         4064    1.1987209            0           91 
-   40000    0.8294437         4062 0.0051262098  -0.19981285    1.0360583    1.6010501         8559           31           31            0        39743        36480         5329         4062    1.2092371            0           91 
-   41000   0.79325147         4079 0.0045273868  -0.26691453   0.91503015    1.4080428         8775           53           53            0        40806        36480         5329         4079    1.1989619            0           91 
-   42000   0.95693891         4027  0.005623893  -0.28919396     1.136645    1.5334192         8509           34           34            0        41793        36480         5329         4027    1.1931035            0           91 
-   43000   0.66458435         4029 0.0035902162  -0.26461209   0.72561859    1.4253918         8559           44           44            0        42768        36480         5329         4029    1.2111853            0           91 
-   44000   0.84442459         4022 0.0050980388  -0.22782802    1.0303646    1.4587515         8522           32           32            0        43812        36480         5329         4022    1.1943268            0           91 
-   45000   0.96505326         4051 0.0057148128  -0.28290855    1.1550208    1.3014361         8496           32           32            0        44803        36480         5329         4051    1.1912109            0           91 
-   46000   0.75345782         4064 0.0040245838  -0.30924351   0.81340864    1.7179797         8568           29           29            0        45795        36480         5329         4064    1.1975591            0           91 
-   47000   0.87187806         4017  0.004406241  -0.40855293   0.89054538    1.3105257         8586           36           36            0        46822        36480         5329         4017    1.1834816            0           91 
-   48000   0.83729235         4078 0.0045115864  -0.33572888   0.91183673    1.3856733         8513           38           38            0        47866        36480         5329         4078    1.1996374            0           91 
-   49000   0.65112065         4048 0.0030445536  -0.35483503   0.61533473    1.2659451         8705           32           32            0        48907        36480         5329         4048    1.1907782            0           91 
-   50000   0.82730473         4066 0.0045492584  -0.31323342   0.91945063    1.1803982         8562           41           41            0        49965        36480         5329         4066    1.1696702            0           91 
-   51000   0.74252279         4048 0.0046741422  -0.16166808   0.94469088    1.5539445         8564           35           35            0        50948        36480         5329         4048    1.1748481            0           91 
-   52000   0.85671386         4051 0.0058575179 -0.092640701     1.183863    1.6307333         8609           19           19            0        51894        36480         5329         4051    1.1770671            0           91 
-   53000    0.7233951         4068 0.0043421658  -0.20026358   0.87759512     1.453924         8582           28           28            0        52893        36480         5329         4068    1.2027667            0           91 
-   54000   0.72117217         4051 0.0040247209  -0.26111018   0.81343635    1.3496518         8679           25           25            0        53831        36480         5329         4051    1.1823115            0           91 
-   55000   0.87940919         4044 0.0047057065  -0.35924936   0.95107033     1.240057         8559           34           34            0        54813        36480         5329         4044    1.1815144            0           91 
-   56000   0.83192698         4044 0.0046298732  -0.30382753   0.93574367     1.547229         8441           37           37            0        55740        36480         5329         4044    1.1761232            0           91 
-   57000   0.91043729         4058 0.0050029377  -0.34540782    1.0111437    1.4951603         8550           32           32            0        56678        36480         5329         4058    1.2024504            0           91 
-   58000   0.97648852         4036 0.0053292287  -0.37787747    1.0770904    1.4058278         8554           31           31            0        57683        36480         5329         4036    1.1746239            0           91 
-   59000   0.72239185         4018 0.0046615138   -0.1342253   0.94213856    1.8337414         8716           35           35            0        58640        36480         5329         4018    1.1697661            0           91 
-   60000   0.73800253         4032 0.0037590001  -0.33989225   0.75973152     1.399426         8561           32           32            0        59593        36480         5329         4032    1.1958194            0           91 
-   61000   0.72778603         4060 0.0042599892  -0.22341476   0.86098642    1.3778202         8541           31           31            0        60573        36480         5329         4060    1.1980875            0           91 
-   62000   0.80350669         4044 0.0042316822  -0.34195968   0.85526529    1.4379455         8487           37           37            0        61608        36480         5329         4044    1.1942365            0           91 
-   63000   0.90084181         4066 0.0043040273  -0.47236734   0.86988695    1.4672845         8504           32           32            0        62670        36480         5329         4066    1.1829834            0           91 
-   64000   0.87220486         4059 0.0047840275  -0.33268544    0.9668998    1.5398216         8588           34           34            0        63605        36480         5329         4059    1.1884975            0           91 
-   65000   0.82469157         4057  0.004405933  -0.33830733   0.89048312    1.5284565         8783           32           32            0        64693        36480         5329         4057    1.1952722            0           91 
-   66000   0.88692288         4081 0.0047264561  -0.36625105   0.95526405    1.3151847         8745           36           36            0        65755        36480         5329         4081    1.1834684            0           91 
-   67000   0.83322374         4031 0.0047732147  -0.27678896   0.96471442    1.5085732         8415           34           34            0        66796        36480         5329         4031       1.1969            0           91 
-   68000   0.75375865         4020 0.0044379413  -0.22614806   0.89695233    1.6351001         8573           30           30            0        67876        36480         5329         4020    1.1911308            0           91 
-   69000   0.91169697         4055 0.0050371842  -0.34036318    1.0180653    1.2495539         8625           20           20            0        68979        36480         5329         4055    1.1860768            0           91 
-   70000   0.80502435         4075 0.0042565586  -0.33919322   0.86029306    1.3194042         8571           36           36            0        69947        36480         5329         4075      1.18994            0           91 
-   71000    0.8928873         4055 0.0050586026   -0.3080079    1.0223942    1.3949364         8698           32           32            0        71037        36480         5329         4055    1.2154821            0           91 
-   72000   0.95397384         4050 0.0052866702  -0.35293209    1.0684889    1.2950893         8613           35           35            0        72090        36480         5329         4050    1.1790804            0           91 
-   73000   0.78742879         4053  0.004378612  -0.28830762   0.88496127    1.5168042         8624           30           30            0        73174        36480         5329         4053    1.2008591            0           91 
-   74000   0.79498726         4046 0.0042999917  -0.31545969   0.86907133    1.3751647         8562           22           22            0        74250        36480         5329         4046    1.1921334            0           91 
-   75000   0.88929145         4051 0.0048995187  -0.33480254   0.99024172    1.6589606         8393           33           33            0        75296        36480         5329         4051    1.1753137            0           91 
-   76000   0.98366685         4045 0.0049217494  -0.47092883   0.99473478    1.5271346         8555           29           29            0        76301        36480         5329         4045    1.2031327            0           91 
-   77000   0.72618119         4051 0.0035028638  -0.37404618    0.7079638    1.5178344         8565           37           37            0        77315        36480         5329         4051    1.1993308            0           91 
-   78000   0.80445682         4028  0.003992176  -0.39178196    0.8068587    1.3682816         8624           32           32            0        78299        36480         5329         4028    1.2065456            0           91 
-   79000     1.091703         4052 0.0063793569  -0.33730561    1.2893318    1.5717928         8677           39           39            0        79249        36480         5329         4052    1.1725194            0           91 
-   80000   0.77212865         4052 0.0041275152  -0.31625959    0.8342121    1.5583982         8526           33           33            0        80284        36480         5329         4052    1.1981751            0           91 
-   81000   0.80732682         4061  0.004618782  -0.26941493   0.93350203    1.5517327         8444           36           36            0        81331        36480         5329         4061    1.2095831            0           91 
-   82000   0.80166933         4057 0.0042732734  -0.33081602   0.86367129    1.3937505         8476           29           29            0        82335        36480         5329         4057    1.2047807            0           91 
-   83000   0.76980598         4049 0.0041331379  -0.31166241   0.83534851    1.1411979         8561           34           34            0        83375        36480         5329         4049    1.1810941            0           91 
-   84000   0.85529188         4076 0.0046148117  -0.34168531   0.93269959    1.3284464         8664           27           27            0        84510        36480         5329         4076     1.192734            0           91 
-   85000   0.96167157         4034 0.0053261317  -0.35642617    1.0764645    1.3195071         8557           36           36            0        85517        36480         5329         4034    1.2000123            0           91 
-   86000   0.88130862         4047 0.0046646382  -0.37037981   0.94277003    1.3595079         8634           36           36            0        86578        36480         5329         4047    1.1654584            0           91 
-   87000   0.68799517         4037 0.0042184867  -0.17251446   0.85259834    1.5087731         8363           40           40            0        87606        36480         5329         4037    1.1833599            0           91 
-   88000   0.83191621         4041 0.0048307277  -0.26321678   0.97633838    1.4008912         8597           39           39            0        88490        36480         5329         4041    1.1607031            0           91 
-   89000   0.71456519         4036 0.0039378285  -0.26882761   0.79587453    1.2251569         8397           36           36            0        89436        36480         5329         4036    1.1991362            0           91 
-   90000   0.75198251         4048 0.0043377839  -0.24374445   0.87670949    1.4896261         8551           29           29            0        90453        36480         5329         4048    1.1899998            0           91 
-   91000   0.83310145         4032 0.0049902932    -0.232733    1.0085882    1.4140378         8583           48           48            0        91563        36480         5329         4032    1.1953029            0           91 
-   92000    0.8819465         4050 0.0058087956  -0.14008461    1.1740157     1.753218         8610           46           46            0        92618        36480         5329         4050    1.1972268            0           91 
-   93000   0.76721608         4048 0.0041923848  -0.29582907    0.8473229    1.4126521         8671           32           32            0        93690        36480         5329         4048    1.2027935            0           91 
-   94000    0.8942606         4050 0.0051973822  -0.28200539    1.0504429    1.5743434         8751           21           21            0        94750        36480         5329         4050    1.1804594            0           91 
-   95000   0.73609582         4036 0.0035091666  -0.38754512   0.70923765      1.28494         8660           31           31            0        95713        36480         5329         4036    1.1883125            0           91 
-   96000   0.79430429         4078 0.0043400156  -0.30635284   0.87716056    1.4351927         8600           38           38            0        96695        36480         5329         4078    1.1704833            0           91 
-   97000   0.74817621         4044 0.0038163094  -0.34346826   0.77131429     1.255104         8377           36           36            0        97683        36480         5329         4044    1.1756023            0           91 
-   98000   0.78160255         4048 0.0039385343  -0.36857064   0.79601716    1.5320263         8350           25           25            0        98631        36480         5329         4048     1.181196            0           91 
-   99000     0.804448         4053  0.004503827  -0.28835905   0.91026848    1.7569548         8506           35           35            0        99687        36480         5329         4053    1.1950898            0           91 
-  100000   0.74975993         4032  0.004263269    -0.255493   0.86164929    1.5983872         8621           33           33            0       100701        36480         5329         4032    1.1910217            0           91 
-Loop time of 13.4746 on 8 procs for 100000 steps with 20211 atoms
-
-Pair  time (%) = 0.0563478 (0.418178)
-Neigh time (%) = 0.794382 (5.89541)
-Comm  time (%) = 1.23773 (9.18569)
-Outpt time (%) = 0.00554895 (0.0411809)
-Other time (%) = 11.3806 (84.4595)
-
-Nlocal:    2526.38 ave 2725 max 2337 min
-Histogram: 2 0 0 1 1 1 1 0 1 1
-Nghost:    23.875 ave 27 max 21 min
-Histogram: 1 1 0 2 0 2 0 0 0 2
-Neighs:    17 ave 25 max 12 min
-Histogram: 3 1 0 1 1 0 0 0 0 2
-
-Total # of neighbors = 136
-Ave neighs/atom = 0.00672901
-Neighbor list builds = 5008
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

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

@@ -1,239 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD viscosity demo - poydisperse spheres
-
-units		lj
-atom_style	sphere
-atom_modify	first big
-dimension	2
-
-# create big particles with 3 different types and diameters
-
-lattice		sq 0.3
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region		box block 0 10 0 10 -0.5 0.5
-create_box	4 box
-Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
-  2 by 4 by 1 MPI processor grid
-create_atoms	1 region box
-Created 100 atoms
-
-group		big type 1
-100 atoms in group big
-set		group big type/fraction 2 0.33 394895
-  35 settings made for type/fraction
-set		group big type/fraction 3 0.5 989894
-  57 settings made for type/fraction
-group		big type 2 3
-100 atoms in group big
-
-set		type 1*3 mass 1.0
-  100 settings made for mass
-velocity	big create 1.44 87287 loop geom
-
-# equilibrate big particles, repulsive only to prevent aggregation
-
-pair_style	lj/cut 1.12
-pair_coeff	1 1 1.0 1.0 1.12
-pair_coeff	2 2 1.0 2.0 2.24
-pair_coeff	3 3 1.0 1.5 1.68
-pair_coeff	4 4 0.0 1.0 0.0
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big nve
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.poly.equil
-
-run		1000
-Memory usage per processor = 2.7472 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44  -0.16013916            0    1.2654608    1.1298975 
-    1000    1.3367862  -0.30816328            0    1.0152551    1.5440006 
-Loop time of 0.0173425 on 8 procs for 1000 steps with 100 atoms
-
-Pair  time (%) = 0.00033614 (1.93825)
-Neigh time (%) = 0.000266045 (1.53407)
-Comm  time (%) = 0.0115004 (66.3132)
-Outpt time (%) = 2.78056e-05 (0.160332)
-Other time (%) = 0.00521213 (30.0541)
-
-Nlocal:    12.5 ave 18 max 10 min
-Histogram: 1 3 1 1 0 1 0 0 0 1
-Nghost:    27.75 ave 31 max 24 min
-Histogram: 1 0 1 0 2 2 0 0 0 2
-Neighs:    19 ave 30 max 16 min
-Histogram: 4 1 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 152
-Ave neighs/atom = 1.52
-Neighbor list builds = 115
-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 250.0
-Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
-create_atoms	4 region plane
-Created 83521 atoms
-
-set		type 4 mass 0.1
-  83521 settings made for mass
-group		small type 4
-83521 atoms in group small
-velocity	small create 1.0 593849 loop geom
-
-# delete overlaps
-# must set *-4 cutoffs to non-zero values
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 1.0 2.0
-pair_coeff	3 3 1.0 1.5
-pair_coeff	1 4 0.0 1.0 0.5
-pair_coeff	2 4 0.0 1.0 1.0
-pair_coeff	3 4 0.0 1.0 0.75
-
-delete_atoms	overlap 1.0 small big
-Deleted 63410 atoms, new total = 20211
-
-# 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 1.12
-pair_coeff	1 1 1.0 1.0 1.12
-pair_coeff	2 2 1.0 2.0 2.24
-pair_coeff	3 3 1.0 1.5 1.68
-pair_coeff	4 4 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 nve
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 		  search 0.2 inside ignore
-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]
-
-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.poly.mp
-
-#dump		1 all image 500 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
-
-run		50000
-SRD info:
-  SRD/big particles = 20111 100
-  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: 73 73 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
-  SRD per actual grid cell = 4.93717
-  SRD viscosity = 0.23322
-  big/SRD mass density ratio = 0.161311
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.19344 7.74495
-  ave/max big velocity = 1.43991 3.5724
-Memory usage per processor = 11.8633 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] 
-       0   0.88820023            0 0.0050232797  -0.30816328    1.0152551    1.5440006            0            0            0            0            0            0            0            0            0            0            0 
-    1000   0.76223471         3964 0.0058318994  0.042955471    1.1786852    3.9611295         7412           29           29            0          611        36480         5329         3964   0.97424113            0            1 
-    2000   0.83394503         3951 0.0050432506  -0.22328672    1.0192914    2.7492771         7829           30           30            0         1225        36480         5329         3951    1.0832295            0            3 
-    3000   0.86856945         3991 0.0048205728  -0.31988251   0.97428597    2.4105317         7961           34           34            0         2000        36480         5329         3991    1.1243219            0            6 
-    4000   0.88106888         4009 0.0066731082  0.035909261    1.3487019     3.025346         8002           33           33            0         2895        36480         5329         4009    1.1359575            0            6 
-    5000    1.0764198         4036 0.0070136315  -0.18634051    1.4175251    2.7617336         8117           36           36            0         3808        36480         5329         4036    1.1147743            0            6 
-    6000    1.0433139         4004 0.0059532709  -0.35132214    1.2032156    2.3597383         8004           23           23            0         4845        36480         5329         4004    1.1192873            0            6 
-    7000    1.1551053         4026 0.0074766715  -0.20999681    1.5111101     2.280806         8269           36           36            0         5873        36480         5329         4026    1.1704244            0            6 
-    8000    1.2222713         4008 0.0078175708  -0.24117508    1.5800092     1.967726         8218           33           33            0         7077        36480         5329         4008    1.1496529            0            6 
-    9000    1.2240884         4012 0.0081583857  -0.17500037    1.6488913    2.3684675         8502           27           27            0         8359        36480         5329         4012    1.1664455            0            6 
-   10000    1.2071315         4035 0.0073838443  -0.30627724    1.4923488     2.124366         8376           33           33            0         9778        36480         5329         4035    1.1942304            0            6 
-   11000    1.1694272         4036 0.0077950192  -0.16699527    1.5754513    2.4203067         8623           40           40            0        11210        36480         5329         4036    1.1802896            0           42 
-   12000    1.0911561         4044 0.0074117515  -0.12783343    1.4979891    2.4859591         8490           30           30            0        12647        36480         5329         4044     1.171701            0           42 
-   13000    1.3535072         4023 0.0091503262  -0.16735325    1.8493724    2.7718999         8320           33           33            0        14082        36480         5329         4023    1.1841757            0           42 
-   14000    1.4191753         4043 0.0095368758  -0.18707328     1.927498    2.8442438         8422           25           25            0        15462        36480         5329         4043    1.1567854            0           42 
-   15000     1.703769         4053  0.010892787  -0.33707457    2.2015412    2.4160876         8123           34           34            0        16985        36480         5329         4053    1.1875794            0           42 
-   16000    1.4270161         4032  0.010142553 -0.076342616    2.0499114    2.9568071         8360           34           34            0        18487        36480         5329         4032     1.164586            0           42 
-   17000    1.2267528         4013 0.0080642511  -0.19799584    1.6298658    2.5084784         8477           27           27            0        20101        36480         5329         4013    1.1529604            0           42 
-   18000    1.4228586         4050   0.01009573 -0.079611446    2.0404479    2.8013833         8519           33           33            0        21633        36480         5329         4050    1.1549291            0           42 
-   19000    1.3041379         4040 0.0082901927  -0.26763462    1.6755308    1.9403854         8483           30           30            0        23194        36480         5329         4040    1.1592747            0           42 
-   20000    1.3837406         4030 0.0092446911  -0.19332904    1.8684445    2.4550531         8425           25           25            0        24761        36480         5329         4030    1.1757648            0           42 
-   21000    1.7882552         4031  0.012076007  -0.22381856    2.4406817    2.4206092         8581           40           40            0        26371        36480         5329         4031    1.1591574            0           42 
-   22000    1.5079803         4015  0.010373742  -0.15025377    2.0966369    2.6321039         8383           33           33            0        27989        36480         5329         4015    1.1495522            0           42 
-   23000    1.3835348         4044 0.0087922321  -0.28446888     1.776998    2.2729548         8441           30           30            0        29575        36480         5329         4044    1.1616377            0           42 
-   24000    1.5854836         4044 0.0099174248  -0.35795983    2.0044107    2.2250073         8462           35           35            0        31298        36480         5329         4044    1.1796851            0           42 
-   25000    1.5314412         4062  0.010880793 -0.082730301    2.1991171    2.6858232         8473           28           28            0        33079        36480         5329         4062    1.1726593            0           54 
-   26000    1.2896316         4070 0.0090198232 -0.098554631    1.8229965    2.3437649         8453           40           40            0        34816        36480         5329         4070    1.1764482            0           54 
-   27000    1.6956611         4035  0.012064024 -0.088275024      2.43826    2.8138661         8380           32           32            0        36453        36480         5329         4035    1.1622504            0           54 
-   28000    1.3560979         4043 0.0088193796  -0.23810107    1.7824848    2.1799536         8611           30           30            0        38202        36480         5329         4043    1.1681248            0           54 
-   29000    1.5837646         4029  0.010790526  -0.17893612    2.1808731    2.3116753         8480           26           26            0        39846        36480         5329         4029    1.1774511            0           54 
-   30000    1.6549448         4035   0.01137773  -0.16631482    2.2995529    2.6236656         8637           30           30            0        41461        36480         5329         4035    1.1538405            0           54 
-   31000     1.445315         4050   0.01013447   -0.1052417    2.0482777    2.4440312         8504           38           38            0        43099        36480         5329         4050    1.1690375            0           54 
-   32000    1.5572315         4037  0.010828477  -0.13173155    2.1885434    2.5911192         8453           30           30            0        44760        36480         5329         4037    1.1612147            0           54 
-   33000     2.018109         4068  0.013467519  -0.28506208    2.7219203    2.5784978         8701           40           40            0        46462        36480         5329         4068    1.1727186            0           54 
-   34000    1.2455134         4066 0.0083640288  -0.16536113    1.6904539    2.3054829         8428           32           32            0        48055        36480         5329         4066    1.1712016            0           54 
-   35000    1.6248596         4012  0.011213824  -0.15461501    2.2664259    2.8697537         8453           31           31            0        49658        36480         5329         4012    1.1693962            0           54 
-   36000    1.5485873         4039   0.01112737 -0.058442367    2.2489527    3.0386676         8529           42           42            0        51330        36480         5329         4039    1.1750818            0           54 
-   37000    1.5561543         4024  0.011313246 -0.032149816    2.2865202    2.7583779         8484           45           45            0        52981        36480         5329         4024    1.1613247            0           54 
-   38000    1.5174762         4043  0.010120957  -0.21549294    2.0455467    2.2489655         8528           37           37            0        54637        36480         5329         4043    1.1692017            0           54 
-   39000    1.5936544         4045  0.010946409  -0.16216642    2.2123787    2.7579117         8460           35           35            0        56452        36480         5329         4045    1.1670575            0           54 
-   40000    1.7884514         4051  0.011913021   -0.2570519    2.4077408     2.494169         8539           37           37            0        58163        36480         5329         4051    1.1744075            0           54 
-   41000    1.4173685         4042 0.0096196931  -0.16764288    1.9442362    1.9949409         8511           42           42            0        59967        36480         5329         4042    1.1747318            0           54 
-   42000    1.4946304         4055 0.0098254549  -0.24117659    1.9858227    1.9958514         8395           39           39            0        61697        36480         5329         4055    1.1745062            0           54 
-   43000    1.6486882         4041  0.011190255  -0.19488288    2.2616625    2.2173122         8473           28           28            0        63447        36480         5329         4041    1.1631975            0           54 
-   44000    1.7473914         4055  0.011743128  -0.23020951    2.3734036    2.3913609         8421           30           30            0        65095        36480         5329         4055    1.1567659            0           54 
-   45000    1.7826681         4027  0.011993913  -0.23208563    2.4240898    2.4582759         8539           35           35            0        66749        36480         5329         4027    1.1513285            0           54 
-   46000    1.3988187         4049 0.0091738733  -0.23010838    1.8541315    2.3866226         8447           38           38            0        68459        36480         5329         4049    1.1728215            0           54 
-   47000    1.8402398         4064   0.01271321  -0.17249031     2.569467    2.7748374         8524           33           33            0        70139        36480         5329         4064    1.1555276            0           54 
-   48000    1.5634287         4042  0.011047794 -0.096639164    2.2328696    2.7173437         8561           33           33            0        71923        36480         5329         4042     1.177462            0           54 
-   49000     1.789207         4058  0.012453079  -0.14902655    2.5168918    2.9310418         8545           38           38            0        73721        36480         5329         4058    1.1581934            0           54 
-   50000    1.3475703         4010 0.0092484369  -0.13867816    1.8692016    2.1619389         8664           32           32            0        75439        36480         5329         4010    1.1589691            0           54 
-Loop time of 6.84 on 8 procs for 50000 steps with 20211 atoms
-
-Pair  time (%) = 0.0295508 (0.432029)
-Neigh time (%) = 0.400359 (5.8532)
-Comm  time (%) = 0.622996 (9.10813)
-Outpt time (%) = 0.00241029 (0.0352382)
-Other time (%) = 5.78468 (84.5714)
-
-Nlocal:    2526.38 ave 2651 max 2342 min
-Histogram: 1 0 0 2 1 0 0 1 1 2
-Nghost:    24.5 ave 27 max 23 min
-Histogram: 1 0 4 0 0 2 0 0 0 1
-Neighs:    17.375 ave 24 max 13 min
-Histogram: 2 2 0 1 1 0 0 0 0 2
-
-Total # of neighbors = 139
-Ave neighs/atom = 0.00687744
-Neighbor list builds = 2502
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

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

@@ -0,0 +1,317 @@
+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 - poydisperse spheres
+
+units           lj
+atom_style      sphere
+atom_modify     first big
+dimension       2
+
+# create big particles with 3 different types and diameters
+
+lattice         sq 0.3
+Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
+region          box block 0 10 0 10 -0.5 0.5
+create_box      4 box
+Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.000 seconds
+
+group           big type 1
+100 atoms in group big
+set             group big type/fraction 2 0.33 394895
+Setting atom values ...
+  35 settings made for type/fraction
+set             group big type/fraction 3 0.5 989894
+Setting atom values ...
+  57 settings made for type/fraction
+group           big type 2 3
+100 atoms in group big
+
+set             type 1*3 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles, repulsive only to prevent aggregation
+
+pair_style      lj/cut 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 0.0 1.0 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.poly.equil
+
+run             1000
+Generated 6 of 6 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 = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 1.27, bins = 15 15 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 4.174 | 4.174 | 4.174 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.16013916     0              1.2654608      1.1298975    
+      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
+Loop time of 0.00622873 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 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    | 0.0015709  | 0.0015709  | 0.0015709  |   0.0 | 25.22
+Neigh   | 0.0014016  | 0.0014016  | 0.0014016  |   0.0 | 22.50
+Comm    | 0.0012066  | 0.0012066  | 0.0012066  |   0.0 | 19.37
+Output  | 6.169e-06  | 6.169e-06  | 6.169e-06  |   0.0 |  0.10
+Modify  | 0.0013508  | 0.0013508  | 0.0013508  |   0.0 | 21.69
+Other   |            | 0.0006926  |            |       | 11.12
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             60 ave          60 max          60 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            152 ave         152 max         152 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 152
+Ave neighs/atom = 1.52
+Neighbor list builds = 115
+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 250.0
+Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
+create_atoms    4 region plane
+Created 83521 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.016 seconds
+
+set             type 4 mass 0.1
+Setting atom values ...
+  83521 settings made for mass
+group           small type 4
+83521 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set *-4 cutoffs to non-zero values
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 1.0 2.0
+pair_coeff      3 3 1.0 1.5
+pair_coeff      1 4 0.0 1.0 0.5
+pair_coeff      2 4 0.0 1.0 1.0
+pair_coeff      3 4 0.0 1.0 0.75
+pair_coeff      4 4 0.0 1.0 0.0
+
+delete_atoms    overlap 1.0 small big
+System init for delete_atoms ...
+Generated 3 of 6 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 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 63410 atoms, new total = 20211
+
+# 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 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 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 nve
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
+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]
+
+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.poly
+
+#dump           1 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
+
+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 3 of 6 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 20111 100
+  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: 73 73 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
+  SRD per actual grid cell = 4.9371727
+  SRD viscosity = 0.23321983
+  big/SRD mass density ratio = 0.16131131
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1934421 7.74495
+  ave/max big velocity = 1.4399093 3.5724039
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 18.257419, 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) = 42 | 42 | 42 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]    
+         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.0181191      3924           0.0076572255   0.030604433    1.5476019      3.7992573      7242           26             26             0              635            15876          5329           3924           0.98110339     0              3            
+      2000   0.69783736     3992           0.0027817464  -0.47755891     0.56221876     1.9887267      7740           34             34             1              1186           15876          5329           3992           1.0611575      0              24           
+      3000   0.89084297     3981           0.004323119   -0.45361044     0.87374558     1.7342893      7775           24             24             0              1923           15876          5329           3981           1.1207371      0              24           
+      4000   0.84391846     4036           0.0045581483  -0.33619115     0.92124735     1.8456288      8060           43             43             0              2734           15876          5329           4036           1.1481354      0              24           
+      5000   0.69548234     4056           0.0030033315  -0.42926535     0.60700333     1.6113509      8260           33             33             0              3638           15876          5329           4056           1.148749       0              24           
+      6000   0.71729125     4023           0.0035318938  -0.35493291     0.71383106     1.673491       8224           29             29             0              4528           15876          5329           4023           1.1602572      0              24           
+      7000   0.90145513     4032           0.0047423524  -0.38469129     0.95847685     1.7537778      8382           31             31             0              5395           15876          5329           4032           1.1543513      0              24           
+      8000   0.6739295      4026           0.0029910322  -0.39963744     0.60451751     1.646528       8409           35             35             0              6293           15876          5329           4026           1.1540519      0              24           
+      9000   0.80563959     4041           0.0042947965  -0.33238166     0.86802133     1.6597032      8429           29             29             0              7164           15876          5329           4041           1.1880521      0              24           
+     10000   0.90407954     4022           0.0046865656  -0.39987673     0.94720178     1.445708       8349           30             30             0              8189           15876          5329           4022           1.171667       0              24           
+Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms
+
+Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 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    | 0.019832   | 0.019832   | 0.019832   |   0.0 |  0.35
+Neigh   | 0.020738   | 0.020738   | 0.020738   |   0.0 |  0.37
+Comm    | 0.056875   | 0.056875   | 0.056875   |   0.0 |  1.01
+Output  | 0.00083247 | 0.00083247 | 0.00083247 |   0.0 |  0.01
+Modify  | 5.4828     | 5.4828     | 5.4828     |   0.0 | 97.05
+Other   |            | 0.06854    |            |       |  1.21
+
+Nlocal:          20211 ave       20211 max       20211 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             49 ave          49 max          49 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            160 ave         160 max         160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 160
+Ave neighs/atom = 0.0079164811
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:11

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

@@ -0,0 +1,317 @@
+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 - poydisperse spheres
+
+units           lj
+atom_style      sphere
+atom_modify     first big
+dimension       2
+
+# create big particles with 3 different types and diameters
+
+lattice         sq 0.3
+Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
+region          box block 0 10 0 10 -0.5 0.5
+create_box      4 box
+Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  2 by 2 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.000 seconds
+
+group           big type 1
+100 atoms in group big
+set             group big type/fraction 2 0.33 394895
+Setting atom values ...
+  35 settings made for type/fraction
+set             group big type/fraction 3 0.5 989894
+Setting atom values ...
+  57 settings made for type/fraction
+group           big type 2 3
+100 atoms in group big
+
+set             type 1*3 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles, repulsive only to prevent aggregation
+
+pair_style      lj/cut 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 0.0 1.0 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.poly.equil
+
+run             1000
+Generated 6 of 6 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 = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 1.27, bins = 15 15 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 4.172 | 4.172 | 4.172 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.16013916     0              1.2654608      1.1298975    
+      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
+Loop time of 0.00891987 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 48431181.463 tau/day, 112109.216 timesteps/s, 11.211 Matom-step/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00039835 | 0.00043547 | 0.00047558 |   0.0 |  4.88
+Neigh   | 0.00033856 | 0.00036829 | 0.00038548 |   0.0 |  4.13
+Comm    | 0.0065535  | 0.0065882  | 0.0066353  |   0.0 | 73.86
+Output  | 1.0991e-05 | 1.2359e-05 | 1.4677e-05 |   0.0 |  0.14
+Modify  | 0.00043639 | 0.00045662 | 0.00050811 |   0.0 |  5.12
+Other   |            | 0.001059   |            |       | 11.87
+
+Nlocal:             25 ave          29 max          23 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:          33.75 ave          35 max          31 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Neighs:             38 ave          46 max          34 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 152
+Ave neighs/atom = 1.52
+Neighbor list builds = 115
+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 250.0
+Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
+create_atoms    4 region plane
+Created 83521 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.006 seconds
+
+set             type 4 mass 0.1
+Setting atom values ...
+  83521 settings made for mass
+group           small type 4
+83521 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set *-4 cutoffs to non-zero values
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 1.0 2.0
+pair_coeff      3 3 1.0 1.5
+pair_coeff      1 4 0.0 1.0 0.5
+pair_coeff      2 4 0.0 1.0 1.0
+pair_coeff      3 4 0.0 1.0 0.75
+pair_coeff      4 4 0.0 1.0 0.0
+
+delete_atoms    overlap 1.0 small big
+System init for delete_atoms ...
+Generated 3 of 6 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 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 63410 atoms, new total = 20211
+
+# 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 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 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 nve
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
+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]
+
+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.poly
+
+#dump           1 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
+
+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 3 of 6 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 20111 100
+  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: 73 73 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
+  SRD per actual grid cell = 4.9371727
+  SRD viscosity = 0.23321983
+  big/SRD mass density ratio = 0.16131131
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1934421 7.74495
+  ave/max big velocity = 1.4399093 3.5724039
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 18.257419, 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) = 19.17 | 19.17 | 19.18 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]    
+         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
+      1000   0.98459665     3968           0.0086216557   0.27547381     1.7425228      4.4010488      7403           34             34             0              663            25600          5329           3968           0.98292304     0              5            
+      2000   0.74381104     4003           0.0041077507  -0.27806095     0.8302175      2.6170187      7746           32             32             0              1272           25600          5329           4003           1.0631936      0              5            
+      3000   0.86305095     3969           0.0048953507  -0.29654658     0.98939933     2.1215334      7834           35             35             0              1974           25600          5329           3969           1.1209619      0              5            
+      4000   0.8262932      4022           0.0049907905  -0.2224882      1.0086887      2.079935       8196           27             27             0              2753           25600          5329           4022           1.1040604      0              5            
+      5000   0.85908819     4038           0.0043301633  -0.40487209     0.87516931     1.7917343      8347           28             28             0              3622           25600          5329           4038           1.1575336      0              5            
+      6000   0.8048766      4024           0.0047529981  -0.2386377      0.96062844     1.8195477      8103           26             26             0              4536           25600          5329           4024           1.1818796      0              5            
+      7000   0.84561126     4047           0.0039459142  -0.46245206     0.79750871     1.4432235      8154           20             20             0              5483           25600          5329           4047           1.1817402      0              5            
+      8000   0.81543891     4037           0.0037591562  -0.45524091     0.75976306     1.7501338      8377           27             27             0              6472           25600          5329           4037           1.168956       0              5            
+      9000   0.71960112     4045           0.0035243955  -0.3598901      0.71231557     1.7333111      8440           30             30             0              7386           25600          5329           4045           1.1765277      0              5            
+     10000   1.0831334      4043           0.0053045911  -0.54175788     1.0721109      1.7434822      8283           33             33             0              8331           25600          5329           4043           1.1696048      0              5            
+Loop time of 1.82855 on 4 procs for 10000 steps with 20211 atoms
+
+Performance: 472504.837 tau/day, 5468.806 timesteps/s, 110.530 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    | 0.0057481  | 0.0069625  | 0.0087051  |   1.3 |  0.38
+Neigh   | 0.0067658  | 0.0070766  | 0.0076303  |   0.4 |  0.39
+Comm    | 0.10613    | 0.10693    | 0.10786    |   0.2 |  5.85
+Output  | 0.00053606 | 0.00059075 | 0.00063891 |   0.0 |  0.03
+Modify  | 1.6117     | 1.6525     | 1.6763     |   1.9 | 90.37
+Other   |            | 0.05449    |            |       |  2.98
+
+Nlocal:        5052.75 ave        5483 max        4509 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:             27 ave          28 max          26 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           39.5 ave          55 max          26 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 158
+Ave neighs/atom = 0.0078175251
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:03

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

@@ -0,0 +1,318 @@
+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 - poydisperse spheres
+
+units           lj
+atom_style      sphere
+atom_modify     first big
+dimension       2
+
+# create big particles with 3 different types and diameters
+
+lattice         sq 0.3
+Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
+region          box block 0 10 0 10 -0.5 0.5
+create_box      4 box
+Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.000 seconds
+
+group           big type 1
+100 atoms in group big
+set             group big type/fraction 2 0.33 394895
+Setting atom values ...
+  35 settings made for type/fraction
+set             group big type/fraction 3 0.5 989894
+Setting atom values ...
+  57 settings made for type/fraction
+group           big type 2 3
+100 atoms in group big
+
+set             type 1*3 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles, repulsive only to prevent aggregation
+
+pair_style      lj/cut 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 0.0 1.0 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.poly.equil
+
+run             1000
+Generated 6 of 6 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 = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 1.27, bins = 15 15 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 4.174 | 4.174 | 4.174 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.16013916     0              1.2654608      1.1298975    
+      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
+Loop time of 0.00627198 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 68877814.583 tau/day, 159439.386 timesteps/s, 15.944 Matom-step/s
+97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0016224  | 0.0016224  | 0.0016224  |   0.0 | 25.87
+Neigh   | 0.0014238  | 0.0014238  | 0.0014238  |   0.0 | 22.70
+Comm    | 0.0011671  | 0.0011671  | 0.0011671  |   0.0 | 18.61
+Output  | 6.058e-06  | 6.058e-06  | 6.058e-06  |   0.0 |  0.10
+Modify  | 0.0013659  | 0.0013659  | 0.0013659  |   0.0 | 21.78
+Other   |            | 0.0006868  |            |       | 10.95
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             60 ave          60 max          60 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            152 ave         152 max         152 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 152
+Ave neighs/atom = 1.52
+Neighbor list builds = 115
+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 250.0
+Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
+create_atoms    4 region plane
+Created 83521 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.017 seconds
+
+set             type 4 mass 0.1
+Setting atom values ...
+  83521 settings made for mass
+group           small type 4
+83521 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set *-4 cutoffs to non-zero values
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 1.0 2.0
+pair_coeff      3 3 1.0 1.5
+pair_coeff      1 4 0.0 1.0 0.5
+pair_coeff      2 4 0.0 1.0 1.0
+pair_coeff      3 4 0.0 1.0 0.75
+pair_coeff      4 4 0.0 1.0 0.0
+
+delete_atoms    overlap 1.0 small big
+System init for delete_atoms ...
+Generated 3 of 6 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 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 63410 atoms, new total = 20211
+
+# 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 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 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 nve
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
+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]
+
+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.poly.mp
+
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
+
+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 3 of 6 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 20111 100
+  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: 73 73 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
+  SRD per actual grid cell = 4.9371727
+  SRD viscosity = 0.23321983
+  big/SRD mass density ratio = 0.16131131
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1934421 7.74495
+  ave/max big velocity = 1.4399093 3.5724039
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 18.257419, 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) = 42 | 42 | 42 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]    
+         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
+      1000   0.9260989      3936           0.007125623    0.060272296    1.4401597      3.9323         7454           34             34             0              666            15876          5329           3936           0.98459206     0              28           
+      2000   0.90353395     4000           0.0052889652  -0.27731283     1.0689528      2.6405627      7698           23             23             0              1382           15876          5329           4000           1.0797162      0              46           
+      3000   0.90859187     3993           0.0052873224  -0.28518115     1.0686207      2.2965966      7968           31             31             0              2142           15876          5329           3993           1.1267833      0              46           
+      4000   0.84755099     4048           0.005174979   -0.21693597     1.045915       2.3794577      8137           36             36             0              3087           15876          5329           4048           1.1357649      0              46           
+      5000   0.970415       4034           0.0070498808  -0.021066942    1.4248514      2.7424457      8202           29             29             0              4119           15876          5329           4034           1.1354594      0              46           
+      6000   1.3230208      4023           0.0094580142  -0.059741745    1.9115593      3.1405056      8259           36             36             0              5151           15876          5329           4023           1.1508111      0              46           
+      7000   1.2356555      4022           0.0076141503  -0.30223075     1.5388959      2.2740088      8336           33             33             0              6277           15876          5329           4022           1.1814599      0              46           
+      8000   1.0470467      4044           0.0077098735  -0.001857114    1.5582425      2.97413        8285           40             40             0              7399           15876          5329           4044           1.1644871      0              46           
+      9000   1.0827168      4054           0.0062150407  -0.35712609     1.2561219      2.0991523      8454           31             31             0              8664           15876          5329           4054           1.1744383      0              46           
+     10000   1.3953419      4031           0.0091083246  -0.23817595     1.8408835      2.4493963      8468           34             34             0              10227          15876          5329           4031           1.1657737      0              62           
+Loop time of 5.74914 on 1 procs for 10000 steps with 20211 atoms
+
+Performance: 150283.390 tau/day, 1739.391 timesteps/s, 35.155 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    | 0.021224   | 0.021224   | 0.021224   |   0.0 |  0.37
+Neigh   | 0.020586   | 0.020586   | 0.020586   |   0.0 |  0.36
+Comm    | 0.057881   | 0.057881   | 0.057881   |   0.0 |  1.01
+Output  | 0.00093386 | 0.00093386 | 0.00093386 |   0.0 |  0.02
+Modify  | 5.579      | 5.579      | 5.579      |   0.0 | 97.04
+Other   |            | 0.06951    |            |       |  1.21
+
+Nlocal:          20211 ave       20211 max       20211 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             50 ave          50 max          50 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            141 ave         141 max         141 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 141
+Ave neighs/atom = 0.006976399
+Neighbor list builds = 503
+Dangerous builds = 0
+Total wall time: 0:00:11

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

@@ -0,0 +1,318 @@
+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 - poydisperse spheres
+
+units           lj
+atom_style      sphere
+atom_modify     first big
+dimension       2
+
+# create big particles with 3 different types and diameters
+
+lattice         sq 0.3
+Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
+region          box block 0 10 0 10 -0.5 0.5
+create_box      4 box
+Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  2 by 2 by 1 MPI processor grid
+create_atoms    1 region box
+Created 100 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.000 seconds
+
+group           big type 1
+100 atoms in group big
+set             group big type/fraction 2 0.33 394895
+Setting atom values ...
+  35 settings made for type/fraction
+set             group big type/fraction 3 0.5 989894
+Setting atom values ...
+  57 settings made for type/fraction
+group           big type 2 3
+100 atoms in group big
+
+set             type 1*3 mass 1.0
+Setting atom values ...
+  100 settings made for mass
+velocity        big create 1.44 87287 loop geom
+
+# equilibrate big particles, repulsive only to prevent aggregation
+
+pair_style      lj/cut 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 0.0 1.0 0.0
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big nve
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.poly.equil
+
+run             1000
+Generated 6 of 6 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 = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 1.27, bins = 15 15 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 4.172 | 4.172 | 4.172 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.16013916     0              1.2654608      1.1298975    
+      1000   1.3367862     -0.30816328     0              1.0152551      1.5440006    
+Loop time of 0.00883083 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 48919544.759 tau/day, 113239.687 timesteps/s, 11.324 Matom-step/s
+99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00040021 | 0.00044336 | 0.00050371 |   0.0 |  5.02
+Neigh   | 0.00033682 | 0.00036617 | 0.00038566 |   0.0 |  4.15
+Comm    | 0.006519   | 0.0065578  | 0.0066015  |   0.0 | 74.26
+Output  | 1.1215e-05 | 1.2252e-05 | 1.4089e-05 |   0.0 |  0.14
+Modify  | 0.00043326 | 0.00044482 | 0.00046058 |   0.0 |  5.04
+Other   |            | 0.001006   |            |       | 11.40
+
+Nlocal:             25 ave          29 max          23 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:          33.75 ave          35 max          31 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Neighs:             38 ave          46 max          34 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 152
+Ave neighs/atom = 1.52
+Neighbor list builds = 115
+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 250.0
+Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
+create_atoms    4 region plane
+Created 83521 atoms
+  using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
+  create_atoms CPU = 0.006 seconds
+
+set             type 4 mass 0.1
+Setting atom values ...
+  83521 settings made for mass
+group           small type 4
+83521 atoms in group small
+velocity        small create 1.0 593849 loop geom
+
+# delete overlaps
+# must set *-4 cutoffs to non-zero values
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 1.0 2.0
+pair_coeff      3 3 1.0 1.5
+pair_coeff      1 4 0.0 1.0 0.5
+pair_coeff      2 4 0.0 1.0 1.0
+pair_coeff      3 4 0.0 1.0 0.75
+pair_coeff      4 4 0.0 1.0 0.0
+
+delete_atoms    overlap 1.0 small big
+System init for delete_atoms ...
+Generated 3 of 6 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 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 63410 atoms, new total = 20211
+
+# 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 1.12
+pair_coeff      1 1 1.0 1.0 1.12
+pair_coeff      2 2 1.0 2.0 2.24
+pair_coeff      3 3 1.0 1.5 1.68
+pair_coeff      4 4 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 nve
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 inside ignore
+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]
+
+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.poly.mp
+
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
+
+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 3 of 6 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 20111 100
+  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: 73 73 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
+  SRD per actual grid cell = 4.9371727
+  SRD viscosity = 0.23321983
+  big/SRD mass density ratio = 0.16131131
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1934421 7.74495
+  ave/max big velocity = 1.4399093 3.5724039
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.54
+  ghost atom cutoff = 2.54
+  binsize = 18.257419, 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) = 19.17 | 19.17 | 19.18 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]    
+         0   0.88820023     0              0.0050232797  -0.30816328     1.0152551      1.5440006      0              0              0              0              0              0              0              0              0              0              0            
+      1000   0.83735494     3964           0.0071370659   0.19481352     1.4424724      3.9770741      7472           25             25             0              603            25600          5329           3964           0.96475118     0              2            
+      2000   0.89694821     3981           0.0057098818  -0.18242861     1.1540242      3.1251883      7672           28             28             0              1238           25600          5329           3981           1.0589985      0              2            
+      3000   0.99778172     3975           0.0051822049  -0.43931933     1.0473754      1.8970896      7814           24             24             0              1968           25600          5329           3975           1.1192504      0              3            
+      4000   0.90067439     4030           0.0045096255  -0.43056442     0.91144042     1.8769981      8104           33             33             0              2911           25600          5329           4030           1.1382082      0              3            
+      5000   0.90625848     4018           0.0055622776  -0.22613322     1.1241919      2.1866405      8287           26             26             0              3900           25600          5329           4018           1.1429442      0              3            
+      6000   1.1284139      4022           0.0065653291  -0.354418       1.3269187      2.0312152      8268           35             35             0              5013           25600          5329           4022           1.1559733      0              3            
+      7000   1.0073477      4043           0.0063924548  -0.2089691      1.291979       2.3332058      8433           39             39             0              6093           25600          5329           4043           1.1308958      0              3            
+      8000   1.0621801      4050           0.00731979    -0.10324558     1.4794028      2.6610716      8353           40             40             0              7194           25600          5329           4050           1.1539521      0              3            
+      9000   1.3173319      4046           0.0085268497  -0.23946297     1.7233616      2.4074596      8290           33             33             0              8498           25600          5329           4046           1.1601502      0              3            
+     10000   1.1754738      4009           0.0074264713  -0.25049186     1.5009641      2.4237351      8305           30             30             0              9811           25600          5329           4009           1.1489476      0              43           
+Loop time of 1.85719 on 4 procs for 10000 steps with 20211 atoms
+
+Performance: 465218.852 tau/day, 5384.477 timesteps/s, 108.826 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    | 0.0056791  | 0.0069765  | 0.0089852  |   1.6 |  0.38
+Neigh   | 0.006991   | 0.0073805  | 0.0079507  |   0.4 |  0.40
+Comm    | 0.10756    | 0.10836    | 0.10942    |   0.2 |  5.83
+Output  | 0.00052479 | 0.0005511  | 0.00062567 |   0.0 |  0.03
+Modify  | 1.6443     | 1.6772     | 1.7031     |   1.7 | 90.31
+Other   |            | 0.0567     |            |       |  3.05
+
+Nlocal:        5052.75 ave        5381 max        4651 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Nghost:           28.5 ave          30 max          26 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+Neighs:          34.75 ave          55 max          26 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 139
+Ave neighs/atom = 0.006877443
+Neighbor list builds = 501
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/ASPHERE/star/in.star

@@ -7,7 +7,7 @@ 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.star fix molprop NULL Molecules
 
 set             type 1 mass 1.0
@@ -108,4 +108,4 @@ thermo		1000
 #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
+run             10000

examples/ASPHERE/star/in.star.mp

@@ -7,7 +7,7 @@ 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.star fix molprop NULL Molecules
 
 set             type 1 mass 1.0
@@ -109,4 +109,4 @@ thermo		1000
 #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
+run             10000

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

@@ -1,290 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD diffusion demo - rigid star 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.star fix molprop NULL Molecules
-  orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  270 atoms
-
-set		type 1 mass 1.0
-  270 settings made for mass
-group		big type 1
-270 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
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big rigid molecule
-30 rigid bodies with 270 atoms
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.star.equil
-
-thermo		100
-run		1000
-Memory usage per processor = 2.64859 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0            0            0            0   0.24721146 
-     100            0     3.291475            0     3.291475   0.69158089 
-     200            0    4.6176595            0    4.6176595   0.71737945 
-     300            0    7.0921814            0    7.0921814    1.2163497 
-     400            0    8.3666709            0    8.3666709   0.50645957 
-     500            0    10.630838            0    10.630838   0.72764487 
-     600            0     12.42157            0     12.42157    1.0130599 
-     700            0    14.349074            0    14.349074   0.74795509 
-     800            0    16.464746            0    16.464746     1.054549 
-     900            0    18.253108            0    18.253108   0.51551753 
-    1000            0    20.699563            0    20.699563    1.8084662 
-Loop time of 0.040709 on 8 procs for 1000 steps with 270 atoms
-
-Pair  time (%) = 0.00249004 (6.11668)
-Neigh time (%) = 0.000995547 (2.44552)
-Comm  time (%) = 0.0116902 (28.7165)
-Outpt time (%) = 0.000232756 (0.571755)
-Other time (%) = 0.0253005 (62.1496)
-
-Nlocal:    33.75 ave 42 max 22 min
-Histogram: 1 0 1 0 0 2 0 1 1 2
-Nghost:    23.375 ave 30 max 14 min
-Histogram: 1 0 1 0 0 2 1 0 1 2
-Neighs:    52.25 ave 69 max 27 min
-Histogram: 1 0 1 0 1 0 1 1 1 2
-
-Total # of neighbors = 418
-Ave neighs/atom = 1.54815
-Neighbor list builds = 176
-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 = 0.108465 0.108465 0.108465
-create_atoms	2 region plane
-Created 60025 atoms
-
-set		type 2 mass 0.1
-  60025 settings made for mass
-group		small type 2
-60025 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 16305 atoms, new total = 43990
-
-# 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
-30 rigid bodies with 270 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.star
-
-#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 = 43720 270
-  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: 106 106 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
-  SRD per actual grid cell = 5.55866
-  SRD viscosity = 0.235582
-  big/SRD mass density ratio = 0.144099
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.19085 7.72582
-  ave/max big velocity = 2.20262 5.4168
-Memory usage per processor = 7.83759 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    18.299191            0   0.25067776    37.859815    40.841906    5.7680841            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000    1.3155168         8201   0.22979575    37.225304    37.439685    8.9588433        14577           56           56            0          687        57680        11236         8201    1.0283377            0            5            0 
-    2000   0.82290815         8187   0.22918912    37.206746    37.340849    6.0607727        14326           56           56            0         1524        57680        11236         8187    1.0127464            0            5            0 
-    3000   0.99928391         8168   0.22921842    37.182777    37.345623    10.268998        14389           68           68            0         2274        57680        11236         8168     1.023497            0            5            0 
-    4000    1.0348458         8200   0.22920437    37.174693    37.343335    9.8954805        14335           51           51            0         3047        57680        11236         8200    1.0156984            0            5            0 
-    5000    1.1496765         8199   0.22939095    37.186379    37.373733    8.0143223        14444           74           74            0         3868        57680        11236         8199    1.0104858            0            5            0 
-    6000   0.91767381         8225    0.2292466    37.200668    37.350215    8.6189298        14131           61           61            0         4594        57680        11236         8225    1.0147272            0            5            0 
-    7000   0.74806752         8203   0.22888634    37.169611    37.291518    9.8613421        14121           53           53            1         5322        57680        11236         8203    1.0198289            0           19            0 
-    8000    1.1177867         8213   0.22924801    37.168286    37.350444     7.911691        14380           62           62            0         6024        57680        11236         8213    1.0066799            0           19            0 
-    9000    1.1258411         8209   0.22939703    37.191253    37.374723    6.7377179        14350           51           51            0         6821        57680        11236         8209    1.0081225            0           19            0 
-   10000    1.0597344         8182   0.22919436    37.169006    37.341703    9.7769156        14372           48           48            0         7543        57680        11236         8182    1.0099373            0           19            0 
-   11000    1.3337199         8159   0.22943046    37.162823     37.38017    6.0897666        14359           58           58            0         8245        57680        11236         8159    1.0046221            0           19            0 
-   12000    1.0280975         8184   0.22894286    37.133186    37.300728     2.555317        14162           51           51            0         8935        57680        11236         8184    1.0010306            0           19            0 
-   13000    1.2318533         8190   0.22921487    37.144299    37.345045    6.1739989        14285           64           64            0         9634        57680        11236         8190    1.0138112            0           19            0 
-   14000    1.1851991         8215   0.22915708    37.142485    37.335629    7.8380175        14151           66           66            0        10407        57680        11236         8215    1.0008011            0           19            0 
-   15000   0.89853218         8214   0.22897294    37.159201    37.305628    4.0743953        14077           61           61            0        11069        57680        11236         8214    1.0041341            0           19            0 
-   16000    1.0295974         8176   0.22891205    37.127921    37.295708    8.7527117        14000           48           48            0        11832        57680        11236         8176    1.0089653            0           23            0 
-   17000    1.1793664         8219   0.22906268    37.128056    37.320249    5.2583304        14268           57           57            0        12490        57680        11236         8219    1.0157079            0           23            0 
-   18000   0.90486919         8180   0.22891008    37.147927    37.295387    4.8498125        13939           64           64            0        13154        57680        11236         8180   0.99700921            0           23            0 
-   19000   0.81486319         8219   0.22881911    37.147773    37.280566    1.6338041        13934           59           59            1        13861        57680        11236         8219    1.0099189            0           23            0 
-   20000    1.0146287         8180   0.22896254    37.138587    37.303934    2.1682593        14057           45           45            0        14593        57680        11236         8180    1.0009466            0           23            0 
-   21000    1.3031463         8164   0.22920646    37.131309    37.343674     6.570906        13944           65           65            0        15323        57680        11236         8164   0.98955239            0           23            0 
-   22000    1.1258162         8174   0.22915084    37.151147    37.334613    9.0817519        14052           56           56            0        16042        57680        11236         8174    1.0083228            0           23            0 
-   23000    1.1421222         8217   0.22906722    37.134865    37.320989    8.0529401        14143           66           66            0        16797        57680        11236         8217    1.0111161            0           23            0 
-   24000   0.77402445         8168   0.22883056    37.156294    37.282431    6.8609899        14258           62           62            0        17559        57680        11236         8168    1.0080535            0           23            0 
-   25000   0.94006632         8215   0.22879533    37.123496    37.276692    3.8570839        14446           48           48            0        18267        57680        11236         8215    1.0087899            0           23            0 
-   26000    1.2808563         8192   0.22933112    37.155253    37.363985    5.3591484        13960           54           54            1        19004        57680        11236         8192    1.0101851            0           79            0 
-   27000    1.0266075         8171   0.22898652    37.140542    37.307841    2.9961422        14049           56           56            1        19683        57680        11236         8171   0.99950217            0           79            0 
-   28000   0.98185838         8199   0.22867129    37.096475    37.256481    12.080529        14106           61           62            0        20417        57680        11236         8199    1.0026548            0           79            0 
-   29000   0.96921352         8192   0.22861802    37.089856    37.247802     8.257635        13891           63           64            0        21169        57680        11236         8192    1.0128041            0           79            0 
-   30000    1.0107665         8223   0.22866616    37.090929    37.255646    9.4280788        14021           61           61            1        21863        57680        11236         8223    1.0034994            0           79            0 
-   31000    1.1859435         8195   0.22877222    37.079661    37.272926    7.3863353        14093           78           78            0        22480        57680        11236         8195    0.9945582            0           79            0 
-   32000    1.2951374         8172   0.22897044    37.094161     37.30522    6.4322363        13792           52           52            0        23151        57680        11236         8172    1.0026092            0           79            0 
-   33000   0.82899919         8176   0.22823894    37.050944    37.186041   0.60210493        13797           62           62            0        23903        57680        11236         8176    1.0051075            0           79            0 
-   34000   0.96685714         8165   0.22828901    37.036637    37.194199    8.1409866        13837           50           50            0        24591        57680        11236         8165    1.0157895            0           79            0 
-   35000   0.95645753         8206   0.22833008    37.045022    37.200889    8.9956195        14130           63           63            0        25340        57680        11236         8206    1.0030424            0           79            0 
-   36000    1.2933379         8197   0.22879201    37.065383     37.27615    8.3938627        13978           80           80            0        26085        57680        11236         8197    1.0094497            0           79            0 
-   37000    1.1511434         8176   0.22861016    37.058929    37.246523    4.9481995        13856           49           49            1        26759        57680        11236         8176    1.0063722            0           79            0 
-   38000   0.93310274         8181   0.22837532    37.056199     37.20826    5.9575015        13949           51           51            0        27445        57680        11236         8181    1.0152607            0           79            0 
-   39000    1.0352467         8215   0.22861437    37.078501    37.247208    9.8519532        14109           69           69            0        28245        57680        11236         8215     1.005523            0           79            0 
-   40000    1.2696427         8193   0.22885162    37.078957    37.285862    8.4680587        13931           54           55            0        28960        57680        11236         8193    1.0014074            0           79            0 
-   41000    1.3270531         8193   0.22909573    37.109374    37.325634    4.3731598        14115           62           62            0        29668        57680        11236         8193    1.0022493            0           79            0 
-   42000    1.3650738         8183   0.22911257    37.105921    37.328377    6.6345101        13659           52           52            0        30400        57680        11236         8183    1.0145834            0           79            0 
-   43000    1.0780084         8209   0.22855316     37.06156    37.237235    5.5147087        14062           52           52            0        31092        57680        11236         8209    1.0031365            0           79            0 
-   44000   0.96146724         8193   0.22846546    37.066263    37.222946    9.7967735        13699           56           56            0        31771        57680        11236         8193    1.0072364            0           79            0 
-   45000    1.1733618         8200    0.2286481    37.061489    37.252703    9.8058881        13967           51           52            0        32532        57680        11236         8200    1.0068663            0           79            0 
-   46000   0.94784989         8211   0.22845052    37.066048    37.220513    5.8834756        13944           34           35            0        33213        57680        11236         8211    1.0080225            0           79            0 
-   47000    1.2354771         8207   0.22859598    37.042876    37.244213    6.1458407        13851           56           56            0        33886        57680        11236         8207    1.0151781            0           79            0 
-   48000    1.0834097         8164   0.22835968    37.029157    37.205712    6.7378814        13944           56           56            0        34578        57680        11236         8164    1.0128575            0           79            0 
-   49000    0.9386786         8208   0.22837254    37.054838    37.207808    5.0809383        13618           53           53            0        35328        57680        11236         8208    1.0045622            0           79            0 
-   50000     1.047176         8154   0.22859126    37.072791    37.243442    4.8016981        13847           55           55            0        36059        57680        11236         8154    1.0005378            0           79            0 
-   51000    1.0943417         8222   0.22844191    37.040773     37.21911    7.9359541        13897           61           61            0        36711        57680        11236         8222    1.0036343            0           79            0 
-   52000    1.2811259         8200   0.22871149    37.054255    37.263031    4.9958687        13744           56           56            0        37402        57680        11236         8200    1.0049188            0           79            0 
-   53000    1.0997162         8218   0.22853173     37.05453    37.233743    4.6772882        13967           65           65            0        38082        57680        11236         8218    1.0054533            0           79            0 
-   54000   0.97625718         8185    0.2283994     37.05309    37.212184    5.9026406        13741           69           69            0        38761        57680        11236         8185   0.99393606            0           79            0 
-   55000   0.97919465         8192   0.22835234    37.044944    37.204516    6.8419755        13990           58           58            0        39453        57680        11236         8192    1.0103052            0           79            0 
-   56000   0.86300824         8181   0.22842164    37.075169    37.215808    6.8288348        13751           57           57            0        40118        57680        11236         8181   0.99683099            0           79            0 
-   57000   0.89429559         8181   0.22851743    37.085677    37.231414     9.378853        13746           72           72            0        40730        57680        11236         8181    1.0086882            0           79            0 
-   58000    1.0853441         8172   0.22857719    37.064279     37.24115    7.4580035        13869           58           58            1        41462        57680        11236         8172    1.0092141            0           79            0 
-   59000    1.0149632         8199   0.22868187    37.092803    37.258205    8.2913359        13720           54           54            0        42159        57680        11236         8199    1.0082738            0           79            0 
-   60000   0.99214038         8241   0.22871146    37.101344    37.263026    7.9905647        13776           67           67            0        42858        57680        11236         8241    1.0027929            0           79            0 
-   61000   0.95721926         8211    0.2285241     37.07651    37.232501    11.837258        13907           62           62            0        43565        57680        11236         8211    1.0201117            0           79            0 
-   62000    1.1457294         8195   0.22866514    37.068769     37.25548    9.7934944        13796           40           40            1        44292        57680        11236         8195     1.005192            0           79            0 
-   63000    1.1096177         8193   0.22863037    37.068989    37.249815    8.0809047        13984           54           55            0        44986        57680        11236         8193    1.0076438            0           79            0 
-   64000    1.1643495         8168   0.22860016    37.055147    37.244893    4.7376475        13857           50           50            1        45657        57680        11236         8168     1.002011            0           79            0 
-   65000    1.2172585         8201   0.22845803    37.023368    37.221736    8.9744616        13610           53           53            0        46295        57680        11236         8201    1.0033999            0           79            0 
-   66000   0.99924611         8189   0.22807344    36.996237    37.159077    8.5854786        13849           49           49            0        46944        57680        11236         8189     1.015528            0           79            0 
-   67000    1.2543542         8165   0.22831075    36.993327     37.19774    5.0081411        13906           57           58            1        47666        57680        11236         8165    1.0189753            0           79            0 
-   68000    1.0360874         8205   0.22812149     36.99806    37.166904    2.2431831        13650           52           52            0        48363        57680        11236         8205    1.0076864            0           79            0 
-   69000   0.69755552         8218   0.22766249    36.978446    37.092121    4.2769033        13654           51           51            0        49044        57680        11236         8218     1.009863            0           79            0 
-   70000   0.90921994         8167   0.22796236    36.992809    37.140978    9.3555738        13927           52           52            0        49793        57680        11236         8167    1.0015807            0           79            0 
-   71000   0.95608837         8177   0.22797832    36.987772    37.143579    8.0740708        13612           63           63            0        50464        57680        11236         8177    1.0097491            0           79            0 
-   72000    1.0374855         8192   0.22803745     36.98414    37.153212    4.4789755        13561           52           52            0        51127        57680        11236         8192   0.99496724            0           79            0 
-   73000   0.90636338         8214   0.22783374     36.97232    37.120024    9.3364171        13598           53           53            0        51799        57680        11236         8214    1.0078219            0           79            0 
-   74000    1.1869638         8179   0.22834625    37.010094    37.203525    4.8292929        13771           51           51            0        52500        57680        11236         8179   0.98865277            0           79            0 
-   75000    1.0177351         8188   0.22826506    37.024443    37.190296    5.1808505        13508           55           55            0        53183        57680        11236         8188   0.99903558            0           79            0 
-   76000     1.062496         8230   0.22820987    37.008158    37.181305    8.1032524        13769           58           58            0        53864        57680        11236         8230   0.99397021            0           79            0 
-   77000    0.9762027         8131   0.22831271    37.038975     37.19806    10.309798        13787           47           47            0        54553        57680        11236         8131    1.0066289            0           79            0 
-   78000    1.0688533         8160   0.22855677     37.06364    37.237824    7.4800503        13224           58           58            0        55248        57680        11236         8160    1.0073477            0           79            0 
-   79000    1.2598513         8151   0.22844942    37.015024    37.220333    7.4724924        13859           63           63            0        55911        57680        11236         8151    1.0065168            0           79            0 
-   80000    1.1044575         8176   0.22834306    37.023019    37.203005    3.0142586        13579           62           62            0        56611        57680        11236         8176    1.0008704            0           79            0 
-   81000    1.2756491         8205   0.22853748    37.026797     37.23468     6.434309        13702           52           52            0        57313        57680        11236         8205    1.0058366            0           79            0 
-   82000    1.1276926         8193   0.22857049    37.056287    37.240059    11.825248        13621           63           63            0        58011        57680        11236         8193    1.0113537            0           79            0 
-   83000   0.96941691         8173   0.22824759    37.029471     37.18745    2.9152799        13478           48           49            0        58712        57680        11236         8173    1.0168819            0           79            0 
-   84000    1.0770325         8186   0.22821292    37.006285    37.181802    5.0626072        13733           60           61            0        59433        57680        11236         8186    1.0177757            0           79            0 
-   85000    1.1959489         8175    0.2284266    37.021719    37.216615    5.3844747        13964           55           55            0        60226        57680        11236         8175     1.007371            0           79            0 
-   86000     1.035779         8204   0.22845952    37.053185    37.221979    7.5428558        13713           64           64            0        60982        57680        11236         8204    1.0110801            0           79            0 
-   87000    1.1878573         8204   0.22836412    37.012859    37.206436    3.1124447        13655           47           47            0        61668        57680        11236         8204    1.0034968            0           79            0 
-   88000   0.98402924         8206   0.22815704    37.012337    37.172698    10.613422        13947           56           56            0        62325        57680        11236         8206    1.0081468            0           79            0 
-   89000   0.83763529         8199   0.22807071    37.022127    37.158631    5.4628281        13966           50           50            0        63012        57680        11236         8199   0.99956322            0           79            0 
-   90000    1.1976672         8187   0.22849599    37.032745    37.227921    5.5583762        13903           43           43            0        63697        57680        11236         8187    1.0047573            0           79            0 
-   91000   0.94863742         8188   0.22818061    37.021945    37.176537     5.157692        13859           46           46            0        64382        57680        11236         8188    1.0041894            0           79            0 
-   92000    1.2038427         8172   0.22846103    37.026042    37.222224     6.685059        13675           57           57            0        65081        57680        11236         8172    1.0036906            0           79            0 
-   93000   0.95835618         8210   0.22828548    37.037446    37.193622    8.0038227        13826           57           58            0        65761        57680        11236         8210    1.0076646            0           79            0 
-   94000    1.2451267         8197   0.22856138    37.035665    37.238575    3.6305666        13918           62           62            0        66462        57680        11236         8197    1.0110913            0           79            0 
-   95000   0.82128549         8206   0.22809174    37.028218    37.162057    8.7024273        13817           44           44            0        67185        57680        11236         8206    1.0032224            0           79            0 
-   96000   0.83473128         8199   0.22820935     37.04519     37.18122    8.1258155        14167           54           54            0        67912        57680        11236         8199    1.0035561            0           79            0 
-   97000   0.98924493         8196   0.22847944    37.064014    37.225225    8.9964529        14039           48           51            0        68608        57680        11236         8196    1.0007515            0           79            0 
-   98000    1.1749668         8211   0.22879851    37.085733     37.27721    7.0283734        13850           58           59            0        69305        57680        11236         8211   0.99525651            0           79            0 
-   99000    1.3269705         8163   0.22890919    37.078994    37.295241    9.7962294        13885           63           63            0        69994        57680        11236         8163     1.011015            0          107            0 
-  100000    1.0020436         8171   0.22867221    37.093336    37.256632    4.9455304        14102           55           56            0        70707        57680        11236         8171    1.0072865            0          107            0 
-Loop time of 33.9872 on 8 procs for 100000 steps with 43990 atoms
-
-Pair  time (%) = 0.379981 (1.11801)
-Neigh time (%) = 2.01801 (5.93757)
-Comm  time (%) = 2.30255 (6.77476)
-Outpt time (%) = 0.00694308 (0.0204285)
-Other time (%) = 29.2797 (86.1492)
-
-Nlocal:    5498.75 ave 6445 max 4431 min
-Histogram: 1 0 0 2 1 1 0 1 1 1
-Nghost:    62.5 ave 70 max 57 min
-Histogram: 3 0 0 1 1 0 1 0 1 1
-Neighs:    207 ave 365 max 92 min
-Histogram: 1 1 1 1 2 0 1 0 0 1
-
-Total # of neighbors = 1656
-Ave neighs/atom = 0.0376449
-Neighbor list builds = 5000
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

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

@@ -1,291 +0,0 @@
-LAMMPS (1 Feb 2014)
-# SRD viscosity demo - rigid star 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.star fix molprop NULL Molecules
-  orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  270 atoms
-
-set		type 1 mass 1.0
-  270 settings made for mass
-group		big type 1
-270 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
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 big rigid molecule
-30 rigid bodies with 270 atoms
-fix		2 all enforce2d
-
-#dump		1 all atom 10 dump.star.equil
-
-thermo		100
-run		1000
-Memory usage per processor = 2.64859 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0            0            0            0   0.24721146 
-     100            0     3.291475            0     3.291475   0.69158089 
-     200            0    4.6176595            0    4.6176595   0.71737945 
-     300            0    7.0921814            0    7.0921814    1.2163497 
-     400            0    8.3666709            0    8.3666709   0.50645957 
-     500            0    10.630838            0    10.630838   0.72764487 
-     600            0     12.42157            0     12.42157    1.0130599 
-     700            0    14.349074            0    14.349074   0.74795509 
-     800            0    16.464746            0    16.464746     1.054549 
-     900            0    18.253108            0    18.253108   0.51551753 
-    1000            0    20.699563            0    20.699563    1.8084662 
-Loop time of 0.0484946 on 8 procs for 1000 steps with 270 atoms
-
-Pair  time (%) = 0.00250834 (5.17242)
-Neigh time (%) = 0.000999629 (2.06132)
-Comm  time (%) = 0.0154877 (31.9369)
-Outpt time (%) = 0.000273734 (0.564464)
-Other time (%) = 0.0292252 (60.2649)
-
-Nlocal:    33.75 ave 42 max 22 min
-Histogram: 1 0 1 0 0 2 0 1 1 2
-Nghost:    23.375 ave 30 max 14 min
-Histogram: 1 0 1 0 0 2 1 0 1 2
-Neighs:    52.25 ave 69 max 27 min
-Histogram: 1 0 1 0 1 0 1 1 1 2
-
-Total # of neighbors = 418
-Ave neighs/atom = 1.54815
-Neighbor list builds = 176
-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 = 0.108465 0.108465 0.108465
-create_atoms	2 region plane
-Created 60025 atoms
-
-set		type 2 mass 0.1
-  60025 settings made for mass
-group		small type 2
-60025 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 16305 atoms, new total = 43990
-
-# 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
-30 rigid bodies with 270 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 1000 dump.star.mp
-
-#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 = 43720 270
-  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: 106 106 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
-  SRD per actual grid cell = 5.55866
-  SRD viscosity = 0.235582
-  big/SRD mass density ratio = 0.144099
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 4.19085 7.72582
-  ave/max big velocity = 2.20262 5.4168
-Memory usage per processor = 7.83759 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    18.299191            0   0.25067776    37.859815    40.841906    5.7680841            0            0            0            0            0            0            0            0            0            0            0            0 
-    1000    1.3197888         8196    0.2296966    37.208454     37.42353    7.4694369        14388           59           59            0          707        57680        11236         8196    1.0259754            0            5            0 
-    2000    1.5789784         8192   0.22993088    37.204387    37.461702    7.6252927        14352           56           56            0         1521        57680        11236         8192    1.0168955            0            7            0 
-    3000     1.286186         8153    0.2296947    37.213621    37.423222    8.8624394        14533           73           73            0         2299        57680        11236         8153    1.0109574            0            7            0 
-    4000    2.0862082         8194   0.23044604     37.20566    37.545635    7.8064365        14228           48           48            0         3068        57680        11236         8194    1.0046224            0            7            0 
-    5000     1.892401         8172   0.23019301    37.196017    37.504409    7.9041579        14290           55           55            0         3866        57680        11236         8172     1.005673            0            7            0 
-    6000    2.1063411         8138   0.23041636    37.197543    37.540799    4.8468885        13803           47           47            0         4638        57680        11236         8138    1.0083722            0            7            0 
-    7000    2.3549938         8174   0.23071159    37.205123      37.5889    6.5703154        13773           58           58            0         5398        57680        11236         8174    1.0039365            0            7            0 
-    8000    3.0660305         8216   0.23155654    37.226914    37.726563    11.977404        13898           65           65            0         6180        57680        11236         8216   0.99586836            0            7            0 
-    9000    3.1510761         8203   0.23143756     37.19367    37.707178    7.2978028        13815           54           54            0         6985        57680        11236         8203   0.99794556            0            7            0 
-   10000    2.7472522         8196   0.23096076    37.181796    37.629496    11.336568        14012           59           59            0         7812        57680        11236         8196   0.99210203            0           11            0 
-   11000    2.1776587         8186   0.23038876    37.181424    37.536302    9.2106614        14063           64           64            0         8627        57680        11236         8186     1.003993            0           11            0 
-   12000    3.0146734         8196    0.2312123    37.179198    37.670478    5.9303705        14077           60           60            0         9436        57680        11236         8196   0.98496016            0           23            0 
-   13000    3.0029829         8179   0.23150759    37.229214    37.718589    7.3329148        14116           74           74            0        10339        57680        11236         8179    1.0039911            0           23            0 
-   14000    3.2942972         8191   0.23166868    37.207985    37.744833    9.6428846        14019           56           57            0        11290        57680        11236         8191   0.99410574            0           23            0 
-   15000    3.8480961         8213   0.23228155    37.217589    37.844686    2.1025549        13746           68           68            0        12175        57680        11236         8213    1.0011325            0           23            0 
-   16000    3.2573043         8195    0.2316418    37.209634    37.740454    8.1255708        13682           55           55            0        13104        57680        11236         8195    1.0061399            0           23            0 
-   17000    3.3579037         8186    0.2315443    37.177356     37.72457    9.8606039        13833           54           54            0        14034        57680        11236         8186     1.004156            0           23            0 
-   18000    4.7903055         8194   0.23307181    37.192799    37.973441    3.8090185        13914           55           55            1        15012        57680        11236         8194   0.98633014            0           23            0 
-   19000    4.4696839         8183   0.23293212    37.222288    37.950681    7.1931333        13499           54           54            0        15960        57680        11236         8183   0.98359656            0           23            0 
-   20000    5.0239019         8126   0.23355887    37.234085    38.052794    5.1504203        13600           58           58            0        16972        57680        11236         8126   0.98555755            0           23            0 
-   21000    4.6595948         8155   0.23275722    37.162845    37.922186    9.0375076        13965           73           74            0        17966        57680        11236         8155   0.99574348            0           23            0 
-   22000     4.043444         8124   0.23247599    37.217434    37.876366    3.9265975        13584           53           53            2        18989        57680        11236         8124    0.9943952            0           23            0 
-   23000    4.9981028         8127   0.23314549    37.170939    37.985445    4.2352191        13589           47           47            0        19958        57680        11236         8127   0.99276741            0           47            0 
-   24000    4.7542655         8145   0.23295434    37.179533    37.954302     7.365415        13753           51           51            0        20955        57680        11236         8145   0.99024306            0           47            0 
-   25000    4.2987054         8177   0.23252979    37.184601    37.885131    10.735771        13536           58           58            0        21994        57680        11236         8177   0.99215977            0           47            0 
-   26000    4.4136261         8170   0.23331629    37.294015    38.013272     14.25925        13842           58           58            0        22979        57680        11236         8170   0.99283174            0           47            0 
-   27000    4.0546007         8173   0.23283443    37.274016    37.934766      6.22969        13877           51           51            0        23997        57680        11236         8173   0.98496361            0           47            0 
-   28000    4.5919614         8151   0.23364384    37.318319    38.066638    4.9917488        13836           60           61            1        25071        57680        11236         8151   0.99390956            0           47            0 
-   29000    4.8025535         8189   0.23313849    37.201667    37.984305    4.7895172        13978           46           47            0        26121        57680        11236         8189   0.99018295            0           47            0 
-   30000    4.2835226         8139   0.23247583    37.178284     37.87634     8.994878        13988           61           61            0        27141        57680        11236         8139   0.98735471            0           47            0 
-   31000    5.4049428         8133   0.23373767    37.201121    38.081927    7.6419291        13771           58           58            0        28207        57680        11236         8133   0.98354883            0           47            0 
-   32000    5.0299584         8177   0.23336211    37.201041    38.020738    8.1206741        14036           55           55            0        29303        57680        11236         8177   0.98239013            0           47            0 
-   33000    4.2993816         8158   0.23320229     37.29406      37.9947    10.745167        13583           51           51            0        30344        57680        11236         8158   0.98952524            0           47            0 
-   34000    5.8334257         8179   0.23458355    37.269109    38.219741    11.094625        13921           62           62            0        31432        57680        11236         8179   0.98822406            0           47            0 
-   35000     6.481318         8168   0.23501133    37.233224    38.289439    7.9397445        13942           56           56            0        32518        57680        11236         8168   0.98830425            0           47            0 
-   36000     4.967891         8186   0.23366927    37.261199    38.070782    8.3979019        13952           51           51            0        33626        57680        11236         8186   0.99579665            0           47            0 
-   37000    5.3458808         8145    0.2337339    37.210132    38.081312    5.4177865        13659           55           55            0        34715        57680        11236         8145    1.0009582            0           47            0 
-   38000    6.3597955         8159   0.23479285    37.217431    38.253842    6.1408411        13754           55           56            0        35754        57680        11236         8159   0.98853252            0           47            0 
-   39000    6.1217173         8195   0.23447066    37.203737     38.20135    9.6016075        13756           70           70            0        36807        57680        11236         8195   0.98652299            0           47            0 
-   40000    5.0218059         8159   0.23370899    37.258886    38.077254    6.6460004        13603           56           56            1        37933        57680        11236         8159   0.98674585            0           47            0 
-   41000    5.5873722         8138   0.23429215     37.26173    38.172265    1.4183057        13634           51           52            1        39050        57680        11236         8138   0.98833769            0           47            0 
-   42000    5.5502013         8170   0.23405343    37.228895    38.133372    7.8338637        13913           72           72            0        40105        57680        11236         8170   0.99124609            0           47            0 
-   43000    4.6854143         8161   0.23326283    37.241013    38.004562     7.857085        13759           48           48            0        41187        57680        11236         8161   0.99649848            0           47            0 
-   44000    6.3172352         8180    0.2348893    37.240081    38.269557     12.59288        13810           55           55            0        42292        57680        11236         8180   0.99164669            0           47            0 
-   45000    6.1213322         8166   0.23449878    37.208381    38.205931    6.3760889        13854           48           49            0        43406        57680        11236         8166   0.98981447            0           47            0 
-   46000    5.0015874         8195   0.23354809    37.235965    38.051038    10.992836        13962           62           62            0        44527        57680        11236         8195   0.99128184            0           47            0 
-   47000    5.0499615         8190   0.23376151    37.262854    38.085811    8.7985849        14105           64           64            0        45653        57680        11236         8190   0.99020272            0           47            0 
-   48000     5.202255         8170   0.23400688    37.278013    38.125788    4.7389097        13754           51           51            0        46705        57680        11236         8170   0.98792999            0           47            0 
-   49000    5.6144741         8167   0.23429848    37.258346    38.173297    6.3247626        13953           51           51            1        47846        57680        11236         8167   0.99270232            0           47            0 
-   50000    6.3027505         8145    0.2347122    37.213588    38.240703    6.4424496        13843           59           59            0        49061        57680        11236         8145   0.99810926            0           47            0 
-   51000    5.2050769         8154   0.23390178     37.26043    38.108665    6.6143765        13999           51           51            0        50075        57680        11236         8154   0.99525977            0           47            0 
-   52000    5.4749884         8175   0.23418567    37.262697    38.154917    8.7256782        13916           51           51            0        51249        57680        11236         8175   0.99508289            0           47            0 
-   53000    5.1367735         8158   0.23393299    37.276645    38.113748    9.3248422        13910           41           41            0        52381        57680        11236         8158   0.98956839            0           47            0 
-   54000    4.8680584         8211   0.23402832    37.335968    38.129281    4.8979582        14214           63           64            0        53439        57680        11236         8211   0.98838908            0           47            0 
-   55000    4.6223848         8167   0.23347097    37.285196    38.038473    6.1898955        14162           46           46            0        54504        57680        11236         8167   0.97935238            0           47            0 
-   56000    4.9075747         8168   0.23409393    37.340218    38.139971     12.20686        13980           60           60            0        55540        57680        11236         8168   0.99885966            0           47            0 
-   57000    4.8736147         8143   0.23354696    37.256636    38.050854    3.9348529        13857           59           59            0        56680        57680        11236         8143   0.98434054            0           47            0 
-   58000    5.6134201         8162   0.23393276    37.198932    38.113711    3.7493067        13866           55           55            2        57767        57680        11236         8162   0.99041155            0           47            0 
-   59000     5.440371         8197   0.23353392    37.162151     38.04873    4.1297786        13748           67           67            0        58894        57680        11236         8197   0.98824623            0           47            0 
-   60000    5.2754075         8148   0.23359083    37.198307    38.058003    7.1427242        13781           55           55            0        60028        57680        11236         8148    0.9831827            0           47            0 
-   61000    5.8228233         8153   0.23438274     37.23812    38.187025    8.8839625        14019           48           48            0        61204        57680        11236         8153   0.98566731            0           47            0 
-   62000    5.7623285         8129   0.23480056    37.316052    38.255098     9.992341        13791           67           68            0        62385        57680        11236         8129   0.97338459            0           47            0 
-   63000     6.095315         8178   0.23455792    37.222257    38.215567    10.722535        14210           54           54            0        63448        57680        11236         8178   0.98135973            0           47            0 
-   64000    5.2494942         8189   0.23380158    37.236866    38.092339    4.4010329        13869           51           51            0        64538        57680        11236         8189   0.98071569            0           47            0 
-   65000    5.6534858         8151   0.23405328    37.212039    38.133348    8.9144953        14065           53           53            0        65661        57680        11236         8151   0.99589337            0           47            0 
-   66000    5.3999138         8165   0.23453061     37.33113    38.211116    7.3102657        13994           61           62            0        66785        57680        11236         8165   0.98715854            0           47            0 
-   67000    6.3619419         8183   0.23459518    37.184875    38.221636    4.0425684        13859           49           49            0        67944        57680        11236         8183   0.98479883            0           47            0 
-   68000    6.2170116         8157   0.23470153    37.225822    38.238965    9.3090925        13598           50           50            0        69121        57680        11236         8157   0.98683618            0           47            0 
-   69000    6.8545121         8179   0.23542272    37.239433    38.356465    9.4175179        13911           59           59            0        70316        57680        11236         8179   0.99828763            0           47            0 
-   70000    5.1476232         8154   0.23389653    37.268937    38.107809    7.6438157        13882           55           55            0        71380        57680        11236         8154   0.99088995            0           47            0 
-   71000    5.9284504         8161   0.23499148    37.320087    38.286205    9.1242845        13968           60           60            0        72478        57680        11236         8161   0.98627289            0           47            0 
-   72000    5.8044136         8180   0.23473312    37.298207    38.244111    6.6084298        14066           56           56            0        73653        57680        11236         8180   0.97959812            0           47            0 
-   73000    5.3690655         8148   0.23424676    37.289911     38.16487    8.7025002        14433           55           55            1        74740        57680        11236         8148   0.97949605            0           47            0 
-   74000    4.8144157         8192   0.23361625    37.277572    38.062144    7.6685178        14425           58           58            1        75918        57680        11236         8192   0.98949387            0           47            0 
-   75000    4.9424688         8143   0.23362551    37.258213    38.063652    5.5882668        13938           42           42            0        77080        57680        11236         8143   0.99602516            0           47            0 
-   76000    6.3017203         8178   0.23500247    37.261048    38.287995    5.2760401        13952           47           47            0        78240        57680        11236         8178   0.98484281            0           47            0 
-   77000    5.3086333         8208   0.23389726    37.242817    38.107928     4.034731        14052           47           47            0        79331        57680        11236         8208    0.9896033            0           47            0 
-   78000    6.1152265         8157   0.23546115    37.366171    38.362726    11.521489        13980           58           58            0        80446        57680        11236         8157   0.98562154            0           47            0 
-   79000    6.5034669         8173   0.23569944    37.341726     38.40155    5.0939756        14030           74           74            0        81663        57680        11236         8173   0.98837711            0           47            0 
-   80000    6.1688245         8182   0.23495003    37.274162    38.279451    6.3337593        14292           50           50            0        82872        57680        11236         8182   0.99316806            0           47            0 
-   81000    6.3818913         8189   0.23516767    37.274899    38.314911    9.0232294        14259           56           56            0        84072        57680        11236         8189   0.98467136            0           47            0 
-   82000     6.502454         8171   0.23498158    37.224932    38.284591    7.6685939        13970           63           63            0        85190        57680        11236         8171   0.99511647            0           47            0 
-   83000    7.2245962         8142   0.23564338    37.215075    38.392416    6.0363083        13789           61           61            0        86416        57680        11236         8142   0.99223565            0           47            0 
-   84000    6.3529888         8192   0.23477435    37.215526    38.250828    7.2109855        14062           52           52            0        87555        57680        11236         8192   0.98623425            0           47            0 
-   85000    6.5185235         8177   0.23516364    37.251976    38.314254     5.266764        14325           52           53            0        88732        57680        11236         8177   0.97895516            0           47            0 
-   86000     5.742959         8170   0.23432816    37.242243    38.178133    6.0834874        13922           48           48            0        89836        57680        11236         8170   0.99203022            0           47            0 
-   87000     6.548676         8177   0.23495538    37.213132    38.280324    6.2502744        14147           48           48            0        91035        57680        11236         8177   0.98829721            0           47            0 
-   88000    5.9500587         8193   0.23446634    37.231006    38.200645    6.2196893        13960           44           44            0        92206        57680        11236         8193   0.98956808            0           47            0 
-   89000    5.0591447         8174   0.23386574    37.278339    38.102793    11.164066        14071           54           54            0        93437        57680        11236         8174   0.99827748            0           47            0 
-   90000    6.4930795         8181   0.23544182    37.301445    38.359576    6.6167028        14183           63           63            1        94640        57680        11236         8181   0.99559871            0           47            0 
-   91000     6.489104         8187   0.23523152    37.267829    38.325313    6.4932786        14223           51           51            1        95718        57680        11236         8187   0.99090796            0           47            0 
-   92000    6.3543839         8184   0.23502776    37.256587    38.292116    7.1553807        14265           66           66            1        96903        57680        11236         8184   0.98979354            0           47            0 
-   93000    5.3818591         8195   0.23393122    37.236417     38.11346    7.9445503        14327           70           70            0        98138        57680        11236         8195    1.0030252            0           47            0 
-   94000    5.6818206         8171    0.2343696    37.258958    38.184885    5.7311019        13943           63           63            0        99306        57680        11236         8171   0.99691591            0           47            0 
-   95000    4.8295204         8160   0.23371941    37.291918    38.078951    4.5703653        13682           48           48            1       100491        57680        11236         8160    1.0078235            0           47            0 
-   96000    6.7415726         8191   0.23539566    37.253429    38.352056    11.837168        13783           53           53            1       101761        57680        11236         8191    1.0010125            0           49            0 
-   97000    6.5298825         8160    0.2354153    37.291126    38.355255    7.6012271        13688           65           65            0       103010        57680        11236         8160   0.99694671            0           49            0 
-   98000    6.2804965         8175   0.23496877    37.259015    38.282504    5.4636503        14041           55           55            0       104259        57680        11236         8175    1.0042653            0           49            0 
-   99000    5.7684681         8173    0.2344998     37.26605    38.206096    1.7807753        14082           58           59            0       105418        57680        11236         8173   0.99124491            0           49            0 
-  100000    6.1371898         8170   0.23495644     37.28036    38.280495    7.7665232        13908           53           53            0       106633        57680        11236         8170   0.98281247            0           49            0 
-Loop time of 34.1892 on 8 procs for 100000 steps with 43990 atoms
-
-Pair  time (%) = 0.361362 (1.05695)
-Neigh time (%) = 2.01143 (5.88324)
-Comm  time (%) = 2.27139 (6.64359)
-Outpt time (%) = 0.00694269 (0.0203067)
-Other time (%) = 29.5381 (86.3959)
-
-Nlocal:    5498.75 ave 6478 max 4726 min
-Histogram: 2 0 1 0 1 2 1 0 0 1
-Nghost:    52.875 ave 59 max 44 min
-Histogram: 1 0 1 0 1 0 1 0 2 2
-Neighs:    186.25 ave 293 max 81 min
-Histogram: 1 0 1 3 0 0 1 0 0 2
-
-Total # of neighbors = 1490
-Ave neighs/atom = 0.0338713
-Neighbor list builds = 5000
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

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

@@ -0,0 +1,321 @@
+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 - rigid star 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.star fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  270 atoms
+  read_data CPU = 0.011 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  270 settings made for mass
+group           big type 1
+270 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
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big rigid molecule
+  30 rigid bodies with 270 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.star.equil
+
+compute         tbig all temp/sphere
+thermo_modify   temp tbig
+
+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 = 38 38 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) = 5.562 | 5.562 | 5.562 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.3101488      0              0              0.21350573     0.32876464   
+       100   5.0954142      3.291475       0              4.1218387      1.0087565    
+       200   13.041252      4.6176595      0              6.7429006      1.5291618    
+       300   11.912727      7.0921814      0              9.0335147      1.9578844    
+       400   17.60886       8.3666709      0              11.236263      1.602563     
+       500   16.786375      10.630838      0              13.366396      1.7725508    
+       600   18.470347      12.42157       0              15.431552      2.1627885    
+       700   19.39794       14.349074      0              17.510219      1.9554238    
+       800   19.082984      16.464746      0              19.574566      2.2424126    
+       900   20.702091      18.253108      0              21.626782      1.8041661    
+      1000   18.299191      20.699563      0              23.681654      2.9475408    
+Loop time of 0.0585091 on 1 procs for 1000 steps with 270 atoms
+
+Performance: 7383466.593 tau/day, 17091.358 timesteps/s, 4.615 Matom-step/s
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.017165   | 0.017165   | 0.017165   |   0.0 | 29.34
+Neigh   | 0.0058479  | 0.0058479  | 0.0058479  |   0.0 |  9.99
+Comm    | 0.0028221  | 0.0028221  | 0.0028221  |   0.0 |  4.82
+Output  | 0.00017384 | 0.00017384 | 0.00017384 |   0.0 |  0.30
+Modify  | 0.03015    | 0.03015    | 0.03015    |   0.0 | 51.53
+Other   |            | 0.00235    |            |       |  4.02
+
+Nlocal:            270 ave         270 max         270 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             73 ave          73 max          73 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            418 ave         418 max         418 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 418
+Ave neighs/atom = 1.5481481
+Neighbor list builds = 176
+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 60025 atoms
+  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  create_atoms CPU = 0.013 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  60025 settings made for mass
+group           small type 2
+60025 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 = 19 19 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 16305 atoms, new total = 43990
+
+# 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
+  30 rigid bodies with 270 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
+
+uncompute       tbig
+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]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
+
+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.star
+
+#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 = 43720 270
+  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: 106 106 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
+  SRD per actual grid cell = 5.5586635
+  SRD viscosity = 0.23558168
+  big/SRD mass density ratio = 0.14409881
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1908497 7.725824
+  ave/max big velocity = 2.202625 5.4167964
+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 = 26.586808, 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) = 41.29 | 41.29 | 41.29 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   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.2074332      8227           0.22959643     37.210444      37.407211      7.9007359      14317          47             47             0              649            28900          11236          8227           1.0260288      0              3              0            
+      2000   1.2044605      8206           0.22945824     37.188414      37.384697      5.8738384      14470          63             63             0              1423           28900          11236          8206           1.018589       0              4              0            
+      3000   1.1060368      8226           0.22936549     37.189341      37.369584      4.7013136      14255          51             51             0              2207           28900          11236          8226           1.0007203      0              4              0            
+      4000   1.2395587      8236           0.2294891      37.187723      37.389725      5.7916781      14371          56             56             0              2916           28900          11236          8236           1.0229966      0              4              0            
+      5000   1.3332555      8236           0.22962818     37.195112      37.412383      10.662157      14373          61             61             0              3740           28900          11236          8236           1.0094713      0              4              0            
+      6000   1.2991744      8192           0.22957221     37.191547      37.403264      1.2016626      14145          56             58             0              4425           28900          11236          8192           1.0215234      0              4              0            
+      7000   1.0110737      8147           0.22923336     37.18329       37.348057      6.2493424      14200          59             59             0              5102           28900          11236          8147           1.0163405      0              4              0            
+      8000   0.79508387     8168           0.22908516     37.194343      37.323912      9.832591       14355          45             45             0              5839           28900          11236          8168           1.0063207      0              4              0            
+      9000   1.0340542      8207           0.2292515      37.1825        37.351013      11.458942      14220          54             54             0              6606           28900          11236          8207           1.0074421      0              4              0            
+     10000   0.96342976     8202           0.22912995     37.174206      37.33121       1.7523017      14308          53             53             0              7379           28900          11236          8202           1.0126923      0              4              0            
+Loop time of 18.5504 on 1 procs for 10000 steps with 43990 atoms
+
+Performance: 46575.737 tau/day, 539.071 timesteps/s, 23.714 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    | 0.21961    | 0.21961    | 0.21961    |   0.0 |  1.18
+Neigh   | 0.055763   | 0.055763   | 0.055763   |   0.0 |  0.30
+Comm    | 0.22073    | 0.22073    | 0.22073    |   0.0 |  1.19
+Output  | 0.0013822  | 0.0013822  | 0.0013822  |   0.0 |  0.01
+Modify  | 17.872     | 17.872     | 17.872     |   0.0 | 96.34
+Other   |            | 0.1812     |            |       |  0.98
+
+Nlocal:          43990 ave       43990 max       43990 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            138 ave         138 max         138 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1587 ave        1587 max        1587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1587
+Ave neighs/atom = 0.036076381
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:20

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

@@ -0,0 +1,321 @@
+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 - rigid star 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.star fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  270 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  270 settings made for mass
+group           big type 1
+270 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
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big rigid molecule
+  30 rigid bodies with 270 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.star.equil
+
+compute         tbig all temp/sphere
+thermo_modify   temp tbig
+
+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 = 38 38 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) = 5.554 | 5.554 | 5.555 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.3101488      0              0              0.21350573     0.32876464   
+       100   5.0954142      3.291475       0              4.1218387      1.0087565    
+       200   13.041252      4.6176595      0              6.7429006      1.5291618    
+       300   11.912727      7.0921814      0              9.0335147      1.9578844    
+       400   17.60886       8.3666709      0              11.236263      1.602563     
+       500   16.786375      10.630838      0              13.366396      1.7725508    
+       600   18.470347      12.42157       0              15.431552      2.1627885    
+       700   19.39794       14.349074      0              17.510219      1.9554238    
+       800   19.082984      16.464746      0              19.574566      2.2424126    
+       900   20.702091      18.253108      0              21.626782      1.8041661    
+      1000   18.299191      20.699563      0              23.681654      2.9475408    
+Loop time of 0.0312248 on 4 procs for 1000 steps with 270 atoms
+
+Performance: 13835169.963 tau/day, 32025.856 timesteps/s, 8.647 Matom-step/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0026978  | 0.0031211  | 0.0033489  |   0.5 | 10.00
+Neigh   | 0.0011292  | 0.0013054  | 0.0014446  |   0.3 |  4.18
+Comm    | 0.010095   | 0.010474   | 0.010975   |   0.3 | 33.54
+Output  | 0.00019592 | 0.00021948 | 0.00027642 |   0.0 |  0.70
+Modify  | 0.013333   | 0.013668   | 0.013952   |   0.2 | 43.77
+Other   |            | 0.002437   |            |       |  7.80
+
+Nlocal:           67.5 ave          80 max          54 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:          29.75 ave          33 max          26 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:          104.5 ave         135 max          72 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 418
+Ave neighs/atom = 1.5481481
+Neighbor list builds = 176
+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 60025 atoms
+  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  create_atoms CPU = 0.003 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  60025 settings made for mass
+group           small type 2
+60025 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 = 19 19 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 16305 atoms, new total = 43990
+
+# 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
+  30 rigid bodies with 270 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
+
+uncompute       tbig
+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]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
+
+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.star
+
+#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 = 43720 270
+  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: 106 106 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
+  SRD per actual grid cell = 5.5586635
+  SRD viscosity = 0.23558168
+  big/SRD mass density ratio = 0.14409881
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1908497 7.725824
+  ave/max big velocity = 2.202625 5.4167964
+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 = 26.586808, 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) = 14.19 | 14.19 | 14.2 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   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.4057114      8217           0.22974151     37.20177       37.430849      11.548865      14197          56             57             0              682            42436          11236          8217           1.0187465      0              3              0            
+      2000   1.0468288      8223           0.22932205     37.191914      37.362508      4.8322766      14185          60             60             0              1452           42436          11236          8223           1.0271433      0              64             0            
+      3000   0.89541606     8240           0.22921893     37.199787      37.345707      9.7555289      14770          60             60             0              2175           42436          11236          8240           1.0157844      0              64             0            
+      4000   1.021344       8222           0.22920858     37.177579      37.344021      6.2834235      14480          50             50             0              2951           42436          11236          8222           1.0130315      0              64             0            
+      5000   1.045809       8222           0.2294309      37.209813      37.380241      2.8847497      14109          59             60             0              3667           42436          11236          8222           1.0126872      0              64             0            
+      6000   1.1527336      8227           0.22933212     37.176296      37.364149      5.4760843      14597          42             42             0              4418           42436          11236          8227           1.0188272      0              64             0            
+      7000   1.1799559      8216           0.22941075     37.18467       37.376959      10.243848      14281          57             57             0              5154           42436          11236          8216           1.0063617      0              64             0            
+      8000   1.1913762      8188           0.22940126     37.181263      37.375413      5.7338518      14497          47             47             0              5878           42436          11236          8188           1.0076169      0              64             0            
+      9000   1.0587094      8230           0.22928172     37.183406      37.355936      5.7323116      14267          62             62             0              6550           42436          11236          8230           1.0108237      0              64             0            
+     10000   1.0359117      8165           0.22944086     37.21305       37.381865      9.4246373      14016          52             52             0              7246           42436          11236          8165           1.0147132      0              64             0            
+Loop time of 6.61179 on 4 procs for 10000 steps with 43990 atoms
+
+Performance: 130675.562 tau/day, 1512.449 timesteps/s, 66.533 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    | 0.041077   | 0.059027   | 0.07409    |   4.8 |  0.89
+Neigh   | 0.015706   | 0.017829   | 0.019903   |   1.1 |  0.27
+Comm    | 0.23742    | 0.25326    | 0.26722    |   2.1 |  3.83
+Output  | 0.00073333 | 0.00077549 | 0.00084859 |   0.0 |  0.01
+Modify  | 6.1477     | 6.174      | 6.2149     |   1.0 | 93.38
+Other   |            | 0.1069     |            |       |  1.62
+
+Nlocal:        10997.5 ave       11924 max       10204 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost:          64.25 ave          71 max          56 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:          395.5 ave         497 max         271 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 1582
+Ave neighs/atom = 0.035962719
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:07

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

@@ -0,0 +1,322 @@
+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 - rigid star 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.star fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  270 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  270 settings made for mass
+group           big type 1
+270 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
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big rigid molecule
+  30 rigid bodies with 270 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.star.equil
+
+compute         tbig all temp/sphere
+thermo_modify   temp tbig
+
+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 = 38 38 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) = 5.562 | 5.562 | 5.562 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.3101488      0              0              0.21350573     0.32876464   
+       100   5.0954142      3.291475       0              4.1218387      1.0087565    
+       200   13.041252      4.6176595      0              6.7429006      1.5291618    
+       300   11.912727      7.0921814      0              9.0335147      1.9578844    
+       400   17.60886       8.3666709      0              11.236263      1.602563     
+       500   16.786375      10.630838      0              13.366396      1.7725508    
+       600   18.470347      12.42157       0              15.431552      2.1627885    
+       700   19.39794       14.349074      0              17.510219      1.9554238    
+       800   19.082984      16.464746      0              19.574566      2.2424126    
+       900   20.702091      18.253108      0              21.626782      1.8041661    
+      1000   18.299191      20.699563      0              23.681654      2.9475408    
+Loop time of 0.0474374 on 1 procs for 1000 steps with 270 atoms
+
+Performance: 9106745.092 tau/day, 21080.428 timesteps/s, 5.692 Matom-step/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.01287    | 0.01287    | 0.01287    |   0.0 | 27.13
+Neigh   | 0.0050573  | 0.0050573  | 0.0050573  |   0.0 | 10.66
+Comm    | 0.0024616  | 0.0024616  | 0.0024616  |   0.0 |  5.19
+Output  | 0.00025461 | 0.00025461 | 0.00025461 |   0.0 |  0.54
+Modify  | 0.024714   | 0.024714   | 0.024714   |   0.0 | 52.10
+Other   |            | 0.00208    |            |       |  4.38
+
+Nlocal:            270 ave         270 max         270 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             73 ave          73 max          73 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            418 ave         418 max         418 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 418
+Ave neighs/atom = 1.5481481
+Neighbor list builds = 176
+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 60025 atoms
+  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  create_atoms CPU = 0.014 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  60025 settings made for mass
+group           small type 2
+60025 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 = 19 19 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 16305 atoms, new total = 43990
+
+# 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
+  30 rigid bodies with 270 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
+
+uncompute       tbig
+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]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
+
+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.star.mp
+
+#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 = 43720 270
+  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: 106 106 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
+  SRD per actual grid cell = 5.5586635
+  SRD viscosity = 0.23558168
+  big/SRD mass density ratio = 0.14409881
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1908497 7.725824
+  ave/max big velocity = 2.202625 5.4167964
+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 = 26.586808, 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) = 41.29 | 41.29 | 41.29 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   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   0.82328749     8250           0.22908506     37.18973       37.323895      6.0611499      14546          54             54             0              691            28900          11236          8250           1.025654       0              3              0            
+      2000   1.314397       8198           0.22953802     37.183497      37.397695      7.6050033      14165          65             65             0              1503           28900          11236          8198           1.0137885      0              3              0            
+      3000   1.4327928      8174           0.22973765     37.196727      37.430219      4.8441566      14378          43             43             0              2274           28900          11236          8174           1.0052401      0              5              0            
+      4000   1.9637993      8194           0.23036966     37.213164      37.533191      4.9697216      14203          51             51             1              3241           28900          11236          8194           1.0129187      0              245            0            
+      5000   1.6886675      8206           0.22987561     37.177507      37.452697      10.972628      14155          56             56             0              4073           28900          11236          8206           1.0024406      0              245            0            
+      6000   1.7377657      8197           0.23000322     37.190296      37.473487      6.3971042      14331          57             57             0              4929           28900          11236          8197           1.0094945      0              245            0            
+      7000   2.4106224      8199           0.23083719     37.216521      37.609363      5.1070917      14144          49             49             0              5822           28900          11236          8199           1.0074275      0              245            0            
+      8000   2.5161884      8202           0.2306663      37.171475      37.581521      12.156127      14263          67             67             0              6667           28900          11236          8202           1.006502       0              245            0            
+      9000   2.9100148      8188           0.23124828     37.202115      37.67634       6.1326598      14171          66             67             0              7443           28900          11236          8188           0.99544201     0              245            0            
+     10000   3.4714177      8206           0.23192306     37.220567      37.78628       5.1293943      14100          48             49             0              8272           28900          11236          8206           1.0022763      0              245            0            
+Loop time of 17.933 on 1 procs for 10000 steps with 43990 atoms
+
+Performance: 48179.444 tau/day, 557.632 timesteps/s, 24.530 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    | 0.22008    | 0.22008    | 0.22008    |   0.0 |  1.23
+Neigh   | 0.054046   | 0.054046   | 0.054046   |   0.0 |  0.30
+Comm    | 0.20917    | 0.20917    | 0.20917    |   0.0 |  1.17
+Output  | 0.001317   | 0.001317   | 0.001317   |   0.0 |  0.01
+Modify  | 17.275     | 17.275     | 17.275     |   0.0 | 96.33
+Other   |            | 0.1731     |            |       |  0.97
+
+Nlocal:          43990 ave       43990 max       43990 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            122 ave         122 max         122 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1569 ave        1569 max        1569 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1569
+Ave neighs/atom = 0.035667197
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:19

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

@@ -0,0 +1,322 @@
+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 - rigid star 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.star fix molprop NULL Molecules
+Reading data file ...
+  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  270 atoms
+  read_data CPU = 0.001 seconds
+
+set             type 1 mass 1.0
+Setting atom values ...
+  270 settings made for mass
+group           big type 1
+270 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
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             1 big rigid molecule
+  30 rigid bodies with 270 atoms
+fix             2 all enforce2d
+
+#dump           1 all atom 10 dump.star.equil
+
+compute         tbig all temp/sphere
+thermo_modify   temp tbig
+
+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 = 38 38 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) = 5.554 | 5.554 | 5.555 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.3101488      0              0              0.21350573     0.32876464   
+       100   5.0954142      3.291475       0              4.1218387      1.0087565    
+       200   13.041252      4.6176595      0              6.7429006      1.5291618    
+       300   11.912727      7.0921814      0              9.0335147      1.9578844    
+       400   17.60886       8.3666709      0              11.236263      1.602563     
+       500   16.786375      10.630838      0              13.366396      1.7725508    
+       600   18.470347      12.42157       0              15.431552      2.1627885    
+       700   19.39794       14.349074      0              17.510219      1.9554238    
+       800   19.082984      16.464746      0              19.574566      2.2424126    
+       900   20.702091      18.253108      0              21.626782      1.8041661    
+      1000   18.299191      20.699563      0              23.681654      2.9475408    
+Loop time of 0.0311841 on 4 procs for 1000 steps with 270 atoms
+
+Performance: 13853197.664 tau/day, 32067.587 timesteps/s, 8.658 Matom-step/s
+97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0027957  | 0.0031644  | 0.0035219  |   0.5 | 10.15
+Neigh   | 0.001171   | 0.0012862  | 0.0014036  |   0.3 |  4.12
+Comm    | 0.0099068  | 0.010544   | 0.011053   |   0.4 | 33.81
+Output  | 0.00014281 | 0.00016091 | 0.00020823 |   0.0 |  0.52
+Modify  | 0.013319   | 0.013618   | 0.014047   |   0.2 | 43.67
+Other   |            | 0.002411   |            |       |  7.73
+
+Nlocal:           67.5 ave          80 max          54 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:          29.75 ave          33 max          26 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:          104.5 ave         135 max          72 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 418
+Ave neighs/atom = 1.5481481
+Neighbor list builds = 176
+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 60025 atoms
+  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
+  create_atoms CPU = 0.003 seconds
+
+set             type 2 mass 0.1
+Setting atom values ...
+  60025 settings made for mass
+group           small type 2
+60025 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 = 19 19 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 16305 atoms, new total = 43990
+
+# 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
+  30 rigid bodies with 270 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
+
+uncompute       tbig
+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]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
+
+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.star.mp
+
+#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 = 43720 270
+  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: 106 106 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
+  SRD per actual grid cell = 5.5586635
+  SRD viscosity = 0.23558168
+  big/SRD mass density ratio = 0.14409881
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 4.1908497 7.725824
+  ave/max big velocity = 2.202625 5.4167964
+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 = 26.586808, 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) = 14.19 | 14.19 | 14.2 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   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
+      1000   1.3506473      8186           0.22968182     37.201018      37.421123      5.6398923      14572          54             54             0              654            42436          11236          8186           1.0228728      0              3              0            
+      2000   0.99412905     8212           0.22952823     37.234094      37.3961        8.5863689      14257          69             69             0              1394           42436          11236          8212           1.0206297      0              12             0            
+      3000   1.4469134      8192           0.22970951     37.189841      37.425634      8.0408437      14439          53             53             0              2178           42436          11236          8192           1.0121272      0              12             0            
+      4000   1.6112802      8172           0.2303679      37.270324      37.532903      8.3379947      14098          57             57             0              2992           42436          11236          8172           1.0171443      0              12             0            
+      5000   2.0436283      8191           0.23016186     37.166298      37.499334      7.1370191      14030          49             49             0              3804           42436          11236          8191           1.0054513      0              12             0            
+      6000   2.2894073      8184           0.2303867      37.162878      37.535967      7.6496143      13970          50             50             0              4662           42436          11236          8184           1.0084738      0              12             0            
+      7000   2.1640822      8183           0.23045121     37.193812      37.546477      7.1526683      13926          56             57             0              5445           42436          11236          8183           1.0046108      0              15             0            
+      8000   2.8851243      8199           0.23121762     37.201176      37.671344      9.1644504      13849          58             58             0              6237           42436          11236          8199           1.0081629      0              15             0            
+      9000   2.6422092      8180           0.23070839     37.157795      37.588377      2.4816571      13651          70             70             0              7007           42436          11236          8180           1.0089869      0              15             0            
+     10000   2.7121051      8189           0.23087145     37.172972      37.614945      11.176036      13901          63             64             0              7845           42436          11236          8189           1.0023484      0              15             0            
+Loop time of 6.56969 on 4 procs for 10000 steps with 43990 atoms
+
+Performance: 131513.146 tau/day, 1522.143 timesteps/s, 66.959 Matom-step/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.037869   | 0.059232   | 0.073664   |   5.4 |  0.90
+Neigh   | 0.015688   | 0.017835   | 0.019891   |   1.1 |  0.27
+Comm    | 0.22905    | 0.24375    | 0.26098    |   2.3 |  3.71
+Output  | 0.00069058 | 0.00071614 | 0.00078869 |   0.0 |  0.01
+Modify  | 6.1124     | 6.1385     | 6.1881     |   1.2 | 93.44
+Other   |            | 0.1096     |            |       |  1.67
+
+Nlocal:        10997.5 ave       12305 max       10259 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:          58.25 ave          73 max          48 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:         402.75 ave         520 max         207 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 1611
+Ave neighs/atom = 0.03662196
+Neighbor list builds = 500
+Dangerous builds = 0
+Total wall time: 0:00:06

examples/ASPHERE/tri/in.tri.srd

@@ -85,7 +85,7 @@ compute		10 all property/atom corner1x corner1y corner1z &
 #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
 #               c_10[7] c_10[8] c_10[9]
 
-run		10000
+run             1000
 
 #undump          1
 #undump          2
@@ -104,4 +104,4 @@ fix	        2 small srd 20 big 1.0 1.0 49894 &
 
 fix             3 all deform 1 xy erate 0.05 units box remap v
 
-run		40000
+run             2000

examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8

@@ -1,812 +0,0 @@
-LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
-WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
-# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
-
-units		lj
-atom_style	tri
-atom_modify	first big map yes
-
-read_data	data.tri.srd
-Reading data file ...
-  orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  1500 atoms
-  1500 triangles
-  read_data CPU = 0.007 seconds
-
-# add small particles as hi density lattice
-
-lattice		sc 0.4
-Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
-region		box block INF INF INF INF INF INF
-lattice		sc 20.0
-Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
-create_atoms	2 region box
-Created 91125 atoms
-  using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
-  create_atoms CPU = 0.002 seconds
-
-group		big type 1
-1500 atoms in group big
-group		small type 2
-91125 atoms in group small
-set		group small mass 0.01
-Setting atom values ...
-  91125 settings made for mass
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 1.5
-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
-
-delete_atoms	overlap 1.5 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 = 1.8
-  ghost atom cutoff = 1.8
-  binsize = 0.9, bins = 19 19 19
-  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/3d
-      bin: standard
-  (2) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
-Deleted 76354 atoms, new total = 16271
-
-# SRD run
-
-reset_timestep	0
-
-velocity	small create 1.44 87287 loop geom
-
-neighbor	0.3 multi
-neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule/intra big include big
-
-comm_modify	mode multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style	tri/lj 3.5
-pair_coeff	1 1 0.1 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/small molecule #langevin 1.0 1.0 0.1 12398
-  create bodies CPU = 0.000 seconds
-  125 rigid bodies with 1500 atoms
-  1.8601881 = max distance from body owner to body atom
-fix	        2 small srd 20 big 1.0 1.0 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip inside ignore
-
-fix		3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
-
-# diagnostics
-
-compute		tsmall small temp/deform
-compute		tbig big temp
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-
-compute_modify  tbig extra/dof -4500
-
-compute		1 big erotate/asphere
-compute		2 all ke
-compute		3 all pe
-variable	toteng equal (c_1+c_2+c_3)/atoms
-
-thermo		100
-thermo_style	custom step f_1 c_tsmall temp press f_2[9] f_2[4]
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
-
-compute		10 all property/atom corner1x corner1y corner1z 		corner2x corner2y corner2z corner3x corner3y corner3z
-
-#dump		1 all custom 500 dump1.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump1.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
-
-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
-WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
-WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
-SRD info:
-  SRD/big particles = 14771 1500
-  big particle diameter max/min = 2.9202881 0.87320391
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 17 17 17
-  SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
-  SRD per actual grid cell = -3.9971745
-  SRD viscosity = -34.162587
-  big/SRD mass density ratio = -3.3753691
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
-WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 19.970837 35.150443
-  ave/max big velocity = 0 0
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 3.8
-  ghost atom cutoff = 3.8
-  binsize = 16.874681, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair tri/lj, perpetual
-      attributes: half, newton on
-      pair build: half/multi/newton
-      stencil: half/multi/3d
-      bin: multi
-Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
-   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
-         0   0              1.4401779      0             -0.15917996     0              0            
-       100   0.36662911     1.1475389      0.24585067     1.0290503      1.1382325      18           
-       200   0.73133134     1.0558153      0.49986673     0.73932383     1.049638       34           
-       300   1.1229361      1.0218621      0.82641583     0.7589689      1.0205369      40           
-       400   1.5826262      0.99541508     1.2201293      0.69171726     0.99190857     52           
-       500   1.8834563      0.99351667     1.4778822      1.0147794      1.0005581      63           
-       600   2.4225372      0.98954834     1.8740966      1.1362893      0.99760042     61           
-       700   3.0172772      0.99153625     2.3351502      1.3284877      0.98731355     39           
-       800   3.5307913      1.0012521      2.6477224      1.1404922      0.9846605      52           
-       900   3.757064       0.99743944     2.7220653      1.4078087      0.97538456     55           
-      1000   4.3165268      1.002214       3.055501       1.2252972      0.99123745     63           
-      1100   4.2796945      1.0075233      3.1022956      1.1893685      1.0139864      69           
-      1200   4.3719315      1.0037271      3.0054509      1.3886162      1.002661       64           
-      1300   4.5628012      0.99368316     3.2690604      1.3621012      0.9810568      56           
-      1400   4.6954389      0.99365088     3.1940001      1.8485712      0.99571089     71           
-      1500   5.0270163      0.99455258     3.4120396      1.5992539      0.98294263     77           
-      1600   5.5897797      1.0021621      3.647347       1.7796904      0.98967622     66           
-      1700   5.5330194      1.0130853      3.6407996      1.8005429      1.0068955      62           
-      1800   5.3606928      1.0090284      3.5863618      1.3308757      1.0214092      59           
-      1900   5.6086195      1.0071865      3.7427101      1.5296314      0.99886937     55           
-      2000   5.3726474      1.0064207      3.603621       1.9473142      0.99999816     54           
-      2100   5.836183       1.0124553      3.7321841      1.7889397      1.0188986      59           
-      2200   5.5090061      1.0113832      3.5884963      1.6617781      1.0071583      59           
-      2300   5.4011211      1.0095947      3.520406       1.8937582      0.99689983     61           
-      2400   5.2219281      1.0053246      3.3699458      1.7231672      0.99899754     59           
-      2500   5.7695275      1.0141459      3.6211469      1.7767598      1.0143133      65           
-      2600   5.4206253      1.0182828      3.521774       2.0800518      1.0081603      70           
-      2700   5.1401099      1.0085209      3.4200563      2.4019836      1.0107652      59           
-      2800   6.5420721      1.0159876      4.1996904      1.863842       1.0160738      61           
-      2900   5.9082962      1.0106921      3.7223419      2.0586998      1.0073885      67           
-      3000   5.6556123      1.0099021      3.6768976      1.921987       1.0068962      76           
-      3100   5.2913762      1.0008567      3.4103831      1.9831969      0.99187526     80           
-      3200   5.1032361      0.99756662     3.1967156      2.2448433      0.99743574     93           
-      3300   5.2622386      1.0024934      3.3325614      2.0078097      1.0047789      86           
-      3400   5.1247527      0.99810102     3.1363556      1.8907269      0.98936508     82           
-      3500   4.9424333      1.0009344      3.2153968      1.9002728      0.99161849     71           
-      3600   5.1243735      1.0037377      3.3117313      2.1267438      1.0078943      65           
-      3700   5.5045819      1.0006119      3.5686193      2.3466538      0.99876164     68           
-      3800   5.5355384      1.0022639      3.6701457      2.0383269      1.0008683      76           
-      3900   6.4915796      1.0137733      4.3225864      2.6996933      1.0064787      79           
-      4000   6.6631737      1.0236248      4.3057163      2.6352666      1.0255232      75           
-      4100   6.2999507      1.0263876      4.0101385      2.5479077      1.0168303      79           
-      4200   6.7902489      1.0247392      4.4616158      2.4926177      1.0191403      91           
-      4300   6.505908       1.0182073      4.0675428      2.168754       1.0177101      74           
-      4400   5.9554283      1.0115938      3.5787297      2.9258144      1.0133896      72           
-      4500   6.2276609      1.0202416      3.8211204      2.5308249      1.0174385      74           
-      4600   6.0485727      1.0195757      3.8217434      2.6421797      1.0201441      78           
-      4700   6.511063       1.0220764      3.933486       2.8591093      1.0147269      83           
-      4800   6.9478172      1.0106414      4.345402       3.3257663      1.00469        85           
-      4900   6.7547045      1.0211842      4.1874576      3.6503845      1.022873       94           
-      5000   7.2603949      1.0234313      4.5393985      3.4667806      1.0222306      105          
-      5100   7.1899652      1.0256566      4.5421834      3.8137207      1.0317242      99           
-      5200   7.1960739      1.026746       4.4288606      3.5523675      1.0242269      97           
-      5300   7.1294458      1.017883       4.5799808      3.3917274      1.0145317      99           
-      5400   6.2810892      1.0291953      4.0109229      2.8604571      1.0289438      97           
-      5500   6.15246        1.0288734      3.8714587      3.2760394      1.0210757      89           
-      5600   6.5860526      1.0192882      4.0272883      3.3124298      1.0096258      93           
-      5700   7.0296116      1.0097293      4.2652722      3.6049788      1.012463       82           
-      5800   6.8372302      1.0140065      4.2205065      4.3686183      1.0088542      93           
-      5900   7.8887098      1.0090612      4.9724078      4.457317       1.0045137      92           
-      6000   10.120663      1.0312443      6.3025192      4.72018        1.0374722      91           
-      6100   9.1318265      1.0304199      5.7084296      4.244548       1.0259056      97           
-      6200   8.9758903      1.0295285      5.1842704      4.870955       1.0178851      95           
-      6300   9.0088218      1.022484       5.3742805      5.1554352      1.0138365      101          
-      6400   10.470322      1.0287848      6.4602103      4.5461489      1.0335978      105          
-      6500   11.100779      1.0347405      6.9630121      4.9840664      1.0339044      99           
-      6600   10.139333      1.0476079      6.4284839      4.5523893      1.0433517      104          
-      6700   8.9706766      1.0386262      5.8387485      4.247024       1.0408151      101          
-      6800   7.7799532      1.0362651      4.9946283      4.6093924      1.0274763      102          
-      6900   8.0866551      1.0337743      4.9942769      4.1679939      1.0454805      102          
-      7000   8.0224277      1.0193598      4.9380527      3.9173115      1.0185001      109          
-      7100   7.8361001      1.0211143      4.872673       5.3471479      1.024779       110          
-      7200   7.8542147      1.0057183      4.8666653      4.668317       0.99980296     122          
-      7300   7.9313852      1.0159181      5.0062527      4.1410294      1.0195705      114          
-      7400   7.2769846      1.0155245      4.6349779      4.9138895      1.0005886      119          
-      7500   7.5974523      1.0196295      4.7918247      4.2525935      1.0211412      124          
-      7600   6.7835063      1.0203187      4.2674694      4.9251624      1.0218296      113          
-      7700   6.4039017      1.0119494      4.1086667      5.5240525      1.0078246      118          
-      7800   7.0715134      1.0149015      4.2450776      4.8796778      1.0164737      125          
-      7900   6.3626535      1.02294        4.202778       4.482164       1.0235878      136          
-      8000   6.2423869      1.0212553      4.0460303      5.2753307      1.0124884      132          
-      8100   6.550891       1.0223318      4.2993545      5.2634985      1.0163244      143          
-      8200   6.9122202      1.008347       4.3551124      5.4108909      1.0084913      142          
-      8300   6.9104634      1.0103936      4.4622206      5.6762373      0.99559355     143          
-      8400   6.4918879      1.0084381      4.1050732      5.8389788      1.0036021      135          
-      8500   7.4377218      1.0216662      4.5229841      5.5431311      1.0260799      123          
-      8600   7.572198       1.0228381      4.9058913      7.1028185      1.0015164      116          
-      8700   8.204675       1.03457        5.2231696      6.4790244      1.0214635      132          
-      8800   8.3118914      1.0381333      5.1795799      6.7437722      1.0290086      132          
-      8900   8.2559198      1.0268665      5.218352       7.2191395      1.019804       138          
-      9000   8.0403128      1.0339414      4.9310394      6.4942331      1.041527       156          
-      9100   7.1773079      1.0397062      4.4993688      7.0272109      1.0388012      167          
-      9200   7.1793935      1.0373589      4.3481663      7.4894459      1.0078785      157          
-      9300   8.3705146      1.0248112      5.1036971      8.2173072      1.010168       156          
-      9400   9.4935002      1.0252907      5.7846951      9.7466018      1.028941       170          
-      9500   9.5208037      1.0371093      5.9635099      7.6444933      1.022673       165          
-      9600   8.9992217      1.0292895      5.6224192      8.8071452      1.0101362      169          
-      9700   8.682661       1.0422224      5.3997636      8.6827834      1.0337928      149          
-      9800   7.6191562      1.0350948      4.7198842      8.6125595      1.0300395      151          
-      9900   8.0910913      1.0319432      4.8843183      7.9013334      1.0272495      167          
-     10000   7.4438347      1.0186098      4.7184985      8.999795       0.99762661     177          
-Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
-
-Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
-99.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 33.647     | 64.106     | 79.639     | 169.5 | 39.49
-Neigh   | 0.30808    | 0.44033    | 0.50863    |   9.8 |  0.27
-Comm    | 26.611     | 43.438     | 74.998     | 215.7 | 26.76
-Output  | 0.0072573  | 0.0087791  | 0.0097993  |   0.9 |  0.01
-Modify  | 53.171     | 54.121     | 55.362     |  12.3 | 33.34
-Other   |            | 0.2104     |            |       |  0.13
-
-Nlocal:        2033.88 ave        2601 max        1413 min
-Histogram: 1 2 0 0 0 0 2 1 1 1
-Nghost:        1647.25 ave        1714 max        1617 min
-Histogram: 4 0 1 0 0 1 1 0 0 1
-Neighs:        12482.8 ave       17009 max        8679 min
-Histogram: 1 1 1 0 1 1 2 0 0 1
-
-Total # of neighbors = 99862
-Ave neighs/atom = 6.1374224
-Neighbor list builds = 562
-Dangerous builds = 0
-
-#undump          1
-#undump          2
-unfix		3
-
-change_box      all triclinic
-Changing box ...
-  triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
-
-fix	        2 small srd 20 big 1.0 1.0 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip tstat yes inside ignore
-
-#dump		1 all custom 500 dump2.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump2.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
-
-fix		3 all deform 1 xy erate 0.05 units box remap v
-
-run		40000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-SRD info:
-  SRD/big particles = 14771 1500
-  big particle diameter max/min = 2.9202881 0.87320391
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 13 13 13
-  SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
-  SRD per actual grid cell = -2.775698
-  SRD viscosity = -12.180602
-  big/SRD mass density ratio = -5.5653033
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
-WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
-  # of rescaled SRD velocities = 1
-  ave/max small velocity = 16.14994 40
-  ave/max big velocity = 1.6952661 5.2200074
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 3.8
-  ghost atom cutoff = 3.8
-  binsize = 13.499745, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair tri/lj, perpetual
-      attributes: half, newton on
-      pair build: half/multi/newton/tri
-      stencil: half/multi/3d/tri
-      bin: multi
-Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
-   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
-     10000   7.4438347      1.0189789      4.7184481      7.9505614      0              0            
-     10100   7.0770142      1.0021471      4.4491455      6.606701       1              141          
-     10200   6.7628072      1.002308       4.152988       8.5190386      1              125          
-     10300   6.5333319      1.0007472      4.1295404      8.2341747      1              109          
-     10400   6.3237519      1.0024029      3.8636034      9.4058128      1              95           
-     10500   6.6411054      1.0026261      4.2975997      7.6122304      1              82           
-     10600   5.7470775      1.0004827      3.7959947      7.3091777      1              67           
-     10700   5.9744919      1.0014977      3.6885649      7.5517197      1              59           
-     10800   5.8028731      1.0029627      3.7553961      6.2787087      1              49           
-     10900   5.3755286      1.0019318      3.5334739      7.1318348      1              41           
-     11000   5.3915962      1.001463       3.483172       7.6362496      1              40           
-     11100   5.8683672      1.0022459      3.6697589      6.9711866      1              33           
-     11200   5.4351801      0.99956703     3.4548447      7.0745257      1              29           
-     11300   4.9397513      1.0008287      3.1990325      6.0917337      1              27           
-     11400   4.9159845      1.0017862      3.0005677      7.653817       1              26           
-     11500   4.9243103      1.0013135      3.1799841      7.744414       1              23           
-     11600   5.2036357      1.0017984      3.2963749      7.540477       1              22           
-     11700   4.8991892      1.0020757      3.1773032      8.7218471      1              27           
-     11800   4.9489399      1.003438       3.1679764      7.1605486      1              26           
-     11900   4.82398        1.0019946      3.1939566      7.1397869      1              21           
-     12000   4.3531411      1.000532       2.8321416      7.6672501      1              23           
-     12100   4.8226081      1.0018898      3.0382137      6.8343432      1              25           
-     12200   4.7456418      1.0032116      2.9186038      7.3067818      1              20           
-     12300   4.4280468      1.0005857      2.734593       8.0365684      1              22           
-     12400   4.7311239      1.0000982      2.8898839      7.9231831      1              22           
-     12500   4.7261054      1.0016127      2.9090517      7.6085854      1              24           
-     12600   4.7719025      1.0016702      2.9736761      7.6101796      1              26           
-     12700   4.386248       1.001394       2.8508378      6.4765102      1              28           
-     12800   4.3313538      1.0019737      2.6258221      6.3164681      1              19           
-     12900   4.2219861      1.0007469      2.5345699      7.0901077      1              22           
-     13000   4.1775643      1.0011891      2.5807017      7.3579938      1              25           
-     13100   4.3060837      1.0008671      2.5974066      6.9301328      1              22           
-     13200   4.3529062      0.99996469     2.7571632      6.7806287      1              21           
-     13300   4.2178709      1.000673       2.7819091      7.6449064      1              18           
-     13400   4.2714169      1.0021294      2.7280794      8.0986691      1              18           
-     13500   4.3430969      1.0037732      2.6768429      8.1267941      1              18           
-     13600   4.3664374      1.0016083      2.6470186      6.2797727      1              20           
-     13700   4.4904769      1.0008993      2.7885718      7.7410193      1              22           
-     13800   4.2966193      1.001532       2.73862        7.9651302      1              21           
-     13900   4.4003185      1.0009984      2.7484129      8.7160439      1              24           
-     14000   4.5948292      1.0011748      2.9051777      7.842121       1              22           
-     14100   4.6901122      1.0001265      2.9404111      8.9953816      1              20           
-     14200   4.8517518      0.99998743     2.9647625      6.6450509      1              22           
-     14300   4.889628       1.0018051      3.0891097      7.2671824      1              20           
-     14400   4.578862       1.0010629      2.8239776      6.1317183      1              23           
-     14500   4.0865406      1.0013917      2.5119661      6.864665       1              19           
-     14600   4.30688        1.0009041      2.6817814      6.9007433      1              18           
-     14700   4.1295726      1.002342       2.6032093      7.1441648      1              15           
-     14800   4.2176021      1.0015157      2.7332903      6.8394683      1              16           
-     14900   4.2012664      0.99986345     2.6498409      7.4568241      1              15           
-     15000   4.6124269      1.0014751      2.9584178      7.9341875      1              16           
-     15100   4.947327       1.0010615      3.0784409      7.6241305      1              21           
-     15200   5.253281       1.002095       3.3093754      8.1872718      1              25           
-     15300   5.2642369      1.0017799      3.1511136      7.4668389      1              25           
-     15400   5.1967916      1.0029407      3.247548       8.0840111      1              23           
-     15500   5.7465412      1.001896       3.468834       9.5990471      1              15           
-     15600   6.2245772      1.0021086      3.6127689      7.8242016      1              19           
-     15700   5.5626191      0.99984979     3.3893723      7.8124588      1              20           
-     15800   5.5945727      1.0010291      3.3442448      7.0116922      1              17           
-     15900   5.4450219      1.0006248      3.3132381      8.4803413      1              15           
-     16000   5.7800459      1.001449       3.5002534      8.7989456      1              19           
-     16100   6.1168718      1.0008109      3.8081142      8.0119729      1              18           
-     16200   5.4901649      1.0020643      3.3673653      7.3483134      1              17           
-     16300   5.4051694      1.0015652      3.3560012      7.4641983      1              19           
-     16400   5.4237612      1.0012686      3.3816406      7.3845086      1              14           
-     16500   5.1935593      1.001754       3.3340381      7.8607712      1              16           
-     16600   5.539343       1.0021073      3.4164309      8.1541097      1              12           
-     16700   5.8922923      1.0013792      3.553426       7.5220576      1              14           
-     16800   5.956937       1.0005959      3.7630589      8.7417987      1              13           
-     16900   5.469721       1.0016219      3.5531223      8.6721994      1              13           
-     17000   5.3110154      1.001142       3.4167244      7.4644182      1              15           
-     17100   5.9226035      0.99918238     4.0244287      6.5172028      1              16           
-     17200   5.4897042      0.99981565     3.4350691      5.6840394      1              20           
-     17300   5.4302636      1.0021571      3.421473       6.4317025      1              21           
-     17400   5.5559131      1.0013807      3.4951403      6.874191       1              24           
-     17500   5.4068006      1.0010448      3.4506835      7.7069504      1              22           
-     17600   4.9283792      1.0007628      3.1736308      7.3098058      1              20           
-     17700   4.9319722      0.99935896     3.0956257      8.2120111      1              15           
-     17800   4.6842391      1.00037        2.9602433      7.4116352      1              17           
-     17900   4.7714682      1.0009332      2.9666778      7.5925131      1              17           
-     18000   4.7233188      1.0035687      3.0991778      7.1636357      1              10           
-     18100   4.6487958      1.0020255      3.10781        6.8468658      1              12           
-     18200   4.6284129      1.0012617      3.089724       6.3082275      1              13           
-     18300   4.7136404      0.99962415     3.1261978      7.3359556      1              15           
-     18400   5.0367681      1.0011016      3.2413493      8.3910633      1              14           
-     18500   4.9658104      1.0025407      3.2420827      7.4701216      1              17           
-     18600   4.6100059      1.0014508      3.0216884      6.553483       1              17           
-     18700   4.3246452      1.0016721      2.7810363      6.7450293      1              19           
-     18800   4.9415788      1.0012406      3.1661907      7.5544034      1              18           
-     18900   5.3930915      1.000138       3.2557456      7.350955       1              21           
-     19000   5.1938599      1.0007364      3.2398733      6.5397956      1              22           
-     19100   5.4433048      1.0019191      3.2699245      8.3625772      1              22           
-     19200   6.1303261      1.0004005      3.7823203      8.0537369      1              22           
-     19300   5.5762518      1.0008117      3.5689121      8.3714373      1              22           
-     19400   5.1316743      0.9999834      3.099381       7.405287       1              23           
-     19500   5.2064799      1.0012007      3.3059455      7.3499127      1              25           
-     19600   5.1650099      1.0023314      3.3759492      7.3637616      1              21           
-     19700   5.8316278      1.0023317      3.601564       7.153887       1              19           
-     19800   5.6435147      1.0010657      3.4967581      6.8899334      1              21           
-     19900   5.4071193      0.99961357     3.4977894      6.1068438      1              20           
-     20000   5.5058495      1.000982       3.5185057      8.5657603      1              19           
-     20100   5.6551271      1.0025852      3.5672369      7.8242273      1              20           
-     20200   5.7196886      1.002283       3.6010925      7.1449072      1              22           
-     20300   5.5593553      1.0009987      3.4363398      8.4141755      1              21           
-     20400   5.5550247      1.001081       3.3950874      8.0222131      1              20           
-     20500   5.4510415      0.99997273     3.5505093      7.5243655      1              18           
-     20600   5.8014064      1.0007611      3.8084579      7.6583499      1              18           
-     20700   5.7337315      1.0020309      3.7973684      8.7376766      1              17           
-     20800   5.2512898      0.99901254     3.5027763      7.8902791      1              14           
-     20900   5.3245034      1.0014504      3.3354615      6.7030716      1              17           
-     21000   5.2071731      1.0020459      3.3881369      5.8616999      1              20           
-     21100   5.3187535      1.0010762      3.2845672      8.1422146      1              21           
-     21200   5.5298545      0.99942313     3.4393978      7.1183144      1              22           
-     21300   5.8430744      1.0008652      3.719408       7.8522038      1              20           
-     21400   5.8190457      1.0017046      3.5624252      7.8150165      1              20           
-     21500   6.004585       1.0035276      3.9161914      7.7719377      1              21           
-     21600   6.7202635      0.99970072     3.9642141      8.7934294      1              18           
-     21700   6.8590346      1.0007883      4.4285217      8.9014638      1              20           
-     21800   6.627638       1.0012117      4.1154082      8.3153026      1              22           
-     21900   7.8281047      1.0008299      4.8842343      8.4016227      1              20           
-     22000   7.200038       1.0014681      4.4141419      9.4091956      1              18           
-     22100   7.7442011      1.0018051      4.7850371      8.9885489      1              15           
-     22200   7.4770203      1.0033558      4.7512643      8.4898148      1              17           
-     22300   8.1080801      1.0000019      5.2725185      9.2314625      1              14           
-     22400   7.8068311      1.0020672      4.9055683      8.4064748      1              12           
-     22500   7.4594636      1.0008427      4.6586396      8.5102986      1              11           
-     22600   6.9380609      1.0024634      4.2435619      10.395118      1              16           
-     22700   6.9338066      1.001056       4.3436179      7.9126284      1              18           
-     22800   6.8049493      1.0020052      4.1443407      7.8228868      1              18           
-     22900   6.2280158      1.0021474      3.7695343      7.3179647      1              20           
-     23000   5.649403       1.0017128      3.5941976      7.2964709      1              19           
-     23100   5.3203116      1.001912       3.3807399      6.6454551      1              15           
-     23200   5.8172882      1.0005742      3.6625896      8.4256312      1              15           
-     23300   5.9647182      1.0015466      3.9106019      8.3303303      1              14           
-     23400   5.9784055      1.0034542      3.7229235      7.7934273      1              14           
-     23500   5.377627       1.00192        3.5481778      6.8195124      1              17           
-     23600   5.4807136      1.0014662      3.563123       7.6356376      1              18           
-     23700   5.8896329      1.0013553      3.7990694      8.5513408      1              13           
-     23800   6.3463707      0.9999403      3.9609397      8.5741923      1              11           
-     23900   6.656669       1.0014998      4.1993183      9.0862996      1              13           
-     24000   7.583723       1.0025057      4.7628652      7.5007245      1              20           
-     24100   6.9868359      1.0014089      4.4369841      7.692833       1              25           
-     24200   7.1966062      1.0013149      4.4384528      9.5264821      1              18           
-     24300   6.7765706      1.0007065      4.3500477      9.4974154      1              16           
-     24400   7.0853466      1.0013246      4.409163       9.2215823      1              17           
-     24500   6.9603823      1.0004247      4.4866051      7.7870058      1              20           
-     24600   6.9208291      0.99953329     4.2298144      6.5732392      1              21           
-     24700   6.5005518      1.0026848      4.0003505      7.8094715      1              22           
-     24800   5.8421948      1.0012055      3.6686768      7.6078157      1              26           
-     24900   5.8410604      1.0023428      3.746177       6.8971309      1              22           
-     25000   5.8728511      1.0001747      3.7170134      7.4456816      1              19           
-     25100   6.0217168      1.000624       3.7756108      6.6542452      1              20           
-     25200   6.1939015      1.0017861      3.8943084      9.395821       1              25           
-     25300   6.161998       1.0010373      3.9255122      6.2228884      1              28           
-     25400   5.5850406      1.0018505      3.5129832      7.2551309      1              24           
-     25500   6.0286276      1.0009028      3.8580887      6.8065265      1              24           
-     25600   5.6262228      1.0005097      3.4574446      7.5061246      1              21           
-     25700   6.1348187      1.0009828      3.8073512      7.4818375      1              17           
-     25800   6.09781        1.0026426      3.9585383      9.0915939      1              21           
-     25900   6.2673667      1.0002269      3.8182813      9.2134822      1              21           
-     26000   6.6001776      1.0020444      4.041386       8.0403555      1              18           
-     26100   6.3063025      1.0016633      3.8649839      8.8149734      1              19           
-     26200   6.0046983      1.002332       3.5380766      8.6145656      1              17           
-     26300   5.9627788      1.0005401      3.56864        6.7821213      1              15           
-     26400   5.0547314      0.9998295      3.2106781      9.2935351      1              15           
-     26500   5.256781       1.0013131      3.2946631      8.8590275      1              15           
-     26600   5.6250355      1.0023929      3.5243033      8.8985058      1              17           
-     26700   6.0197165      1.0018323      3.7973947      7.3093402      1              17           
-     26800   5.4556541      1.0015309      3.4295107      8.2342049      1              18           
-     26900   5.420428       1.0024996      3.4374201      7.1444636      1              16           
-     27000   6.165624       1.0019174      3.8726016      8.6588275      1              20           
-     27100   6.7131697      1.0006541      4.266264       8.7063389      1              24           
-     27200   6.4855163      1.0016139      4.2029778      7.667611       1              29           
-     27300   6.0525608      1.000478       3.9169723      7.4515279      1              25           
-     27400   6.1426194      1.0014522      3.9176108      6.8689671      1              24           
-     27500   6.5981349      1.0001143      4.0620686      8.6804552      1              27           
-     27600   6.7827138      1.0016694      4.2764286      9.3912843      1              21           
-     27700   6.6368902      1.0025149      4.1452128      9.1814523      1              24           
-     27800   6.9791025      1.0019486      4.3989933      7.9446882      1              24           
-     27900   6.617142       1.0015736      4.360571       9.3732108      1              26           
-     28000   7.2818263      1.0014101      4.6041512      8.2398587      1              28           
-     28100   7.2543709      1.0007625      4.5724787      7.7373488      1              22           
-     28200   7.0631847      1.0023922      4.4021705      8.3290554      1              29           
-     28300   7.2999952      1.0012593      4.4655563      8.612666       1              27           
-     28400   7.4124538      1.0014043      4.5011335      8.379391       1              29           
-     28500   7.0350937      1.0011392      4.3528091      7.8167375      1              24           
-     28600   7.9659642      1.0031684      4.8732467      8.0661929      1              30           
-     28700   7.2865919      1.0010958      4.6650146      8.0325989      1              32           
-     28800   7.7039529      1.0027912      4.8299888      9.5471747      1              30           
-     28900   8.3288847      1.0012438      5.0785288      8.8964877      1              31           
-     29000   7.9348665      1.0021794      4.9393968      9.5531767      1              31           
-     29100   8.2473389      1.0013795      4.9890359      9.7697184      1              29           
-     29200   8.6383362      1.0018356      4.9856954      7.6402719      1              25           
-     29300   8.2504592      1.0011048      4.9631793      7.9466724      1              24           
-     29400   8.0502922      1.0010516      5.2521065      8.4515028      1              26           
-     29500   7.9475896      1.0012951      4.8584644      9.1225463      1              19           
-     29600   8.5641641      1.0016228      5.4361335      9.2045399      1              23           
-     29700   8.9932021      1.0011848      5.5727205      8.6045729      1              23           
-     29800   8.0320178      1.0019073      5.2837013      8.9335413      1              22           
-     29900   8.2676522      1.0012734      5.2213798      8.8966896      1              24           
-     30000   9.1848984      1.001747       5.9147628      12.096129      1              27           
-     30100   10.184519      0.99977427     6.4260136      11.140491      1              27           
-     30200   9.271472       1.0023983      6.0252189      9.6954338      1              30           
-     30300   9.0751572      1.000851       5.6010295      9.734426       1              28           
-     30400   9.4581261      1.0018449      5.6987258      9.70456        1              34           
-     30500   9.1574751      0.99944001     5.582217       9.300318       1              27           
-     30600   8.619312       1.001388       5.3503985      8.2759155      1              26           
-     30700   7.9370031      1.0026674      5.0702831      8.5368014      1              28           
-     30800   7.9221619      1.0019077      5.1278637      11.046922      1              26           
-     30900   9.9722884      1.0025903      6.4055506      10.167311      1              25           
-     31000   8.8648667      0.99962676     5.4777514      10.142102      1              21           
-     31100   8.576344       1.000906       5.3216342      8.7984921      1              18           
-     31200   7.8480974      1.0010341      4.9584917      9.0696437      1              16           
-     31300   8.3536183      1.0005758      5.208516       9.7971514      1              15           
-     31400   8.5301933      1.0007603      5.2241536      9.0257241      1              17           
-     31500   8.5196226      1.0018215      5.0576064      8.8847294      1              19           
-     31600   8.1470823      1.0023147      4.9182956      9.0205413      1              20           
-     31700   8.1475888      1.0005764      5.1814113      9.0603162      1              16           
-     31800   7.8629717      1.0014194      4.9221218      9.366291       1              16           
-     31900   7.7206559      1.0021082      4.9167636      7.4136735      1              16           
-     32000   7.5152809      1.0004752      4.6330638      8.830959       1              16           
-     32100   8.2693974      1.0011751      4.9094804      9.427636       1              13           
-     32200   8.3067661      0.9997006      4.9036865      9.0374633      1              17           
-     32300   7.2068514      1.0007866      4.3580755      8.6445065      1              17           
-     32400   6.885063       1.0011887      4.1528011      8.1199454      1              16           
-     32500   6.9147014      1.0020825      4.160405       7.5398034      1              19           
-     32600   6.8809668      1.000971       4.3312782      8.2157688      1              16           
-     32700   6.4818892      1.0000885      3.9433899      7.309605       1              22           
-     32800   6.6875555      1.0018674      4.1017504      7.2327183      1              22           
-     32900   7.6118502      0.99975736     4.4498951      8.5072395      1              19           
-     33000   7.7576909      1.0022061      4.7239551      9.2132467      1              22           
-     33100   7.8616235      1.000482       5.0031322      9.349805       1              20           
-     33200   8.2620563      1.0015059      5.2482188      10.286446      1              17           
-     33300   8.0217099      1.0015466      5.1166876      9.1381844      1              20           
-     33400   7.6565746      1.0024855      4.7594208      9.2646824      1              22           
-     33500   7.9633887      1.0010334      4.6754116      9.1085184      1              23           
-     33600   7.9566834      1.0024542      4.6712679      9.2046594      1              25           
-     33700   8.2639384      1.0003021      5.1326892      8.0930215      1              24           
-     33800   8.5648917      1.0000947      5.2099387      8.8127486      1              21           
-     33900   8.3593557      1.0002488      5.1291354      8.5938391      1              25           
-     34000   8.1922068      1.0030011      5.1441189      7.1529563      1              24           
-     34100   8.4260308      1.0004639      5.5876122      9.0450303      1              28           
-     34200   8.3014654      1.0002204      5.1964772      8.4920822      1              33           
-     34300   7.4736545      1.0010306      4.7932244      7.8442244      1              30           
-     34400   7.0023126      1.0024002      4.5665168      8.4702188      1              29           
-     34500   7.3797703      1.000813       4.7224014      8.4098954      1              30           
-     34600   7.7158761      0.99973161     4.7441628      8.5818592      1              29           
-     34700   7.6135895      1.0015768      4.6612844      7.2195952      1              28           
-     34800   7.0458078      0.99992638     4.2805357      7.4162305      1              32           
-     34900   7.6190708      1.0007146      4.8064968      8.2709405      1              27           
-     35000   7.4614294      1.0006051      4.7807207      7.7137359      1              28           
-     35100   7.7008336      1.0008263      4.6823621      7.0208513      1              26           
-     35200   8.1510766      1.000271       5.1781834      7.3231692      1              24           
-     35300   7.5106275      1.0010438      4.6988185      8.9418343      1              25           
-     35400   7.8116652      1.0009688      4.8622216      7.4624002      1              17           
-     35500   7.2159785      1.0027484      4.543984       8.3177043      1              21           
-     35600   7.6978875      1.0004834      4.7021203      8.3706905      1              20           
-     35700   7.7827655      1.0019919      4.775879       8.6083292      1              15           
-     35800   7.8433537      1.001844       4.7506574      7.3250009      1              15           
-     35900   7.9456497      1.0004336      4.7925775      7.9824359      1              18           
-     36000   8.1044513      1.0022261      5.1213755      9.211699       1              16           
-     36100   7.6657532      1.0025661      4.751804       8.9770412      1              19           
-     36200   7.909323       1.0035462      4.8435293      10.232493      1              21           
-     36300   8.4188244      1.0016775      5.4337725      9.2060079      1              24           
-     36400   8.7352689      1.0011274      5.6313351      8.6202832      1              24           
-     36500   8.3459273      1.0005659      5.187336       6.9333716      1              21           
-     36600   7.7118105      1.0018769      4.9293347      8.2789615      1              14           
-     36700   7.8069879      1.0014021      4.7782709      8.4841233      1              15           
-     36800   7.862085       1.0005342      4.8680692      8.1055023      1              16           
-     36900   7.9469362      1.0027815      4.9339095      9.157722       1              16           
-     37000   7.9085375      1.0024851      5.0921374      8.9374239      1              16           
-     37100   8.9464869      1.0005734      5.6837772      8.806998       1              16           
-     37200   8.1482632      1.0021175      5.1266453      8.5772094      1              18           
-     37300   7.7958072      1.0026336      4.788431       8.3233372      1              19           
-     37400   7.3647655      1.0015482      4.4786134      9.6606112      1              23           
-     37500   7.3071882      1.0003912      4.681549       8.6319438      1              17           
-     37600   7.8672509      1.0000478      4.7981944      8.3051478      1              14           
-     37700   7.9306696      0.99923102     4.9316544      9.3672856      1              15           
-     37800   7.7397949      0.99948557     5.1168552      8.5978047      1              17           
-     37900   7.9121039      1.0020122      4.9866234      7.640888       1              14           
-     38000   7.433451       1.0007901      4.6254894      8.0853539      1              14           
-     38100   7.4636908      1.0021552      4.8472833      8.1975615      1              10           
-     38200   7.4453077      1.0010305      4.6910943      7.8192603      1              13           
-     38300   7.0488536      1.0012587      4.5490462      8.190036       1              16           
-     38400   8.0686748      1.0016782      5.0747029      7.7242015      1              15           
-     38500   7.9575875      1.0007137      4.8361776      8.05268        1              15           
-     38600   7.6690498      1.0027522      4.8823286      9.1926516      1              20           
-     38700   7.1567         1.002374       4.5600354      10.098089      1              19           
-     38800   6.9100518      1.0008695      4.4101446      7.8832032      1              19           
-     38900   6.8021882      1.0017647      4.1844125      8.1858761      1              21           
-     39000   8.3996464      1.0010263      4.8183813      8.0997387      1              16           
-     39100   8.4533834      1.0021643      5.074254       11.291904      1              19           
-     39200   8.2406701      1.002062       5.0117425      8.778159       1              24           
-     39300   8.3134114      1.0008218      5.0067136      7.9871787      1              22           
-     39400   7.4307571      1.0014205      4.5858283      8.8596594      1              25           
-     39500   7.1146821      1.0016367      4.5021057      7.4890018      1              22           
-     39600   8.0048978      0.99992107     4.9235747      7.8770845      1              24           
-     39700   8.070853       1.0029024      5.0842957      9.020664       1              21           
-     39800   7.6939108      1.0012543      4.8986595      8.3306129      1              20           
-     39900   7.2915444      1.00267        4.5038291      8.3844384      1              20           
-     40000   7.3023994      1.0020441      4.4960911      8.1023709      1              18           
-     40100   7.0221648      1.0033695      4.6374149      8.3756822      1              24           
-     40200   7.4114756      1.0019246      4.6733475      7.6547258      1              23           
-     40300   7.5323108      1.0005472      4.8284493      8.2820085      1              26           
-     40400   7.3890772      1.0010491      4.6599273      8.9203575      1              19           
-     40500   7.5786764      1.0016114      4.8166885      8.6760107      1              25           
-     40600   8.165763       1.0006961      5.1488995      7.9321524      1              22           
-     40700   8.1277597      0.99933464     5.0441567      10.069551      1              16           
-     40800   8.1050904      1.0024705      5.4408599      8.3244459      1              21           
-     40900   7.805318       1.0022992      4.9965408      9.7193723      1              21           
-     41000   9.0130932      1.0006842      5.7931112      6.1646073      1              20           
-     41100   8.0387975      1.0017359      5.3355655      9.6123191      1              21           
-     41200   8.4484723      1.0014151      5.4461007      8.5146504      1              27           
-     41300   8.6181909      1.0007562      5.2963876      9.1122306      1              30           
-     41400   9.6762899      1.0010931      5.950456       9.2851025      1              25           
-     41500   9.9414226      1.0016186      6.1433384      10.741453      1              24           
-     41600   9.3348435      1.0003483      5.9291766      11.460717      1              20           
-     41700   9.6125587      1.0013661      5.8530052      9.2105722      1              19           
-     41800   11.383056      1.0032034      7.1988684      10.312945      1              22           
-     41900   10.884524      1.0034888      6.9126707      10.775457      1              20           
-     42000   11.071218      1.0026753      7.0004189      10.740627      1              20           
-     42100   11.054304      1.0008347      6.9602414      8.9885498      1              22           
-     42200   22.478691      1.0020466      14.997099      12.72513       1              19           
-     42300   18.303508      1.0027626      11.336523      12.638769      1              18           
-     42400   15.998712      1.0030312      9.4092725      11.070501      1              24           
-     42500   15.034488      1.0024472      9.3543751      11.48052       1              28           
-     42600   14.538257      1.0033153      9.2523745      10.909576      1              27           
-     42700   13.986613      1.001458       8.5544184      10.765136      1              29           
-     42800   13.240256      1.0027899      8.2014429      10.506497      1              32           
-     42900   12.784336      1.0001406      8.0823431      12.258209      1              33           
-     43000   13.374145      1.0012996      8.4207155      10.32817       1              31           
-     43100   13.142334      1.0022503      8.5908808      10.152205      1              32           
-     43200   12.669284      1.0018944      7.8511966      10.580104      1              32           
-     43300   13.155032      1.001144       8.0337768      10.6652        1              39           
-     43400   12.155928      1.0019472      7.5886584      11.234772      1              35           
-     43500   12.385603      1.0007639      7.8865245      9.3868914      1              32           
-     43600   12.236179      1.0027456      7.7521353      10.456701      1              42           
-     43700   11.49535       1.0008758      7.3633144      8.8490079      1              40           
-     43800   11.469157      1.0015845      7.0035577      10.594522      1              41           
-     43900   11.228266      1.0013014      7.0137223      8.0653711      1              38           
-     44000   10.56742       1.0016631      6.6908938      8.1094154      1              35           
-     44100   9.8964699      1.0008351      6.3550438      8.6578181      1              36           
-     44200   9.041539       1.0019541      5.6721401      8.6518043      1              38           
-     44300   9.0767434      1.0034191      5.7446596      8.3838528      1              38           
-     44400   9.2299608      1.0019526      5.7117964      8.3106491      1              37           
-     44500   9.458981       1.0030409      5.7612138      7.7679755      1              37           
-     44600   8.9611997      1.0014848      5.6490756      6.9224078      1              37           
-     44700   8.0853184      1.0018894      5.2288749      8.0910912      1              32           
-     44800   7.9999755      1.0015853      4.8088312      7.1854304      1              30           
-     44900   7.6598023      1.0009751      4.6690664      7.1999858      1              28           
-     45000   7.4939315      1.0010307      4.8119666      7.9615769      1              26           
-     45100   7.4690079      0.99913423     4.9704428      7.6026835      1              32           
-     45200   7.7001199      1.001626       4.9315953      7.4926686      1              25           
-     45300   7.8794405      1.0011648      4.8624857      8.0804457      1              26           
-     45400   7.493909       1.0016257      4.7631808      8.0330626      1              26           
-     45500   7.5963141      1.0005825      4.7220659      7.0971298      1              23           
-     45600   7.9028612      1.0017008      4.9561022      8.440428       1              23           
-     45700   7.2285584      1.0006033      4.5521456      9.385579       1              23           
-     45800   7.5687284      1.0024318      4.8557498      8.3052658      1              23           
-     45900   7.8938604      1.0013937      5.1393944      5.5323667      1              26           
-     46000   8.318466       1.0020803      5.4761811      8.2227801      1              25           
-     46100   7.9169512      1.0024598      5.0406355      8.64365        1              27           
-     46200   7.5535458      1.0016318      4.8010133      9.370726       1              26           
-     46300   7.8926896      1.0001525      5.18463        7.9830196      1              27           
-     46400   7.487145       1.002671       4.7718312      8.300134       1              29           
-     46500   7.3564658      1.0006114      4.6762189      7.34947        1              26           
-     46600   7.2261291      1.0005569      4.4751221      6.5847138      1              27           
-     46700   7.2943203      1.0020164      4.3335327      7.7296507      1              25           
-     46800   8.5849411      1.0014634      5.4501531      9.0933014      1              25           
-     46900   10.176752      1.0023799      6.0456779      9.4050423      1              16           
-     47000   9.1913098      1.0029076      5.7577256      9.1826215      1              22           
-     47100   9.5479771      1.0022102      6.1100973      8.9440056      1              28           
-     47200   9.9944172      1.0004924      6.3649417      9.1507264      1              25           
-     47300   9.3543283      1.0013246      6.0873147      10.41657       1              24           
-     47400   8.594101       1.0020068      5.6864295      9.2388304      1              24           
-     47500   9.3191964      1.002411       6.0537511      9.3506828      1              23           
-     47600   8.1615734      1.001364       5.3757905      10.303962      1              30           
-     47700   8.3615046      1.0003075      5.2727936      9.3162209      1              32           
-     47800   8.3566467      1.0026031      5.4379524      7.7644422      1              33           
-     47900   8.4062556      1.0006471      5.3098736      8.0181121      1              33           
-     48000   8.2233307      1.0012304      4.9650027      9.2644288      1              34           
-     48100   8.4495256      1.000088       4.9940422      10.01023       1              27           
-     48200   8.8068097      1.0014275      5.4732649      8.410093       1              31           
-     48300   8.0008187      1.0017459      4.7732764      9.25726        1              27           
-     48400   7.7242529      1.0026909      4.9084505      8.7147295      1              30           
-     48500   8.3752816      1.001333       5.1071228      8.2267308      1              32           
-     48600   9.0777805      1.0019328      5.7331841      9.6679383      1              29           
-     48700   9.3623061      1.0001767      5.7117062      8.396895       1              25           
-     48800   8.1186637      1.0013185      5.2697427      8.6058372      1              27           
-     48900   7.3685497      1.0007173      4.6097553      7.8047228      1              24           
-     49000   7.1661421      1.0023152      4.5389038      8.8759552      1              22           
-     49100   6.9857144      1.0016394      4.6489319      8.2022359      1              24           
-     49200   6.7160336      1.0018413      4.2488082      8.3393245      1              25           
-     49300   7.9703755      1.0010628      5.2328567      7.968278       1              28           
-     49400   8.2628465      1.0010877      5.2292977      8.0196533      1              27           
-     49500   8.1436558      1.0015175      5.0344712      8.0712037      1              30           
-     49600   8.5182498      1.0021589      5.1029028      8.6869789      1              28           
-     49700   8.3604444      1.0015016      5.0333696      9.4861656      1              25           
-     49800   7.336335       1.0020055      4.6365173      8.7210022      1              30           
-     49900   7.432996       1.0016415      4.7090587      8.7033033      1              29           
-     50000   7.4937053      1.001014       4.7212573      9.0890363      1              29           
-Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
-
-Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
-99.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 293.48     | 403.7      | 545.29     | 357.5 | 40.39
-Neigh   | 2.4176     | 3.2721     | 3.8303     |  25.2 |  0.33
-Comm    | 163.58     | 305.88     | 419.83     | 416.7 | 30.60
-Output  | 0.032483   | 0.034794   | 0.040514   |   1.2 |  0.00
-Modify  | 281.15     | 285.67     | 293.8      |  24.3 | 28.58
-Other   |            | 1.023      |            |       |  0.10
-
-Nlocal:        2033.88 ave        2657 max        1198 min
-Histogram: 2 0 0 0 0 2 1 0 1 2
-Nghost:        1628.12 ave        1719 max        1569 min
-Histogram: 2 0 1 1 2 1 0 0 0 1
-Neighs:          13566 ave       18212 max        8488 min
-Histogram: 1 0 0 1 2 1 2 0 0 1
-
-Total # of neighbors = 108528
-Ave neighs/atom = 6.6700264
-Neighbor list builds = 2447
-Dangerous builds = 2
-Total wall time: 0:19:22

examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.1

@@ -0,0 +1,343 @@
+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
+# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
+
+units           lj
+atom_style      tri
+atom_modify     first big map yes
+
+read_data       data.tri.srd
+Reading data file ...
+  orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1500 atoms
+  1500 triangles
+  read_data CPU = 0.013 seconds
+
+# add small particles as hi density lattice
+
+lattice         sc 0.4
+Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
+region          box block INF INF INF INF INF INF
+lattice         sc 20.0
+Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
+create_atoms    2 region box
+Created 91125 atoms
+  using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  create_atoms CPU = 0.014 seconds
+
+group           big type 1
+1500 atoms in group big
+group           small type 2
+91125 atoms in group small
+set             group small mass 0.01
+Setting atom values ...
+  91125 settings made for mass
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 1.5
+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
+
+delete_atoms    overlap 1.5 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 = 1.8
+  ghost atom cutoff = 1.8
+  binsize = 0.9, bins = 19 19 19
+  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/3d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 76354 atoms, new total = 16271
+
+# SRD run
+
+reset_timestep  0
+
+velocity        small create 1.44 87287 loop geom
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+neigh_modify    exclude molecule/intra big include big
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      tri/lj 3.5
+pair_coeff      1 1 0.1 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/small molecule #langevin 1.0 1.0 0.1 12398
+  create bodies CPU = 0.000 seconds
+  125 rigid bodies with 1500 atoms
+  1.8601881 = max distance from body owner to body atom
+fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip inside ignore
+
+fix             3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
+
+# diagnostics
+
+compute         tsmall small temp/deform
+compute         tbig big temp
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+
+compute_modify  tbig extra/dof -4500
+
+compute         1 big erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+thermo          100
+thermo_style    custom step f_1 c_tsmall temp press f_2[9] f_2[4]
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+
+compute         10 all property/atom corner1x corner1y corner1z                 corner2x corner2y corner2z corner3x corner3y corner3z
+
+#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump1.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]
+
+run             1000
+
+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
+WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
+WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 17 17 17
+  SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
+  SRD per actual grid cell = -3.9971745
+  SRD viscosity = -34.162587
+  big/SRD mass density ratio = -3.3753691
+WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 19.970837 35.150443
+  ave/max big velocity = 0 0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 16.874681, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/3d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 381.8 | 381.8 | 381.8 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+         0   0              1.4502537      0             -0.15976045     0              0            
+       100   0.41802172     1.152223       0.27557714     1.0421065      1.1470081      283          
+       200   0.79710339     1.0669332      0.5813323      0.97699684     1.0361619      534          
+       300   1.3739181      1.0275476      1.0869716      0.81001536     1.0211312      658          
+       400   1.9355117      1.0155457      1.5813236      1.7798798      0.99354559     831          
+       500   2.8557382      1.0005021      2.267698       3.3903849      0.98597972     927          
+       600   4.7851916      1.0156689      3.730334       2.838776       0.99140534     1053         
+       700   5.3647697      1.0176657      3.9593121      5.1189107      0.9972029      1218         
+       800   8.23688        1.0268086      5.899689       6.8199153      0.99310516     1349         
+       900   9.9330758      1.0356047      7.0260595      7.2596589      0.98360014     1607         
+      1000   9.8719995      1.043178       6.9903792      10.05101       1.0045416      1805         
+Loop time of 79.2664 on 1 procs for 1000 steps with 16271 atoms
+
+Performance: 1089.995 tau/day, 12.616 timesteps/s, 205.270 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    | 57.961     | 57.961     | 57.961     |   0.0 | 73.12
+Neigh   | 0.34589    | 0.34589    | 0.34589    |   0.0 |  0.44
+Comm    | 0.28615    | 0.28615    | 0.28615    |   0.0 |  0.36
+Output  | 0.0022784  | 0.0022784  | 0.0022784  |   0.0 |  0.00
+Modify  | 20.644     | 20.644     | 20.644     |   0.0 | 26.04
+Other   |            | 0.02724    |            |       |  0.03
+
+Nlocal:          16271 ave       16271 max       16271 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4612 ave        4612 max        4612 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          99463 ave       99463 max       99463 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 99463
+Ave neighs/atom = 6.1129003
+Neighbor list builds = 72
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
+
+fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip tstat yes inside ignore
+
+#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump2.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]
+
+fix             3 all deform 1 xy erate 0.05 units box remap v
+
+run             2000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 13 13 13
+  SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
+  SRD per actual grid cell = -2.775698
+  SRD viscosity = -12.180602
+  big/SRD mass density ratio = -5.5653033
+WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
+  # of rescaled SRD velocities = 3
+  ave/max small velocity = 16.23763 40
+  ave/max big velocity = 1.9825234 5.257255
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 13.499745, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton/tri
+      stencil: half/multi/3d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 278.4 | 278.4 | 278.4 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+      1000   9.8719995      1.0317167      6.98982        4.0948969      0              0            
+      1100   7.6460335      1.0028444      5.2446585      6.6348814      1              1320         
+      1200   6.2789381      1.0012003      4.5257435      6.3278972      1              1024         
+      1300   5.5060209      1.002182       3.7063549      7.0004503      1              794          
+      1400   5.4107119      1.002291       3.594515       7.9511695      1              621          
+      1500   5.072582       1.0001037      3.2501353      8.6993671      1              503          
+      1600   4.7912016      0.99982803     3.1208274      6.464157       1              416          
+      1700   4.5518848      1.0030059      2.9084074      6.3278992      1              346          
+      1800   4.368682       1.000831       2.807184       6.7382017      1              282          
+      1900   4.458655       1.0012568      2.7966515      6.0124309      1              246          
+      2000   4.1256128      1.0004032      2.763649       6.3707442      1              208          
+      2100   3.7040346      1.0004125      2.4398152      5.4213931      1              181          
+      2200   4.2347861      1.002625       2.6206986      6.6832437      1              151          
+      2300   4.254984       1.0028871      2.6794167      7.1661525      1              127          
+      2400   4.1017692      1.0028508      2.6371178      8.388599       1              105          
+      2500   3.9285571      1.0002888      2.5002741      6.0806187      1              95           
+      2600   3.6239964      1.0012152      2.2573993      6.7863124      1              80           
+      2700   3.4085702      1.0023974      2.1179914      6.7351139      1              68           
+      2800   3.1399303      1.0005349      2.0163219      6.4502765      1              61           
+      2900   3.1277562      1.0004013      2.0453134      6.6485498      1              51           
+      3000   3.0737732      1.0022962      1.997382       6.797214       1              44           
+Loop time of 206.387 on 1 procs for 2000 steps with 16271 atoms
+
+Performance: 837.264 tau/day, 9.691 timesteps/s, 157.675 katom-step/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 173.6      | 173.6      | 173.6      |   0.0 | 84.12
+Neigh   | 1.0077     | 1.0077     | 1.0077     |   0.0 |  0.49
+Comm    | 0.58656    | 0.58656    | 0.58656    |   0.0 |  0.28
+Output  | 0.0042824  | 0.0042824  | 0.0042824  |   0.0 |  0.00
+Modify  | 31.128     | 31.128     | 31.128     |   0.0 | 15.08
+Other   |            | 0.05664    |            |       |  0.03
+
+Nlocal:          16271 ave       16271 max       16271 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4521 ave        4521 max        4521 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          94777 ave       94777 max       94777 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 94777
+Ave neighs/atom = 5.8249032
+Neighbor list builds = 100
+Dangerous builds = 0
+Total wall time: 0:04:47

examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.4

@@ -0,0 +1,343 @@
+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
+# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
+
+units           lj
+atom_style      tri
+atom_modify     first big map yes
+
+read_data       data.tri.srd
+Reading data file ...
+  orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  1500 atoms
+  1500 triangles
+  read_data CPU = 0.010 seconds
+
+# add small particles as hi density lattice
+
+lattice         sc 0.4
+Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
+region          box block INF INF INF INF INF INF
+lattice         sc 20.0
+Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
+create_atoms    2 region box
+Created 91125 atoms
+  using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  create_atoms CPU = 0.005 seconds
+
+group           big type 1
+1500 atoms in group big
+group           small type 2
+91125 atoms in group small
+set             group small mass 0.01
+Setting atom values ...
+  91125 settings made for mass
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style      lj/cut 1.5
+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
+
+delete_atoms    overlap 1.5 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 = 1.8
+  ghost atom cutoff = 1.8
+  binsize = 0.9, bins = 19 19 19
+  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/3d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
+Deleted 76354 atoms, new total = 16271
+
+# SRD run
+
+reset_timestep  0
+
+velocity        small create 1.44 87287 loop geom
+
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
+neigh_modify    exclude molecule/intra big include big
+
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
+
+# no pairwise interactions with small particles
+
+pair_style      tri/lj 3.5
+pair_coeff      1 1 0.1 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/small molecule #langevin 1.0 1.0 0.1 12398
+  create bodies CPU = 0.000 seconds
+  125 rigid bodies with 1500 atoms
+  1.8601881 = max distance from body owner to body atom
+fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip inside ignore
+
+fix             3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
+
+# diagnostics
+
+compute         tsmall small temp/deform
+compute         tbig big temp
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+
+compute_modify  tbig extra/dof -4500
+
+compute         1 big erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+thermo          100
+thermo_style    custom step f_1 c_tsmall temp press f_2[9] f_2[4]
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
+
+compute         10 all property/atom corner1x corner1y corner1z                 corner2x corner2y corner2z corner3x corner3y corner3z
+
+#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump1.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]
+
+run             1000
+
+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
+WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
+WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 17 17 17
+  SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
+  SRD per actual grid cell = -3.9971745
+  SRD viscosity = -34.162587
+  big/SRD mass density ratio = -3.3753691
+WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 19.970837 35.150443
+  ave/max big velocity = 0 0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 16.874681, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton
+      stencil: half/multi/3d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 184.3 | 184.9 | 185.4 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+         0   0              1.4502537      0             -0.15949051     0              0            
+       100   0.39689465     1.1495173      0.26931663     1.0004927      1.1170389      279          
+       200   0.82155086     1.0684809      0.60689485     0.81307973     1.0433122      467          
+       300   1.3210872      1.0334277      1.0368935      1.0853416      0.99443391     621          
+       400   1.9755695      1.0149146      1.6438403      1.7258285      0.9925525      788          
+       500   3.0111365      1.0121291      2.4285289      2.5210058      0.99688885     922          
+       600   4.5413799      1.014305       3.4727946      3.8290233      0.99002027     1063         
+       700   6.6071849      1.0062952      4.9025772      3.9595327      0.99573591     1186         
+       800   7.6256618      1.0151252      5.3662442      5.0088255      0.99640985     1371         
+       900   8.1578206      1.0148959      5.7716683      6.6059298      0.96053165     1555         
+      1000   10.749617      1.0282309      7.6209538      11.277602      1.0012602      1844         
+Loop time of 28.4136 on 4 procs for 1000 steps with 16271 atoms
+
+Performance: 3040.793 tau/day, 35.194 timesteps/s, 572.647 katom-step/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.454     | 15.242     | 17.781     |  48.4 | 53.64
+Neigh   | 0.093078   | 0.094516   | 0.097759   |   0.6 |  0.33
+Comm    | 0.48732    | 2.9927     | 5.7363     | 107.5 | 10.53
+Output  | 0.00080706 | 0.0008431  | 0.00086933 |   0.0 |  0.00
+Modify  | 10.015     | 10.063     | 10.111     |   1.4 | 35.42
+Other   |            | 0.02046    |            |       |  0.07
+
+Nlocal:        4067.75 ave        4467 max        3606 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost:         2313.5 ave        2327 max        2296 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:          24883 ave       26066 max       24145 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 99532
+Ave neighs/atom = 6.1171409
+Neighbor list builds = 70
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
+
+fix             2 small srd 20 big 1.0 1.0 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip tstat yes inside ignore
+
+#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump2.tri.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #               c_10[7] c_10[8] c_10[9]
+
+fix             3 all deform 1 xy erate 0.05 units box remap v
+
+run             2000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 13 13 13
+  SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
+  SRD per actual grid cell = -2.775698
+  SRD viscosity = -12.180602
+  big/SRD mass density ratio = -5.5653033
+WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
+  # of rescaled SRD velocities = 3
+  ave/max small velocity = 16.10299 40
+  ave/max big velocity = 2.0311414 11.34118
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 13.499745, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton/tri
+      stencil: half/multi/3d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 148.8 | 149.5 | 150 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+      1000   10.749616      1.0167438      7.6203704      5.4893075      0              0            
+      1100   9.0727748      1.003438       6.1822573      8.6707036      1              1339         
+      1200   7.1960998      1.0003968      4.8077632      6.7809972      1              1039         
+      1300   6.2680889      1.0011134      4.3139658      8.2260362      1              861          
+      1400   5.8199503      1.0024475      3.9876867      7.0322957      1              692          
+      1500   5.399935       0.99757802     3.4552534      7.905565       1              577          
+      1600   5.0830248      1.0023727      3.1330433      7.6897887      1              479          
+      1700   4.8728937      1.0027203      3.0838267      7.606406       1              389          
+      1800   4.8443541      1.0018057      3.115321       7.4547572      1              317          
+      1900   5.0622362      1.0007126      2.9336473      6.514338       1              268          
+      2000   5.022699       1.0030275      3.1244763      7.2999286      1              223          
+      2100   4.4605894      1.0019457      2.9262733      8.3475145      1              196          
+      2200   4.6544992      1.0023701      3.0140329      7.3670747      1              164          
+      2300   4.1954825      1.0012089      2.5802739      7.5553707      1              142          
+      2400   4.0806819      1.0000292      2.6492187      7.5648723      1              122          
+      2500   3.7437189      0.99949605     2.3660722      8.2155316      1              104          
+      2600   4.2333926      1.0002823      2.5704515      7.2839635      1              106          
+      2700   3.7542455      1.001394       2.4146222      6.3785983      1              86           
+      2800   3.4011329      0.99832028     2.141193       6.3869497      1              78           
+      2900   3.4579019      1.0007319      2.1839274      6.241817       1              64           
+      3000   3.6128019      1.0017345      2.2982426      5.8975992      1              55           
+Loop time of 67.0194 on 4 procs for 2000 steps with 16271 atoms
+
+Performance: 2578.358 tau/day, 29.842 timesteps/s, 485.561 katom-step/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 36.774     | 43.583     | 50.126     |  71.5 | 65.03
+Neigh   | 0.29299    | 0.3134     | 0.32399    |   2.2 |  0.47
+Comm    | 0.75102    | 7.2688     | 14.075     | 174.8 | 10.85
+Output  | 0.0016347  | 0.0017229  | 0.0018802  |   0.2 |  0.00
+Modify  | 15.794     | 15.808     | 15.828     |   0.3 | 23.59
+Other   |            | 0.04379    |            |       |  0.07
+
+Nlocal:        4067.75 ave        4560 max        3583 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:        2256.75 ave        2292 max        2241 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:          23706 ave       24669 max       22450 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+
+Total # of neighbors = 94824
+Ave neighs/atom = 5.8277918
+Neighbor list builds = 108
+Dangerous builds = 0
+Total wall time: 0:01:36

examples/PACKAGES/mgpt/in.bcc0

@@ -1,7 +1,5 @@
 # script for mgpt t=0 eos in bulk bcc structure
 
-echo screen
-
 units           electron
 atom_style      atomic
 
@@ -36,7 +34,7 @@ neigh_modify	every 1 delay 0 check yes
 fix             1 all nve
 
 # Dump coordinates to file every 50 timesteps
-dump		id all atom 50 dump.bcc0
+#dump            id all atom 50 dump.bcc0
 
 # Output thermodynamical data every 10 timesteps
 thermo          10

examples/PACKAGES/mgpt/in.vac0-bcc

@@ -1,8 +1,6 @@
 # script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
 # input for unrelaxed vacancy formation energy at constant atomic volume
 
-echo screen
-
 units           electron
 atom_style      atomic
 
@@ -44,7 +42,7 @@ neigh_modify	every 1 delay 0 check yes
 fix             1 all nve
 
 # Dump coordinates to file every 50 timesteps
-dump		id all atom 50 dump.vac0-bcc
+# dump            id all atom 50 dump.vac0-bcc
 
 # Output thermodynamical data every 10 timesteps
 thermo          10

examples/PACKAGES/mgpt/in.vacmin-bcc

@@ -1,8 +1,6 @@
 # script for mgpt t=0 eos with relaxed vacancy in bcc structure:
 # input for relaxed vacancy formation energy at constant pressure
 
-echo screen
-
 units           electron
 atom_style      atomic
 
@@ -38,7 +36,7 @@ neighbor	0.1 bin
 neigh_modify    every 1 delay 0 check yes
 
 # Dump coordinates to file every 50 timesteps
-dump		id all atom 50 dump.vacmin-bcc
+# dump            id all atom 50 dump.vacmin-bcc
 
 # Output thermodynamical data every 10 timesteps
 thermo          10