Merge branch 'develop' into rheo

.github/workflows/check-cpp23.yml

@@ -0,0 +1,92 @@
+# GitHub action to build LAMMPS on Linux with gcc and C++23
+name: "Check for C++23 Compatibility"
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build with C++23 support enabled
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 2
+
+    - name: Install extra packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ccache \
+                                libeigen3-dev \
+                                libcurl4-openssl-dev \
+                                mold \
+                                mpi-default-bin \
+                                mpi-default-dev \
+                                ninja-build \
+                                python3-dev
+
+    - name: Create Build Environment
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: linux-cpp23-ccache-${{ github.sha }}
+        restore-keys: linux-cpp23-ccache-
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      run: |
+        ccache -z
+        python3 -m venv linuxenv
+        source linuxenv/bin/activate
+        python3 -m pip install numpy
+        python3 -m pip install pyyaml
+        cmake -S cmake -B build \
+              -C cmake/presets/most.cmake \
+              -C cmake/presets/kokkos-openmp.cmake \
+              -D CMAKE_CXX_STANDARD=23 \
+              -D CMAKE_CXX_COMPILER=g++ \
+              -D CMAKE_C_COMPILER=gcc \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_BUILD_TYPE=Debug \
+              -D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
+              -D DOWNLOAD_POTENTIALS=off \
+              -D BUILD_MPI=on \
+              -D BUILD_SHARED_LIBS=on \
+              -D BUILD_TOOLS=off \
+              -D ENABLE_TESTING=off \
+              -D MLIAP_ENABLE_ACE=on \
+              -D MLIAP_ENABLE_PYTHON=off \
+              -D PKG_AWPMD=on \
+              -D PKG_GPU=on \
+              -D GPU_API=opencl \
+              -D PKG_KOKKOS=on \
+              -D PKG_LATBOLTZ=on \
+              -D PKG_MDI=on \
+              -D PKG_MANIFOLD=on \
+              -D PKG_ML-PACE=on \
+              -D PKG_ML-RANN=off \
+              -D PKG_MOLFILE=on \
+              -D PKG_RHEO=on \
+              -D PKG_PTM=on \
+              -D PKG_PYTHON=on \
+              -D PKG_QTB=on \
+              -D PKG_SMTBQ=on \
+              -G Ninja
+        cmake --build build
+        ccache -s

.github/workflows/kokkos-regression.yaml

@@ -0,0 +1,124 @@
+# GitHub action to build LAMMPS on Linux and run selected regression tests
+name: "Kokkos OpenMP Regression Test"
+
+on:
+  pull_request:
+    branches:
+      - develop
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build LAMMPS with Kokkos OpenMP
+    # restrict to official LAMMPS repository
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
+    strategy:
+      max-parallel: 4
+      matrix:
+        idx: [ 'pair', 'fix', 'compute', 'misc' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 2
+        show-progress: false
+
+    - name: Install extra packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ccache ninja-build libeigen3-dev \
+                     libcurl4-openssl-dev python3-dev \
+                     mpi-default-bin mpi-default-dev
+
+    - name: Create Build Environment
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: linux-kokkos-ccache-${{ github.sha }}
+        restore-keys: linux-kokkos-ccache-
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      run: |
+        ccache -z
+        python3 -m venv linuxenv
+        source linuxenv/bin/activate
+        python3 -m pip install --upgrade pip
+        python3 -m pip install numpy pyyaml junit_xml
+        cmake -S cmake -B build \
+              -C cmake/presets/gcc.cmake \
+              -C cmake/presets/basic.cmake \
+              -C cmake/presets/kokkos-openmp.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D BUILD_SHARED_LIBS=off \
+              -D DOWNLOAD_POTENTIALS=off \
+              -D PKG_AMOEBA=on \
+              -D PKG_ASPHERE=on \
+              -D PKG_BROWNIAN=on \
+              -D PKG_CLASS2=on \
+              -D PKG_COLLOID=on \
+              -D PKG_CORESHELL=on \
+              -D PKG_DIPOLE=on \
+              -D PKG_DPD-BASIC=on \
+              -D PKG_EXTRA-COMPUTE=on \
+              -D PKG_EXTRA-FIX=on \
+              -D PKG_EXTRA-MOLECULE=on \
+              -D PKG_EXTRA-PAIR=on \
+              -D PKG_GRANULAR=on \
+              -D PKG_LEPTON=on \
+              -D PKG_MC=on \
+              -D PKG_MEAM=on \
+              -D PKG_POEMS=on \
+              -D PKG_PYTHON=on \
+              -D PKG_QEQ=on \
+              -D PKG_REAXFF=on \
+              -D PKG_REPLICA=on \
+              -D PKG_SRD=on \
+              -D PKG_VORONOI=on \
+              -G Ninja
+        cmake --build build
+        ccache -s
+
+    - name: Run Regression Tests for Selected Examples
+      shell: bash
+      run: |
+        source linuxenv/bin/activate
+        python3 tools/regression-tests/get_kokkos_input.py \
+               --examples-top-level=examples \
+               --filter-out="balance;fire;gcmc;granregion;mdi;mliap;neb;pace;prd;pour;python;snap"
+
+        python3 tools/regression-tests/run_tests.py \
+               --lmp-bin=build/lmp \
+               --config-file=tools/regression-tests/config_kokkos_openmp.yaml \
+               --list-input=input-list-${{ matrix.idx }}-kk.txt \
+               --output-file=output-${{ matrix.idx }}.xml \
+               --progress-file=progress-${{ matrix.idx }}.yaml \
+               --log-file=run-${{ matrix.idx }}.log \
+               --quick-max=100 --verbose
+
+        tar -cvf kokkos-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: kokkos-regression-test-artifact-${{ matrix.idx }}
+        path: kokkos-regression-test-${{ matrix.idx }}.tar
+
+  merge:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Merge Artifacts
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: merged-kokkos-regresssion-artifact
+          pattern: kokkos-regression-test-artifact-*

cmake/CMakeLists.txt

@@ -118,7 +118,7 @@ endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
@@ -141,7 +141,7 @@ endif()
 
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
+  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma -Xcudafe --diag_suppress=128")
 endif()
 
 # we require C++11 without extensions. Kokkos requires at least C++17 (currently)
@@ -165,6 +165,7 @@ if(MSVC)
     add_compile_options(/wd4267)
     add_compile_options(/wd4250)
     add_compile_options(/EHsc)
+    add_compile_options(/utf-8)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -822,9 +823,15 @@ foreach(_DEF ${LAMMPS_DEFINES})
   set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
 endforeach()
 if(BUILD_SHARED_LIBS)
-  install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(TARGETS lammps EXPORT LAMMPS_Targets
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   if(NOT BUILD_MPI)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets
+            LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   endif()
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)

cmake/Modules/Documentation.cmake

@@ -110,6 +110,7 @@ if(BUILD_DOC)
   add_custom_command(
     OUTPUT html
     DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
+    COMMAND ${Python3_EXECUTABLE} ${LAMMPS_DOC_DIR}/utils/make-globbed-tocs.py -d ${LAMMPS_DOC_DIR}/src
     COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
     COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
     COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF

cmake/Modules/FindVORO.cmake

@@ -21,9 +21,9 @@ if(VORO_FOUND)
   set(VORO_LIBRARIES ${VORO_LIBRARY})
   set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
 
-  if(NOT TARGET VORO::VORO)
+  if(NOT TARGET VORO::voro++)
-    add_library(VORO::VORO UNKNOWN IMPORTED)
+    add_library(VORO::voro++ UNKNOWN IMPORTED)
-    set_target_properties(VORO::VORO PROPERTIES
+    set_target_properties(VORO::voro++ PROPERTIES
       IMPORTED_LOCATION "${VORO_LIBRARY}"
       INTERFACE_INCLUDE_DIRECTORIES "${VORO_INCLUDE_DIR}")
   endif()

cmake/Modules/Packages/H5MD.cmake

@@ -3,7 +3,7 @@ enable_language(C)
 # we don't use the parallel i/o interface.
 set(HDF5_PREFER_PARALLEL FALSE)
 
-find_package(HDF5 REQUIRED)
+find_package(HDF5 COMPONENTS C REQUIRED)
 
 # parallel HDF5 will import incompatible MPI headers with a serial build
 if((NOT BUILD_MPI) AND HDF5_IS_PARALLEL)

cmake/Modules/Packages/VORONOI.cmake

@@ -54,5 +54,5 @@ else()
   if(NOT VORO_FOUND)
     message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
   endif()
-  target_link_libraries(lammps PRIVATE VORO::VORO)
+  target_link_libraries(lammps PRIVATE VORO::voro++)
 endif()

cmake/presets/kokkos-sycl-intel.cmake

@@ -6,13 +6,24 @@ set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SYCL   ON CACHE BOOL "" FORCE)
 
+set(FFT "MKL" CACHE STRING "" FORCE)
+set(FFT_KOKKOS "MKL_GPU" CACHE STRING "" FORCE)
+
+unset(USE_INTERNAL_LINALG)
+unset(USE_INTERNAL_LINALG CACHE)
+set(BLAS_VENDOR "Intel10_64_dyn")
+
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 
 set(CMAKE_CXX_COMPILER icpx CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER icx CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
 # Silence everything
 set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
-set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-max-parallel-link-jobs=32 -fsycl-targets=spir64_gen -Xsycl-target-backend \"-device 12.60.7\" " CACHE STRING "" FORCE)
+#set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
+#set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
+set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel " CACHE STRING "" FORCE)

cmake/presets/oneapi.cmake

@@ -3,26 +3,9 @@
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
-unset(HAVE_OMP_H_INCLUDE CACHE)
+# force using internal BLAS/LAPCK since external ones may not be ABI compatible
-set(OpenMP_C "icx" CACHE STRING "" FORCE)
+set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

doc/.gitignore

@@ -17,3 +17,10 @@
 *.el
 /utils/sphinx-config/_static/mathjax
 /utils/sphinx-config/_static/polyfill.js
+/src/pairs.rst
+/src/bonds.rst
+/src/angles.rst
+/src/dihedrals.rst
+/src/impropers.rst
+/src/computes.rst
+/src/fixes.rst

doc/Makefile

@@ -83,7 +83,10 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+globbed-tocs:
+	$(PYTHON) $(BUILDDIR)/utils/make-globbed-tocs.py -d $(RSTDIR)
+
+html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -113,7 +116,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
@@ -132,7 +135,7 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf fasthtml/PDF/.[sg]*
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
-spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; \
@@ -143,7 +146,7 @@ spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives
 	)
 	@echo "Spell check finished."
 
-epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
@@ -166,7 +169,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi

doc/src/Commands_fix.rst

@@ -178,6 +178,7 @@ OPT.
    * :doc:`python/move <fix_python_move>`
    * :doc:`qbmsst <fix_qbmsst>`
    * :doc:`qeq/comb (o) <fix_qeq_comb>`
+   * :doc:`qeq/ctip <fix_qeq>`
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`

doc/src/Commands_pair.rst

@@ -44,7 +44,7 @@ OPT.
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
    * :doc:`born/gauss <pair_born_gauss>`
    * :doc:`bpm/spring <pair_bpm_spring>`
-   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian (ko) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
    * :doc:`buck (giko) <pair_buck>`
    * :doc:`buck/coul/cut (giko) <pair_buck>`
@@ -59,6 +59,7 @@ OPT.
    * :doc:`comb (o) <pair_comb>`
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
+   * :doc:`coul/ctip <pair_coul>`
    * :doc:`coul/cut (gko) <pair_coul>`
    * :doc:`coul/cut/dielectric <pair_dielectric>`
    * :doc:`coul/cut/global (o) <pair_coul>`

doc/src/Howto_bioFF.rst

@@ -1,5 +1,5 @@
-CHARMM, AMBER, COMPASS, and DREIDING force fields
+CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
-=================================================
+=======================================================
 
 A compact summary of the concepts, definitions, and properties of
 force fields with explicit bonded interactions (like the ones discussed
@@ -236,6 +236,40 @@ documentation for the formula it computes.
 
 * :doc:`special_bonds <special_bonds>` dreiding
 
+OPLS
+----
+
+OPLS (Optimized Potentials for Liquid Simulations) is a general force
+field for atomistic simulation of organic molecules in solvent.  It was
+developed by the `Jorgensen group
+<https://traken.chem.yale.edu/oplsaam.html>`_ at Purdue University and
+later at Yale University.  Multiple versions of the OPLS parameters
+exist for united atom representations (OPLS-UA) and for all-atom
+representations (OPLS-AA).
+
+This force field is based on atom types mapped to specific functional
+groups in organic and biological molecules.  Each atom includes a
+static, partial atomic charge reflecting the oxidation state of the
+element derived from its bonded neighbors :ref:`(Jorgensen)
+<howto-jorgensen>` and computed based on increments determined by the
+atom type of the atoms bond to it.
+
+The interaction styles listed below compute force field formulas that
+are fully or in part consistent with the OPLS style force fields.  See
+each command's documentation for the formula it computes.  Some are only
+compatible with a subset of OPLS interactions.
+
+* :doc:`bond_style <bond_harmonic>` harmonic
+* :doc:`angle_style <angle_harmonic>` harmonic
+* :doc:`dihedral_style <dihedral_opls>` opls
+* :doc:`improper_style <improper_cvff>` cvff
+* :doc:`improper_style <improper_fourier>` fourier
+* :doc:`improper_style <improper_harmonic>` harmonic
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
+* :doc:`pair_modify <pair_modify>` geometric
+* :doc:`special_bonds <special_bonds>` lj/coul 0.0 0.0 0.5
+
 ----------
 
 .. _Typelabel2:
@@ -266,3 +300,6 @@ documentation for the formula it computes.
 
 **(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
 
+.. _howto-Jorgensen:
+
+**(Jorgensen)** Jorgensen, Tirado-Rives (1988). J Am Chem Soc, 110, 1657-1666. https://doi.org/10.1021/ja00214a001

doc/src/Howto_bpm.rst

@@ -42,7 +42,8 @@ Currently, there are two types of bonds included in the BPM package. The
 first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
 pairwise, central body forces. Point particles must have :doc:`bond atom
 style <atom_style>` and may be thought of as nodes in a spring
-network. Alternatively, the second bond style, :doc:`bond bpm/rotational
+network. An optional multibody term can be used to adjust the network's
+Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational
 <bond_bpm_rotational>`, resolves tangential forces and torques arising
 with the shearing, bending, and twisting of the bond due to rotation or
 displacement of particles.  Particles are similar to those used in the
@@ -55,8 +56,9 @@ orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
 In addition to bond styles, a new pair style :doc:`pair bpm/spring
 <pair_bpm_spring>` was added to accompany the bpm/spring bond
-style. This pair style is simply a hookean repulsion with similar
+style. By default, this pair style is simply a hookean repulsion with
-velocity damping as its sister bond style.
+similar velocity damping as its sister bond style, but optional
+arguments can be used to modify the force.
 
 ----------
 

doc/src/Howto_chunk.rst

@@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
 ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
 
 Note that this compute allows the per-atom output of other
-:doc:`computes <compute>`, :doc:`fixes <fix>`, and
+:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
-:doc:`variables <variable>` to be used to define chunk IDs for each
+<variable>` to be used to define chunk IDs for each atom.  This means
-atom.  This means you can write your own compute or fix to output a
+you can write your own compute or fix to output a per-atom quantity to
-per-atom quantity to use as chunk ID.  See the :doc:`Modify <Modify>`
+use as chunk ID.  See the :doc:`Modify <Modify>` doc pages for info on
-doc pages for info on how to do this.  You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
+how to do this.  You can also define a :doc:`per-atom variable
-generate a chunk ID for each atom.
+<variable>` in the input script that uses a formula to generate a chunk
+ID for each atom.
 
 Fix ave/chunk command:
 ----------------------
 
-This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  For each chunk,
+This fix takes the ID of a :doc:`compute chunk/atom
-it then sums one or more specified per-atom values over the atoms in
+<compute_chunk_atom>` command as input.  For each chunk, it then sums
-each chunk.  The per-atom values can be any atom property, such as
+one or more specified per-atom values over the atoms in each chunk.  The
-velocity, force, charge, potential energy, kinetic energy, stress,
+per-atom values can be any atom property, such as velocity, force,
-etc.  Additional keywords are defined for per-chunk properties like
+charge, potential energy, kinetic energy, stress, etc.  Additional
-density and temperature.  More generally any per-atom value generated
+keywords are defined for per-chunk properties like density and
-by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
+temperature.  More generally any per-atom value generated by other
+:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
+variables <variable>`, can be summed over atoms in each chunk.
 
 Similar to other averaging fixes, this fix allows the summed per-chunk
 values to be time-averaged in various ways, and output to a file.  The
-fix produces a global array as output with one row of values per
+fix produces a global array as output with one row of values per chunk.
-chunk.
 
 Compute \*/chunk commands:
 --------------------------
@@ -97,17 +99,20 @@ category:
 * :doc:`compute torque/chunk <compute_vcm_chunk>`
 * :doc:`compute vcm/chunk <compute_vcm_chunk>`
 
-They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  As their names
+They each take the ID of a :doc:`compute chunk/atom
-indicate, they calculate the center-of-mass, radius of gyration,
+<compute_chunk_atom>` command as input.  As their names indicate, they
-moments of inertia, mean-squared displacement, temperature, torque,
+calculate the center-of-mass, radius of gyration, moments of inertia,
-and velocity of center-of-mass for each chunk of atoms.  The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
+mean-squared displacement, temperature, torque, and velocity of
-count of atoms in each chunk and extract other per-chunk properties.
+center-of-mass for each chunk of atoms.  The :doc:`compute
+property/chunk <compute_property_chunk>` command can tally the count of
+atoms in each chunk and extract other per-chunk properties.
 
-The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
+The reason these various calculations are not part of the :doc:`fix
+ave/chunk command <fix_ave_chunk>`, is that each requires a more
 complicated operation than simply summing and averaging over per-atom
-values in each chunk.  For example, many of them require calculation
+values in each chunk.  For example, many of them require calculation of
-of a center of mass, which requires summing mass\*position over the
+a center of mass, which requires summing mass\*position over the atoms
-atoms and then dividing by summed mass.
+and then dividing by summed mass.
 
 All of these computes produce a global vector or global array as
 output, with one or more values per chunk.  The output can be used in
@@ -118,9 +123,10 @@ various ways:
 * As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
   histogram values across chunks.  E.g. a histogram of cluster sizes or
   molecule diffusion rates.
-* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave().  E.g. to
+* As input to special functions of :doc:`equal-style variables
-  find the largest cluster or fastest diffusing molecule or average
+  <variable>`, like sum() and max() and ave().  E.g. to find the largest
-  radius-of-gyration of a set of molecules (chunks).
+  cluster or fastest diffusing molecule or average radius-of-gyration of
+  a set of molecules (chunks).
 
 Other chunk commands:
 ---------------------
@@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
 
 The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
 peratom value across the atoms in each chunk to produce a value per
-chunk.  When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
+chunk.  When used with the :doc:`compute chunk/spread/atom
-create peratom values that induce a new set of chunks with a second
+<compute_chunk_spread_atom>` command it can create peratom values that
-:doc:`compute chunk/atom <compute_chunk_atom>` command.
+induce a new set of chunks with a second :doc:`compute chunk/atom
+<compute_chunk_atom>` command.
 
 Example calculations with chunks
 --------------------------------

doc/src/Intro_portability.rst

@@ -31,18 +31,19 @@ Operating systems
 ^^^^^^^^^^^^^^^^^
 
 The primary development platform for LAMMPS is Linux.  Thus, the chances
-for LAMMPS to compile without problems on Linux machines are the best.
+for LAMMPS to compile without problems are the best on Linux machines.
 Also, compilation and correct execution on macOS and Windows (using
-Microsoft Visual C++) is checked automatically for largest part of the
+Microsoft Visual C++) is checked automatically for the largest part of
-source code.  Some (optional) features are not compatible with all
+the source code.  Some (optional) features are not compatible with all
 operating systems, either through limitations of the corresponding
-LAMMPS source code or through source code or build system
+LAMMPS source code or through incompatibilities of source code or
-incompatibilities of required libraries.
+build system of required external libraries or packages.
 
 Executables for Windows may be created natively using either Cygwin or
 Visual Studio or with a Linux to Windows MinGW cross-compiler.
 
-Additionally, FreeBSD and Solaris have been tested successfully.
+Additionally, FreeBSD and Solaris have been tested successfully to
+run LAMMPS and produce results consistent with those on Linux.
 
 Compilers
 ^^^^^^^^^

doc/src/Packages_details.rst

@@ -880,7 +880,7 @@ groups of atoms that interact with the remaining atoms as electrolyte.
 
 **Authors:** The ELECTRODE package is written and maintained by Ludwig
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
-Robert Meissner (TUHH, Hamburg, Germany).
+Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
 
 .. versionadded:: 4May2022
 

doc/src/Run_windows.rst

@@ -3,71 +3,70 @@ Running LAMMPS on Windows
 
 To run a serial (non-MPI) executable, follow these steps:
 
-* Get a command prompt by going to Start->Run... ,
+* Install a LAMMPS installer package from https://packages.lammps.org/windows.html
-  then typing "cmd".
+* Open the "Command Prompt" or "Terminal" app.
-* Move to the directory where you have your input script,
+* Change to the directory where you have your input script,
   (e.g. by typing: cd "Documents").
-* At the command prompt, type "lmp -in in.file", where
+* At the command prompt, type "lmp -in in.file.lmp", where
-  in.file is the name of your LAMMPS input script.
+  ``in.file.lmp`` is the name of your LAMMPS input script.
 
 Note that the serial executable includes support for multi-threading
-parallelization from the styles in the OPENMP packages.  To run with
+parallelization from the styles in the OPENMP and KOKKOS packages.
-4 threads, you can type this:
+To run with 4 threads, you can type this:
 
 .. code-block:: bash
 
-   lmp -in in.lj -pk omp 4 -sf omp
+   lmp -in in.lj.lmp -pk omp 4 -sf omp
+   lmp -in in.lj.lmp -k on t 4 -sf kk
+
+Alternately, you can also install a package with LAMMPS-GUI included and
+open the LAMMPS-GUI app (the package includes the command line version
+of LAMMPS as well) and open the input file in the GUI and run it from
+there.  For details on LAMMPS-GUI, see :doc:`Howto_lammps_gui`.
 
 ----------
 
-For the MPI executable, which allows you to run LAMMPS under Windows
+For the MS-MPI executables, which allow you to run LAMMPS under Windows
-in parallel, follow these steps.
+in parallel using MPI rather than multi-threading, follow these steps.
 
-Download and install a compatible MPI library binary package:
+Download and install the MS-MPI runtime package ``msmpisetup.exe`` from
-
+https://www.microsoft.com/en-us/download/details.aspx?id=105289 (Note
-* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
+that the ``msmpisdk.msi`` is **only** required for **compilation** of
-* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
+LAMMPS from source on Windows using Microsoft Visual Studio). After
-
+installation of MS-MPI perform a reboot.
-The LAMMPS Windows installer packages will automatically adjust your
-path for the default location of this MPI package. After the
-installation of the MPICH2 software, it needs to be integrated into
-the system.  For this you need to start a Command Prompt in
-*Administrator Mode* (right click on the icon and select it). Change
-into the MPICH2 installation directory, then into the subdirectory
-**bin** and execute **smpd.exe -install**\ . Exit the command window.
-
-* Get a new, regular command prompt by going to Start->Run... ,
-  then typing "cmd".
-* Move to the directory where you have your input file
-  (e.g. by typing: cd "Documents").
 
 Then you can run the executable in serial like in the example above
 or in parallel using MPI with one of the following commands:
 
 .. code-block:: bash
 
-   mpiexec -localonly 4 lmp -in in.file
+   mpiexec -localonly 4 lmp -in in.file.lmp
-   mpiexec -np 4 lmp -in in.file
+   mpiexec -np 4 lmp -in in.file.lmp
 
-where in.file is the name of your LAMMPS input script. For the latter
+where ``in.file.lmp`` is the name of your LAMMPS input script. For the
-case, you may be prompted to enter the password that you set during
+latter case, you may be prompted to enter the password that you set
-installation of the MPI library software.
+during installation of the MPI library software.
 
 In this mode, output may not immediately show up on the screen, so if
 your input script takes a long time to execute, you may need to be
 patient before the output shows up.
 
-The parallel executable can also run on a single processor by typing
+Note that the parallel executable also includes OpenMP multi-threading
-something like this:
+through both the OPENMP and the KOKKOS package, which can be combined
+with MPI using something like:
 
 .. code-block:: bash
 
-   lmp -in in.lj
+   mpiexec -localonly 2 lmp -in in.lj.lmp -pk omp 2 -sf omp
+   mpiexec -localonly 2 lmp -in in.lj.lmp -kokkos on t 2 -sf kk
 
-Note that the parallel executable also includes OpenMP
+-------------
-multi-threading, which can be combined with MPI using something like:
-
-.. code-block:: bash
-
-   mpiexec -localonly 2 lmp -in in.lj -pk omp 2 -sf omp
 
+MPI parallelization will work for *all* functionality in LAMMPS and in
+many cases the MPI parallelization is more efficient than
+multi-threading since LAMMPS was designed from ground up for MPI
+parallelization using domain decomposition.  Multi-threading is only
+available for selected styles and implemented on top of the MPI
+parallelization.  Multi-threading is most useful for systems with large
+load imbalances when using domain decomposition and a smaller number
+of threads (<= 8).

doc/src/angles.rst

@@ -1,8 +0,0 @@
-Angle Styles
-############
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   angle_*

doc/src/bond_bpm_spring.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/spring keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor*
 
   .. parsed-literal::
 
@@ -36,6 +36,9 @@ Syntax
        *break* value = *yes* or *no*
           indicates whether bonds break during a run
 
+       *volume/factor* value = *yes* or *no*
+          indicates whether forces include the volumetric contribution
+
 Examples
 """"""""
 
@@ -44,6 +47,9 @@ Examples
    bond_style bpm/spring
    bond_coeff 1 1.0 0.05 0.1
 
+   bond_style bpm/spring volume/factor yes
+   bond_coeff 1 1.0 0.05 0.1 0.5
+
    bond_style bpm/spring myfix 1000 time id1 id2
    dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
    dump_modify 1 write_header no
@@ -97,15 +103,6 @@ approach the critical strain
 
    w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
 
-The following coefficients must be defined for each bond type via the
-:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
-the data file or restart files read by the :doc:`read_data
-<read_data>` or :doc:`read_restart <read_restart>` commands:
-
-* :math:`k`             (force/distance units)
-* :math:`\epsilon_c`    (unit less)
-* :math:`\gamma`        (force/velocity units)
-
 If the *normalize* keyword is set to *yes*, the elastic bond force will be
 normalized by :math:`r_0` such that :math:`k` must be given in force units.
 
@@ -123,6 +120,43 @@ during a simulation run. This will prevent some unnecessary calculation.
 However, if a bond reaches a strain greater than :math:`\epsilon_c`,
 it will trigger an error.
 
+.. versionadded:: TBD
+
+The *volume/factor* keyword toggles whether an additional multibody
+contribution is added to he force using the formulation in
+:ref:`(Clemmer2) <multibody-Clemmer>`,
+
+.. math::
+
+   \alpha_v \left(\left[\frac{V_i + V_j}{V_{0,i} + V_{0,j}}\right]^{1/3} - \frac{r_{ij}}{r_{0,ij}}\right)
+
+where :math:`\alpha_v` is a user specified coefficient and :math:`V_i`
+and :math:`V_{0,i}` are estimates of the current and local volume
+of atom :math:`i`. These volumes are calculated as the sum of current
+or initial bond lengths cubed. In 2D, the volume is replaced with an area
+calculated using bond lengths squared and the cube root in the above equation
+is accordingly replaced with a square root. This approximation assumes bonds
+are evenly distributed on a spherical surface and neglects constant prefactors
+which are irrelevant since only the ratio of volumes matters. This term may be
+used to adjust the Poisson's ratio.
+
+If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
+(or adding) that bond's contribution.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* :math:`k`             (force/distance units)
+* :math:`\epsilon_c`    (unit less)
+* :math:`\gamma`        (force/velocity units)
+
+Additionally, if *volume/factor* is set to *yes*, a fourth coefficient
+must be provided:
+
+* :math:`a_v`           (force units)
+
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
@@ -213,7 +247,7 @@ Related commands
 Default
 """""""
 
-The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
+The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, *break* = *yes*, and *volume/factor* = *no*
 
 ----------
 
@@ -224,3 +258,7 @@ The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *
 .. _Groot4:
 
 **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _multibody-Clemmer:
+
+**(Clemmer2)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

doc/src/bonds.rst

@@ -1,8 +0,0 @@
-Bond Styles
-###########
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   bond_*

doc/src/compute_angle_local.rst

@@ -78,7 +78,7 @@ system and output the statistics in various ways:
    compute 2 all angle/local eng theta v_cos v_cossq set theta t
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo

doc/src/compute_bond_local.rst

@@ -139,7 +139,7 @@ output the statistics in various ways:
    compute 2 all bond/local engpot dist v_dsq set dist d
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo

doc/src/compute_composition_atom.rst

@@ -88,6 +88,10 @@ too frequently.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/compute_dihedral_local.rst

@@ -76,7 +76,7 @@ angle in the system and output the statistics in various ways:
    compute 2 all dihedral/local phi v_cos v_cossq set phi p
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo

doc/src/compute_pressure.rst

@@ -125,10 +125,6 @@ where thermo_temp is the ID of a similarly defined compute of style
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Output info
 """""""""""
 

doc/src/compute_reduce.rst

@@ -206,11 +206,13 @@ IDs and the bond stretch will be printed with thermodynamic output.
 
 The *inputs* keyword allows selection of whether all the inputs are
 per-atom or local quantities.  As noted above, all the inputs must be
-the same kind (per-atom or local).  Per-atom is the default setting.
+the same kind (per-atom or local).  Per-atom is the default setting.  If
-If a compute or fix is specified as an input, it must produce per-atom
+a compute or fix is specified as an input, it must produce per-atom or
-or local data to match this setting.  If it produces both, e.g. for
+local data to match this setting.  If it produces both, like for example
 the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
-this keyword selects between them.
+this keyword selects between them.  If a compute *only* produces local
+data, like for example the :doc:`compute bond/local command
+<compute_bond_local>`, the setting "inputs local" is *required*.
 
 ----------
 

doc/src/compute_reduce_chunk.rst

@@ -37,55 +37,57 @@ Description
 
 Define a calculation that reduces one or more per-atom vectors into
 per-chunk values.  This can be useful for diagnostic output.  Or when
-used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
+used in conjunction with the :doc:`compute chunk/spread/atom
-used to create per-atom values that induce a new set of chunks with a
+<compute_chunk_spread_atom>` command it can be used to create per-atom
-second :doc:`compute chunk/atom <compute_chunk_atom>` command.  An
+values that induce a new set of chunks with a second :doc:`compute
-example is given below.
+chunk/atom <compute_chunk_atom>` command.  An example is given below.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
-to a single chunk (or no chunk).  The ID for this command is specified
+chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
-as chunkID.  For example, a single chunk could be the atoms in a
+single chunk (or no chunk).  The ID for this command is specified as
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+chunkID.  For example, a single chunk could be the atoms in a molecule
-doc pages for details of how chunks can be defined and examples of how
+or atoms in a spatial bin.  See the :doc:`compute chunk/atom
-they can be used to measure properties of a system.
+<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
+details of how chunks can be defined and examples of how they can be
+used to measure properties of a system.
 
 For each atom, this compute accesses its chunk ID from the specified
-*chunkID* compute.  The per-atom value from an input contributes
+*chunkID* compute.  The per-atom value from an input contributes to a
-to a per-chunk value corresponding the the chunk ID.
+per-chunk value corresponding the chunk ID.
 
 The reduction operation is specified by the *mode* setting and is
 performed over all the per-atom values from the atoms in each chunk.
-The *sum* option adds the pre-atom values to a per-chunk total.  The
+The *sum* option adds the per-atom values to a per-chunk total.  The
-*min* or *max* options find the minimum or maximum value of the
+*min* or *max* options find the minimum or maximum value of the per-atom
-per-atom values for each chunk.
+values for each chunk.
 
-Note that only atoms in the specified group contribute to the
+Note that only atoms in the specified group contribute to the reduction
-reduction operation.  If the *chunkID* compute returns a 0 for the
+operation.  If the *chunkID* compute returns a 0 for the chunk ID of an
-chunk ID of an atom (i.e., the atom is not in a chunk defined by the
+atom (i.e., the atom is not in a chunk defined by the :doc:`compute
-:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
+chunk/atom <compute_chunk_atom>` command), that atom will also not
-also not contribute to the reduction operation.  An input that is a
+contribute to the reduction operation.  An input that is a compute or
-compute or fix may define its own group which affects the quantities
+fix may define its own group which affects the quantities it returns.
-it returns.  For example, a compute with return a zero value for atoms
+For example, a compute will return a zero value for atoms that are not
-that are not in the group specified for that compute.
+in the group specified for that compute.
 
 Each listed input is operated on independently.  Each input can be the
-result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
+result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
-of an atom-style :doc:`variable <variable>`.
+evaluation of an atom-style :doc:`variable <variable>`.
 
-Note that for values from a compute or fix, the bracketed index I can
+Note that for values from a compute or fix, the bracketed index I can be
-be specified using a wildcard asterisk with the index to effectively
+specified using a wildcard asterisk with the index to effectively
 specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If :math:`N` is the size of the vector (for *mode* = scalar) or the
+"m\*n".  If :math:`N` is the size of the vector (for *mode* = scalar) or
-number of columns in the array (for *mode* = vector), then an asterisk
+the number of columns in the array (for *mode* = vector), then an
-with no numeric values means all indices from 1 to :math:`N`.  A leading
+asterisk with no numeric values means all indices from 1 to :math:`N`.
-asterisk means all indices from 1 to n (inclusive).  A trailing
+A leading asterisk means all indices from 1 to n (inclusive).  A
-asterisk means all indices from n to :math:`N` (inclusive).  A middle asterisk
+trailing asterisk means all indices from n to :math:`N` (inclusive).  A
-means all indices from m to n (inclusive).
+middle asterisk means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  For example, the following two compute reduce/chunk
+had been listed one by one.  For example, the following two compute
-commands are equivalent, since the
+reduce/chunk commands are equivalent, since the :doc:`compute
-:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
+property/chunk <compute_property_chunk>` command creates a per-atom
 array with 3 columns:
 
 .. code-block:: LAMMPS
@@ -164,13 +166,14 @@ Output info
 """""""""""
 
 This compute calculates a global vector if a single input value is
-specified, otherwise a global array is output.  The number of columns
+specified, otherwise a global array is output.  The number of columns in
-in the array is the number of inputs provided.  The length of the
+the array is the number of inputs provided.  The length of the vector or
-vector or the number of vector elements or array rows = the number of
+the number of vector elements or array rows = the number of chunks
-chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The vector or array can
+*Nchunk* as calculated by the specified :doc:`compute chunk/atom
-be accessed by any command that uses global values from a compute as
+<compute_chunk_atom>` command.  The vector or array can be accessed by
-input.  See the :doc:`Howto output <Howto_output>` page for an
+any command that uses global values from a compute as input.  See the
-overview of LAMMPS output options.
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+options.
 
 The per-atom values for the vector or each column of the array will be
 in whatever :doc:`units <units>` the corresponding input value is in.
@@ -183,7 +186,9 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
+:doc:`compute chunk/atom <compute_chunk_atom>`,
+:doc:`compute reduce <compute_reduce>`,
+:doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
 
 Default
 """""""

doc/src/compute_rheo_property_atom.rst

@@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
 Many properties require their respective fixes, listed below in related
 commands, be defined. For instance, the *viscosity* attribute is the
 viscosity of a particle calculated by
-:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
 properties is described below.
 
 The *phase* property indicates whether the particle is in a fluid state,

doc/src/compute_stress_mop.rst

@@ -129,6 +129,9 @@ package <Build_package>` doc page on for more info.
 The method is implemented for orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
+Contributions from bonds, angles, and dihedrals are not compatible
+with MPI parallel runs.
+
 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

doc/src/compute_temp_deform.rst

@@ -128,6 +128,12 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
 thermostatting.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/compute_temp_partial.rst

@@ -82,12 +82,6 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
 thermostatting.
 
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
 Output info
 """""""""""
 

doc/src/computes.rst

@@ -1,8 +0,0 @@
-Computes
-########
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   compute_*

doc/src/dihedrals.rst

@@ -1,8 +0,0 @@
-Dihedral Styles
-###############
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   dihedral_*

doc/src/fix.rst

@@ -357,6 +357,7 @@ accelerated styles exist.
 * :doc:`python/move <fix_python_move>` - move particles using a Python function during a simulation run
 * :doc:`qbmsst <fix_qbmsst>` - quantum bath multi-scale shock technique time integrator
 * :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential
+* :doc:`qeq/ctip <fix_qeq>` - charge equilibration for CTIP potential
 * :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
 * :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
 * :doc:`qeq/point <fix_qeq>` - charge equilibration via point method

doc/src/fix_adapt.rst

@@ -322,29 +322,33 @@ all types from 1 to :math:`N`.  A leading asterisk means all types from
 If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
 sub-style name. The bond styles that currently work with fix adapt are:
 
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`class2 <bond_class2>`                       | r0                        | type bonds |
+| :doc:`class2 <bond_class2>`                         | k2,k3,k4,r0               | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`fene <bond_fene>`                           | k,r0                      | type bonds |
+| :doc:`fene <bond_fene>`                             | k,r0                      | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`fene/expand <bond_fene_expand>`             | k,r0,epsilon,sigma,shift  | type bonds |
+| :doc:`fene/expand <bond_fene_expand>`               | k,r0,epsilon,sigma,shift  | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`fene/nm <bond_fene>`                        | k,r0                      | type bonds |
+| :doc:`fene/nm <bond_fene>`                          | k,r0                      | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`gromos <bond_gromos>`                       | k,r0                      | type bonds |
+| :doc:`gaussian <bond_gaussian>`                     | alpha,width,r0            | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`harmonic <bond_harmonic>`                   | k,r0                      | type bonds |
+| :doc:`gromos <bond_gromos>`                         | k,r0                      | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`harmonic/shift <bond_harmonic_shift>`       | k,r0,r1                   | type bonds |
+| :doc:`harmonic <bond_harmonic>`                     | k,r0                      | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k                         | type bonds |
+| :doc:`harmonic/restrain <bond_harmonic_restrain>`   | k                         | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`mm3 <bond_mm3>`                             | k,r0                      | type bonds |
+| :doc:`harmonic/shift <bond_harmonic_shift>`         | k,r0,r1                   | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`morse <bond_morse>`                         | r0                        | type bonds |
+| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1                   | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
-| :doc:`nonlinear <bond_nonlinear>`                 | epsilon,r0                | type bonds |
+| :doc:`mm3 <bond_mm3>`                               | k,r0                      | type bonds |
-+---------------------------------------------------+---------------------------+------------+
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`morse <bond_morse>`                           | d0,alpha,r0               | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`nonlinear <bond_nonlinear>`                   | lamda,epsilon,r0          | type bonds |
++-----------------------------------------------------+---------------------------+------------+
 
 ----------
 
@@ -367,31 +371,37 @@ all types from 1 to :math:`N`.  A leading asterisk means all types from
 If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
 sub-style name. The angle styles that currently work with fix adapt are:
 
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`harmonic <angle_harmonic>`                                   | k,theta0        | type angles |
+| :doc:`harmonic <angle_harmonic>`                                   | k,theta0           | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`charmm <angle_charmm>`                                       | k,theta0        | type angles |
+| :doc:`charmm <angle_charmm>`                                       | k,theta0           | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`class2 <angle_class2>`                                       | k2,k3,k4,theta0 | type angles |
+| :doc:`class2 <angle_class2>`                                       | k2,k3,k4,theta0    | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`cosine <angle_cosine>`                                       | k               | type angles |
+| :doc:`cosine <angle_cosine>`                                       | k                  | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`cosine/periodic <angle_cosine_periodic>`                     | k,b,n           | type angles |
+| :doc:`cosine/delta <angle_cosine_delta>`                           | k                  | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0        | type angles |
+| :doc:`cosine/periodic <angle_cosine_periodic>`                     | k,b,n              | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`dipole <angle_dipole>`                                       | k,gamma0        | type angles |
+| :doc:`cosine/squared <angle_cosine_squared>`                       | k,theta0           | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`fourier <angle_fourier>`                                     | k,c0,c1,c2      | type angles |
+| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0           | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`fourier/simple <angle_fourier_simple>`                       | k,c,n           | type angles |
+| :doc:`dipole <angle_dipole>`                                       | k,gamma0           | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`mm3 <angle_mm3>`                                             | k,theta0        | type angles |
+| :doc:`fourier <angle_fourier>`                                     | k,c0,c1,c2         | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`quartic <angle_quartic>`                                     | k2,k3,k4,theta0 | type angles |
+| :doc:`fourier/simple <angle_fourier_simple>`                       | k,c,n              | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
-| :doc:`spica <angle_spica>`                                         | k,theta0        | type angles |
+| :doc:`gaussian <angle_gaussian>`                                   | alpha,width,theta0 | type angles |
-+--------------------------------------------------------------------+-----------------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`mm3 <angle_mm3>`                                             | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`quartic <angle_quartic>`                                     | k2,k3,k4,theta0    | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`spica <angle_spica>`                                         | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
 
 Note that internally, theta0 is stored in radians, so the variable
 this fix uses to reset theta0 needs to generate values in radians.

doc/src/fix_addforce.rst

@@ -115,10 +115,6 @@ correctly, the minimization will not converge properly.
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_atom_swap.rst

@@ -119,15 +119,14 @@ groups of atoms that have different charges, these charges will not be
 changed when the atom types change.
 
 Since this fix computes total potential energies before and after
-proposed swaps, so even complicated potential energy calculations are
+proposed swaps, even complicated potential energy calculations are
-OK, including the following:
+acceptable, including the following:
 
 * long-range electrostatics (:math:`k`-space)
 * many body pair styles
-* hybrid pair styles
+* hybrid pair styles (with restrictions)
-* eam pair styles
+* EAM pair styles
 * triclinic systems
-* need to include potential energy contributions from other fixes
 
 Some fixes have an associated potential energy. Examples of such fixes
 include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
@@ -181,6 +180,10 @@ 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.
 
+When this fix is used with a :doc:`hybrid pair style <pair_hybrid>`
+system, only swaps between atom types of the same sub-style (or
+combination of sub-styles) are permitted.
+
 This fix cannot be used with systems that do not have per-type masses
 (e.g. atom style sphere) since the implemented algorithm pre-computes
 velocity rescaling factors from per-type masses and ignores any per-atom

doc/src/fix_aveforce.rst

@@ -71,10 +71,6 @@ to it.
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_gcmc.rst

@@ -50,8 +50,8 @@ Syntax
        *intra_energy* value = intramolecular energy (energy units)
        *tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
        *overlap_cutoff* value = maximum pair distance for overlap rejection (distance units)
-       *max* value = Maximum number of molecules allowed in the system
+       *max* value = Maximum number of atoms allowed in the fix group (and region)
-       *min* value = Minimum number of molecules allowed in the system
+       *min* value = Minimum number of atoms allowed in the fix group (and region)
 
 Examples
 """"""""
@@ -380,10 +380,11 @@ an infinite positive energy to all new configurations that place any
 pair of atoms closer than the specified overlap cutoff distance.
 
 The *max* and *min* keywords allow for the restriction of the number of
-atoms in the simulation. They automatically reject all insertion or
+atoms in the fix group (and region in case the *region* keyword is
-deletion moves that would take the system beyond the set boundaries.
+used).  They automatically reject all insertion or deletion moves that
-Should the system already be beyond the boundary, only moves that bring
+would take the system beyond the set boundaries.  Should the system
-the system closer to the bounds may be accepted.
+already be beyond the boundary, only moves that bring the system closer
+to the bounds may be accepted.
 
 The *group* keyword adds all inserted atoms to the :doc:`group <group>`
 of the group-ID value. The *grouptype* keyword adds all inserted atoms

doc/src/fix_halt.rst

@@ -101,7 +101,7 @@ hstyle = bondmax option.
 .. code-block:: LAMMPS
 
    compute         bdist all bond/local dist
-   compute         bmax all reduce max c_bdist
+   compute         bmax all reduce max c_bdist inputs local
    variable        bondmax equal c_bmax
 
 Thus these two versions of a fix halt command will do the same thing:

doc/src/fix_langevin.rst

@@ -231,12 +231,6 @@ the particles.  As described below, this energy can then be printed
 out or added to the potential energy of the system to monitor energy
 conservation.
 
-.. note::
-
-   This accumulated energy does NOT include kinetic energy removed
-   by the *zero* flag. LAMMPS will print a warning when both options are
-   active.
-
 The keyword *zero* can be used to eliminate drift due to the
 thermostat. Because the random forces on different atoms are
 independent, they do not sum exactly to zero.  As a result, this fix

doc/src/fix_nonaffine_displacement.rst

@@ -102,7 +102,6 @@ zeroed. The *update* reference style implies the reference state will be updated
 *nstep* timesteps. The *offset* reference will update the reference state *nstep*
 timesteps before a multiple of *nevery* timesteps.
 
-
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
@@ -129,6 +128,12 @@ This compute 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.
 
+As this fix depends on a run including specific reference timesteps, it
+currently does not update peratom values if used in conjunction with the
+:doc:`rerun command <rerun>` since it cannot ensure the necessary reference
+timesteps are included.
+
+
 Related commands
 """"""""""""""""
 

doc/src/fix_nph_body.rst

@@ -79,8 +79,6 @@ It also means that changing attributes of *thermo_temp* or
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_npt_body.rst

@@ -103,8 +103,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_nvt_body.rst

@@ -85,8 +85,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_pour.rst

@@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
    the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
    for the temperature compute you are using.
 
+.. admonition:: Implementation Notes
+  :class: Hint
+
+  The exact insertion procedure depends on many factors (e.g. the range of
+  diameters inserted or whether molecules are being inserted). However, in
+  the simplest scenario of monodisperse atoms, the procedure works as
+  follows. First, the number of timesteps between two insertion events is
+  calculated as the time for a particle to fall through the insertion region,
+  accounting for gravity and any region motion. Next, the target number of
+  particles inserted per event (assuming no failed insertions due to overlaps)
+  is calculated as the product of the volume fraction and the volume of the
+  insertion region divided by the volume of a particle (or area in 2D).
+  Events are repeated until all N particles have been inserted, where
+  the final event is likely interrupted upon reaching N. Estimates of this
+  process are printed to the log/screen at the start of a run.
+
 ----------
 
 All other keywords are optional with defaults as shown below.

doc/src/fix_qeq.rst

@@ -1,6 +1,7 @@
 .. index:: fix qeq/point
 .. index:: fix qeq/shielded
 .. index:: fix qeq/slater
+.. index:: fix qeq/ctip
 .. index:: fix qeq/dynamic
 .. index:: fix qeq/fire
 
@@ -13,6 +14,9 @@ fix qeq/shielded command
 fix qeq/slater command
 ======================
 
+fix qeq/ctip command
+====================
+
 fix qeq/dynamic command
 =======================
 
@@ -27,18 +31,20 @@ Syntax
    fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
+* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/ctip* or *qeq/dynamic* or *qeq/fire*
 * Nevery = perform charge equilibration every this many steps
 * cutoff = global cutoff for charge-charge interactions (distance unit)
 * tolerance = precision to which charges will be equilibrated
 * maxiter = maximum iterations to perform charge equilibration
-* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
+* qfile = a filename with QEq parameters or *coul/streitz* or *coul/ctip* or *reaxff*
 * zero or more keyword/value pairs may be appended
-* keyword = *alpha* or *qdamp* or *qstep* or *warn*
+* keyword = *alpha* or *cdamp* or *maxrepeat* or *qdamp* or *qstep* or *warn*
 
   .. parsed-literal::
 
        *alpha* value = Slater type orbital exponent (qeq/slater only)
+       *cdamp* value = damping parameter for Coulomb interactions (qeq/ctip only)
+       *maxrepeat* value = number of equilibration cycles allowed to ensure no atoms cross charge bounds (qeq/ctip only)
        *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
        *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
        *warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
@@ -51,6 +57,7 @@ Examples
    fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
    fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
    fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+   fix 1 all qeq/ctip 1 12 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
    fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
    fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
 
@@ -103,7 +110,7 @@ equalizes the derivative of energy with respect to charge of all the
 atoms) by adjusting the partial charge on individual atoms based on
 interactions with their neighbors within *cutoff*\ .  It requires a few
 parameters in the appropriate units for each atom type which are read
-from a file specified by *qfile*\ .  The file has the following format
+from a file specified by *qfile*\ .  The file has the following format:
 
 .. parsed-literal::
 
@@ -112,20 +119,32 @@ from a file specified by *qfile*\ .  The file has the following format
    ...
    Ntype chi eta gamma zeta qcore
 
+except for fix style *qeq/ctip* where the format is:
+
+.. parsed-literal::
+
+   1 chi eta gamma zeta qcore qmin qmax omega
+   2 chi eta gamma zeta qcore qmin qmax omega
+   ...
+   Ntype chi eta gamma zeta qcore qmin qmax omega
+
 There have to be parameters given for every atom type. Wildcard entries
 are possible using the same type range syntax as for "coeff" commands
 (i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
-Empty lines or any text following the pound sign (#) are ignored.
+Empty lines or any text following the pound sign (#) are ignored.  Each
-Each line starts with the atom type followed by five parameters.
+line starts with the atom type followed by eight parameters.  Only a
-Only a subset of the parameters is used by each QEq style as described
+subset of the parameters is used by each QEq style as described below,
-below, thus the others can be set to 0.0 if desired, but all five
+thus the others can be set to 0.0 if desired, but all eight entries per
-entries per line are required.
+line are required.
 
 * *chi* = electronegativity in energy units
 * *eta* = self-Coulomb potential in energy units
 * *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
 * *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
 * *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
+* *qmin* = lower bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
+* *qmax* = upper bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
+* *omega* = penalty parameter used to enforce charge bounds defined by the :ref:`CTIP <CTIP1>` potential in energy units
 
 The fix qeq styles will print a warning if the charges are not
 equilibrated within *tolerance* by *maxiter* steps, unless the
@@ -171,6 +190,22 @@ on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
 usually a good number.  Keyword *alpha* can be used to change the Slater
 type orbital exponent.
 
+.. versionadded:: TBD
+
+The *qeq/ctip* style describes partial charges on atoms in the same way
+as style *qeq/shielded* but also enables the definition of charge
+bounds.  Only the *chi*, *eta*, *gamma*, *qmin*, *qmax*, and *omega*
+parameters from the *qfile* file are used.  When using the string
+*coul/ctip* as filename, these parameters are extracted directly from an
+active *coul/ctip* pair style.  This style solves partial charges on
+atoms via the matrix inversion method.  Keyword *cdamp* can be used to
+change the damping parameter used to calculate Coulomb interactions.
+Keyword *maxrepeat* can be used to adjust the number of equilibration
+cycles allowed to ensure no atoms have crossed the charge bounds.  A
+value of 10 is usually a good choice.  A tolerance between 1.0e-6 and
+1.0e-8 is usually a good choice but should be checked in conjunction
+with the timestep for adequate energy conservation during dynamic runs.
+
 The *qeq/dynamic* style describes partial charges on atoms as point
 charges that interact through 1/r, but the extended Lagrangian method is
 used to solve partial charges on atoms.  Only the *chi* and *eta*
@@ -186,7 +221,7 @@ minimization algorithm to solve for equilibrium charges.  Keyword
 *qdamp* can be used to change the damping factor, while keyword *qstep*
 can be used to change the time step size.
 
-Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe
+Note that *qeq/point*, *qeq/shielded*, *qeq/slater*, and *qeq/ctip* describe
 different charge models, whereas the matrix inversion method and the
 extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
 different solvers.
@@ -266,6 +301,11 @@ Chemistry, 95, 3358-3363 (1991).
 **(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
 16, 11996 (1994)
 
+.. _CTIP1:
+
+**(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
+in preparation
+
 .. _vanDuin:
 
 **(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J

doc/src/fix_rheo.rst

@@ -16,8 +16,7 @@ Syntax
 * kstyle = *quintic* or *RK0* or *RK1* or *RK2*
 * zmin = minimal number of neighbors for reproducing kernels
 * zero or more keyword/value pairs may be appended to args
-* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
+* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
-            *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
 
   .. parsed-literal::
 

doc/src/fix_wall_flow.rst

@@ -123,6 +123,12 @@ also be potentially mitigated by using more multiple walls.
   conservative as possible (every timestep if needed).  Those are the
   default settings.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fixes.rst

@@ -1,8 +0,0 @@
-Fixes
-#####
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   fix_*

doc/src/group.rst

@@ -162,7 +162,7 @@ potential energy is above the threshold value :math:`-3.0`.
    compute         1 all pe/atom
    compute         2 all reduce sum c_1
    thermo_style    custom step temp pe c_2
-   run             0
+   run             0 post no
 
    variable        eatom atom "c_1 > -3.0"
    group           hienergy variable eatom
@@ -173,7 +173,7 @@ Note that these lines
 
    compute         2 all reduce sum c_1
    thermo_style    custom step temp pe c_2
-   run             0
+   run             0 post no
 
 are necessary to ensure that the "eatom" variable is current when the
 group command invokes it.  Because the eatom variable computes the

doc/src/impropers.rst

@@ -1,8 +0,0 @@
-Improper Styles
-###############
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   improper_*

doc/src/min_style.rst

@@ -3,6 +3,8 @@
 min_style cg command
 ====================
 
+Accelerator Variant: *cg/kk*
+
 min_style hftn command
 ======================
 

doc/src/pair_bpm_spring.rst

@@ -8,7 +8,14 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   pair_style bpm/spring
+   pair_style bpm/spring keyword value  ...
+
+* optional keyword = *anharmonic*
+
+  .. parsed-literal::
+
+       *anharmonic* value = *yes* or *no*
+          whether forces include the anharmonic term
 
 Examples
 """"""""
@@ -17,7 +24,8 @@ Examples
 
    pair_style bpm/spring
    pair_coeff * * 1.0 1.0 1.0
-   pair_coeff 1 1 1.0 1.0 1.0
+   pair_style bpm/spring anharmonic yes
+   pair_coeff 1 1 1.0 1.0 1.0 50.0
 
 Description
 """""""""""
@@ -28,12 +36,16 @@ Style *bpm/spring* computes pairwise forces with the formula
 
 .. math::
 
-   F = k (r - r_c)
+   F = k (r - r_c) + k_a (r - r_c)^3
 
-where :math:`k` is a stiffness and :math:`r_c` is the cutoff length.
+where :math:`k` is a stiffness, :math:`r_c` is the cutoff
-An additional damping force is also applied to interacting
+length, and :math:`k_a` is an optional anharmonic cubic prefactor
-particles. The force is proportional to the difference in the
+that can be enabled using the *anharmonic* keyword. The anharmonic
-normal velocity of particles
+term may be useful in scenarios that need to prevent large particle overlap.
+
+An additional damping force is also applied to interacting particles.
+The force is proportional to the difference in the normal velocity of
+particles
 
 .. math::
 
@@ -73,6 +85,12 @@ commands, or by mixing as described below:
 * :math:`r_c`           (distance units)
 * :math:`\gamma`        (force/velocity units)
 
+.. versionadded:: TBD
+
+Additionally, if *anharmonic* is set to *yes*, a fourth coefficient
+must be provided:
+
+* :math:`k_a`           (force/distance\^3 units)
 
 ----------
 
@@ -117,4 +135,5 @@ Related commands
 Default
 """""""
 
-none
+The option defaults are *anharmonic* = *no*
+

doc/src/pair_brownian.rst

@@ -1,12 +1,13 @@
 .. index:: pair_style brownian
 .. index:: pair_style brownian/omp
+.. index:: pair_style brownian/kk
 .. index:: pair_style brownian/poly
 .. index:: pair_style brownian/poly/omp
 
 pair_style brownian command
 ===========================
 
-Accelerator Variants: *brownian/omp*
+Accelerator Variants: *brownian/omp*, *brownian/kk*
 
 pair_style brownian/poly command
 ================================

doc/src/pair_coul.rst

@@ -4,6 +4,7 @@
 .. index:: pair_style coul/cut/omp
 .. index:: pair_style coul/cut/global
 .. index:: pair_style coul/cut/global/omp
+.. index:: pair_style coul/ctip
 .. index:: pair_style coul/debye
 .. index:: pair_style coul/debye/gpu
 .. index:: pair_style coul/debye/kk
@@ -38,6 +39,9 @@ pair_style coul/cut/global command
 
 Accelerator Variants: *coul/cut/omp*
 
+pair_style coul/ctip command
+============================
+
 pair_style coul/debye command
 =============================
 
@@ -79,7 +83,6 @@ pair_style tip4p/long command
 
 Accelerator Variants: *tip4p/long/omp*
 
-
 Syntax
 """"""
 
@@ -87,6 +90,7 @@ Syntax
 
    pair_style coul/cut cutoff
    pair_style coul/cut/global cutoff
+   pair_style coul/ctip alpha cutoff
    pair_style coul/debye kappa cutoff
    pair_style coul/dsf alpha cutoff
    pair_style coul/exclude cutoff
@@ -116,6 +120,9 @@ Examples
    pair_coeff * *
    pair_coeff 2 2 3.5
 
+   pair_style coul/ctip 0.30 12.0
+   pair_coeff * * NiO.ctip Ni O
+
    pair_style coul/debye 1.4 3.0
    pair_coeff * *
    pair_coeff 2 2 3.5
@@ -173,6 +180,33 @@ coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
 
 ----------
 
+.. versionadded:: TBD
+
+Style *coul/ctip* computes the Coulomb interactions as described in
+:ref:`Plummer <Plummer1>`. It uses the the damped shifted model as in
+style *coul/dsf* but is further extended to the second derivative of the
+potential and incorporates empirical charge shielding meant to
+approximate the more expensive Coulomb integrals used in style
+*coul/streitz*.  More details can be found in the referenced paper. Like
+the style *coul/streitz*, style *coul/ctip* is a variable charge
+potential and must be hybridized with a short-range potential via the
+:doc:`pair_style hybrid/overlay <pair_hybrid>` command. Charge
+equilibration must be performed with the :doc:`fix qeq/ctip <fix_qeq>`
+command. For example:
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
+   pair_coeff * * eam/fs NiO.eam.fs Ni O
+   pair_coeff * * coul/ctip NiO.ctip Ni O
+   fix 1 all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
+
+See the examples/ctip directory for an example input script using the
+CTIP potential. An Ni-O CTIP and EAM/FS parameterization are included
+for use with the example.
+
+----------
+
 Style *coul/debye* adds an additional exp() damping factor to the
 Coulombic term, given by
 
@@ -399,16 +433,18 @@ Restrictions
 """"""""""""
 
 The *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles are
-part of the KSPACE package.  The *coul/cut/global*, *coul/exclude* styles are
+part of the KSPACE package.  The *coul/cut/global*, *coul/exclude*, and
-part of the EXTRA-PAIR package.  The *tip4p/cut* style is part of the MOLECULE
+*coul/ctip* styles are part of the EXTRA-PAIR package.  The *tip4p/cut*
-package.  A pair style is only enabled if LAMMPS was built with its
+style is part of the MOLECULE package.  A pair style is only enabled if
-corresponding package.  See the :doc:`Build package <Build_package>`
+LAMMPS was built with its corresponding package.  See the
-doc page for more info.
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
+:doc:`pair_coeff <pair_coeff>`,
+:doc:`pair_style hybrid/overlay <pair_hybrid>`,
+:doc:`kspace_style <kspace_style>`
 
 Default
 """""""
@@ -432,6 +468,11 @@ Phys, 110, 8254 (1999).
 **(Streitz)** F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
 (1994).
 
+.. _Plummer1:
+
+**(Plummer)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
+in preparation
+
 .. _Jorgensen3:
 
 **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem

doc/src/pair_coul_diel.rst

@@ -71,6 +71,10 @@ The global cutoff (:math:`r_c`) specified in the pair_style command is used.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_coul_slater.rst

@@ -77,6 +77,10 @@ The global decay length of the charge (:math:`\lambda`) specified in the pair_st
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_granular.rst

@@ -741,10 +741,6 @@ atom types.
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_mesodpd.rst

@@ -287,6 +287,10 @@ concentration profiles of the two chemical species as
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_mie.rst

@@ -62,6 +62,10 @@ cutoff specified in the pair_style command is used.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_sph_heatconduction.rst

@@ -39,6 +39,10 @@ above.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_sph_lj.rst

@@ -43,6 +43,10 @@ above.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_sph_taitwater.rst

@@ -52,6 +52,10 @@ above.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_style.rst

@@ -151,6 +151,7 @@ accelerated styles exist.
 * :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
 * :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
 * :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
+* :doc:`coul/ctip <pair_coul>` - Charge Transfer Interatomic (Coulomb) Potential
 * :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential
 * :doc:`coul/cut/dielectric <pair_dielectric>` -
 * :doc:`coul/cut/global <pair_coul>` - cutoff Coulomb potential

doc/src/pairs.rst

@@ -1,8 +0,0 @@
-Pair Styles
-###########
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   pair_*

doc/src/read_dump.rst

@@ -115,10 +115,11 @@ to tell LAMMPS how many parallel files exist, via its specified
 
 The format of the dump file is selected through the *format* keyword.
 If specified, it must be the last keyword used, since all remaining
-arguments are passed on to the dump reader.  The *native* format is
+arguments are passed on to the dump reader.  The *native* format is for
-for native LAMMPS dump files, written with a :doc:`dump atom <dump>`
+native LAMMPS dump files, written with a :doc:`dump atom <dump>` or
-or :doc:`dump custom <dump>` command.  The *xyz* format is for generic XYZ
+:doc:`dump custom <dump>` command.  The *xyz* format is for generic XYZ
-formatted dump files.  These formats take no additional values.
+formatted dump files (see details below).  These formats take no
+additional values.
 
 The *molfile* format supports reading data through using the `VMD <vmd_>`_
 molfile plugin interface. This dump reader format is only available,
@@ -230,23 +231,39 @@ will then have a label corresponding to the fix-ID rather than "x" or
 "xs".  The *label* keyword can also be used to specify new column
 labels for fields *id* and *type*\ .
 
-For dump files in *xyz* format, only the *x*, *y*, and *z* fields are
+For dump files in *xyz* format, only the *type*, *x*, *y*, and *z*
-supported.  The dump file does not store atom IDs, so these are
+fields are supported.  There are many variants of the XYZ file format.
-assigned consecutively to the atoms as they appear in the dump file,
+LAMMPS will read the number of atoms from the first line of each frame,
-starting from 1.  Thus you should ensure that order of atoms is
+ignore the second (title) line, and then read one line for each atom in the format:
-consistent from snapshot to snapshot in the XYZ dump file.  See
+
-the :doc:`dump_modify sort <dump_modify>` command if the XYZ dump file
+.. parsed-literal::
-was written by LAMMPS.
+
+   <label> <x coordinate>  <y coordinate> <z coordinate>
+
+
+If the atom label is a numeric integer (like with XYZ files created by
+created with default settings by :doc:`dump style <dump>` *xyz*), that
+number will be used as the atom type.  If the atom label is a string,
+then a type map must be created using the :doc:`labelmap command
+<labelmap>`.  This map needs to associate each (numeric) atom type with
+a string label. The numeric atom type is stored internally.
+
+The xyz format dump file does not store atom IDs, so these are assigned
+consecutively to the atoms as they appear in the dump file, starting
+from 1.  Thus you should ensure that the order of atoms is consistent
+from snapshot to snapshot in the XYZ dump file.  See the
+:doc:`dump_modify sort <dump_modify>` command if the XYZ dump file was
+written by LAMMPS.
 
 For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and
 *vz* fields can be specified.  However, not all molfile formats store
 velocities, or their respective plugins may not support reading of
-velocities.  The molfile dump files do not store atom IDs, so these
+velocities.  The molfile dump files do not store atom IDs, so these are
-are assigned consecutively to the atoms as they appear in the dump
+assigned consecutively to the atoms as they appear in the dump file,
-file, starting from 1.  Thus you should ensure that order of atoms are
+starting from 1.  Thus you should ensure that the order of atoms are
-consistent from snapshot to snapshot in the molfile dump file.
+consistent from snapshot to snapshot in the molfile dump file.  See the
-See the :doc:`dump_modify sort <dump_modify>` command if the dump file
+:doc:`dump_modify sort <dump_modify>` command if the dump file was
-was written by LAMMPS.
+written by LAMMPS.
 
 The *adios* format supports all fields that the *native* format supports
 except for the *q* charge field.

doc/utils/check-styles.py

@@ -61,16 +61,51 @@ region = {}
 total = 0
 
 index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
+accel_pattern = re.compile(r"^.. include::\s+accel_styles.rst$")
 style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
+cmd_pattern = re.compile(r"^.. index:: ([a-zA-Z0-9/_]+)$")
 upper = re.compile("[A-Z]+")
-gpu = re.compile("(.+)/gpu$")
+gpu = re.compile("(.+)/gpu\\s*$")
-intel = re.compile("(.+)/intel$")
+intel = re.compile("(.+)/intel\\s*$")
-kokkos = re.compile("(.+)/kk$")
+kokkos = re.compile("(.+)/kk$\\s*")
-kokkos_skip = re.compile("(.+)/kk/(host|device)$")
+kokkos_skip = re.compile("(.+)/kk/(host|device)\\s*$")
-omp = re.compile("(.+)/omp$")
+omp = re.compile("(.+)/omp\\s*$")
-opt = re.compile("(.+)/opt$")
+opt = re.compile("(.+)/opt\\s*$")
 removed = re.compile("(.*)Deprecated$")
 
+accel_pattern = re.compile(r"^.. include::\s+accel_styles.rst$")
+
+def require_accel_include(path):
+    found = False
+    needs = False
+    # handle exceptions
+    if path == "src/min_style.rst" : needs = True
+    if path == "src/atom_style.rst" : needs = True
+    if path == "src/region.rst" : needs = True
+    # check file
+    with open(path, 'r') as reader:
+        for line in reader:
+            m = accel_pattern.match(line)
+            if m: found = True
+            m = index_pattern.match(line)
+            if m:
+                if gpu.match(line): needs = True
+                if omp.match(line): needs = True
+                if kokkos.match(line): needs = True
+                if intel.match(line): needs = True
+                if opt.match(line): needs = True
+            m = cmd_pattern.match(line)
+            if m:
+                if gpu.match(line): needs = True
+                if omp.match(line): needs = True
+                if kokkos.match(line): needs = True
+                if intel.match(line): needs = True
+                if opt.match(line): needs = True
+    if needs and not found:
+        print("Missing '.. include:: accel_style.rst' in file ", path)
+    if not needs and found:
+        print("Have '.. include:: accel_style.rst' without accelerated styles in file ", path)
+
 def load_index_entries_in_file(path):
     entries = []
     with open(path, 'r') as reader:
@@ -82,6 +117,11 @@ def load_index_entries_in_file(path):
                 entries.append((command_type, style))
     return entries
 
+def check_accel_includes():
+    rst_files = glob(os.path.join(doc_dir, '*.rst'))
+    for f in rst_files:
+        require_accel_include(f)
+
 def load_index_entries():
     index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
              'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
@@ -249,6 +289,8 @@ Total number of styles (including suffixes): %d""" \
        len(fix), len(improper), len(integrate), len(kspace), \
        len(minimize), len(pair), len(reader), len(region), total))
 
+check_accel_includes()
+
 index = load_index_entries()
 
 total_index = 0

doc/utils/converters/.gitignore

@@ -1 +1,2 @@
 *.egg-info
+/build

doc/utils/make-globbed-tocs.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python3
+
+"""
+Script to emulate globbed toctrees with the added feature
+to avoid adding files that are already included elsewhere.
+"""
+
+import os, re
+import filecmp
+import tempfile
+import shutil
+from glob import glob
+from argparse import ArgumentParser
+
+LAMMPS_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), '..', '..'))
+
+parser = ArgumentParser(prog='make-globbed-tocs.py',
+                        description="Create toctree files from patterns with exclusions")
+parser.add_argument("-v", "--verbose", action='store_true', help="Enable verbose output")
+parser.add_argument("-d", "--doc", help="Path to LAMMPS documentation sources")
+
+args = parser.parse_args()
+verbose = args.verbose
+if args.doc:
+    docsrc = os.path.realpath(args.doc)
+else:
+    docsrc = os.path.join(LAMMPS_DIR, 'doc', 'src')
+
+if not os.path.isdir(docsrc):
+    sys.exit(f"LAMMPS manual source dir {docsrc} does not exist")
+
+def glob_tocfile(style, name, head, exclude):
+
+    newname = None
+    exclude_re = re.compile(exclude)
+    if verbose: print("Processing style ", style)
+    with tempfile.NamedTemporaryFile(prefix=style + '.', delete=False) as f:
+        newname = f.name
+        if verbose: print("Temporary file: ", newname)
+        f.write(head.encode('utf-8'))
+        for doc in sorted(glob(os.path.join(docsrc, style + '_*.rst'))):
+            d,e = os.path.splitext(os.path.basename(doc))
+            if exclude_re.match(d):
+                if verbose: print("skipping file ", d)
+                continue
+            if verbose: print("processing file ", d)
+            f.write(("   " + d + "\n").encode('utf-8'))
+
+    oldname = os.path.join(docsrc, name)
+    if os.path.exists(oldname) and filecmp.cmp(newname, oldname, shallow=False):
+        print("File ", name, " is unchanged")
+        os.remove(newname)
+    else:
+        print("Overwriting file ", name, " with new version")
+        shutil.move(newname, os.path.join(docsrc, name))
+
+##################################
+
+pair_head = """Pair Styles
+###########
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('pair', 'pairs.rst', pair_head, r"pair_(coeff|modify|style|write)")
+
+bond_head = """Bond Styles
+###########
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('bond', 'bonds.rst', bond_head, r"bond_(coeff|modify|style|write)")
+
+angle_head = """Angle Styles
+############
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('angle', 'angles.rst', angle_head, r"angle_(coeff|modify|style|write)")
+
+dihedral_head = """Dihedral Styles
+###############
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('dihedral', 'dihedrals.rst', dihedral_head, r"dihedral_(coeff|modify|style|write)")
+
+improper_head = """Improper Styles
+###############
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('improper', 'impropers.rst', improper_head, r"improper_(coeff|modify|style|write)")
+
+compute_head = """Compute Styles
+###############
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('compute', 'computes.rst', compute_head, r"compute_modify")
+
+fix_head = """Fix Styles
+##########
+
+.. toctree::
+   :maxdepth: 1
+
+"""
+glob_tocfile('fix', 'fixes.rst', fix_head, r"fix_modify(|_atc_commands)")

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <7.5
+Sphinx >= 5.3.0, <8.2.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 sphinx-design

doc/utils/sphinx-config/false_positives.txt

@@ -639,6 +639,7 @@ cstyle
 csvr
 ctest
 ctilde
+ctip
 ctrl
 ctrn
 ctypes
@@ -1285,6 +1286,7 @@ gcc
 gcmc
 gdot
 GeC
+Geesthacht
 Geier
 gencode
 Geocomputing
@@ -3664,6 +3666,7 @@ Tanmoy
 Tartakovsky
 taskset
 taubi
+Tavenner
 taylor
 tb
 tchain
@@ -4217,6 +4220,7 @@ zeeman
 Zeeman
 Zemer
 zenodo
+Zentrum
 Zepeda
 zflag
 Zhang

examples/ASPHERE/line/in.line

@@ -13,11 +13,11 @@ neigh_modify    delay 0 every 1 check yes
 neigh_modify    exclude molecule/intra all
 
 pair_style      line/lj 2.5
-pair_coeff      * * 1.0 1.0 1.0 0.25 2.5
+pair_coeff      * * 0.25 0.25 1.0 0.25 2.5
 
 fix             2 all rigid molecule langevin 2.0 2.0 1.0 492983
 
-fix             3 all deform 1 x scale 0.3 y scale 0.3
+fix             3 all deform 5 x scale 0.8 y scale 0.8
 fix             4 all enforce2d
 
 compute         10 all property/atom end1x end1y end2x end2y
@@ -26,7 +26,7 @@ compute         10 all property/atom end1x end1y end2x end2y
 #dump           2 all custom 500 dump1.line id type &
 #               c_10[1] c_10[2] c_10[3] c_10[4]
 
-timestep        0.004
+timestep        0.001
 
 compute         1 all erotate/asphere
 compute         2 all ke

examples/ASPHERE/line/in.line.srd

@@ -21,10 +21,10 @@ set             group small mass 0.01
 # delete overlaps
 # must set 1-2 cutoff to non-zero value
 
-pair_style      lj/cut 1.5
+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
+pair_coeff      1 2 1.0 1.0
 
 delete_atoms    overlap 1.5 small big
 
@@ -34,7 +34,7 @@ reset_timestep  0
 
 velocity        small create 1.44 87287 loop geom
 
-neighbor        0.3 multi
+neighbor        0.8 multi
 neigh_modify    delay 0 every 1 check yes
 neigh_modify    exclude molecule/intra big include big
 
@@ -44,21 +44,21 @@ neigh_modify    include big
 # no pairwise interactions with small particles
 
 pair_style      line/lj 2.5
-pair_coeff      1 1 1.0 1.0 1.0 1.0 2.5
+pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
-pair_coeff      2 2 0.0 0.0 0.0 1.0 0.0
+pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
-pair_coeff      1 2 1.0 0.0 0.0 1.0 0.0
+pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5
 
 # use fix SRD to push small particles out from inside big ones
 # if comment out, big particles won't see SRD particles
 
-timestep        0.001
+timestep        0.0001
 
 fix             1 big rigid molecule
 fix             2 small srd 20 big 1.0 0.25 49894 &
                 search 0.2 cubic warn 0.0001 shift yes 49829 &
                 overlap yes collision noslip
 
-fix             3 all deform 1 x scale 0.35 y scale 0.35
+fix             3 all deform 1 x scale 1.25 y scale 1.25
 fix             4 all enforce2d
 
 # diagnostics
@@ -96,12 +96,12 @@ change_box      all triclinic
 
 fix             2 small srd 20 big 1.0 0.25 49894 &
                 search 0.2 cubic warn 0.0001 shift yes 49829 &
-                overlap yes collision noslip tstat yes
+                overlap yes collision noslip #tstat yes
 
 #dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
 #dump           2 all custom 500 dump2.line.srd id type &
 #               c_10[1] c_10[2] c_10[3] c_10[4]
 
-fix             3 all deform 1 xy erate 0.05 units box remap v
+fix             3 all deform 1 xy erate 0.0002 units box remap v
 
-run             40000
+run             30000

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

@@ -1,213 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
-
-units		lj
-atom_style	line
-dimension	2
-
-read_data	data.line
-  orthogonal box = (-22.5539 -22.5539 -0.5) to (22.5539 22.5539 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  350 atoms
-  350 lines
-
-velocity	all create 1.44 320984 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule all
-
-pair_style	line/lj 2.5
-pair_coeff	* * 1.0 0.25
-
-fix		2 all rigid molecule langevin 2.0 2.0 1.0 492983
-100 rigid bodies with 350 atoms
-
-fix		3 all deform 1 x scale 0.3 y scale 0.3
-fix		4 all enforce2d
-
-compute		10 all property/atom end1x end1y end2x end2y
-
-#dump		1 all custom 500 dump1.atom id type x y z ix iy iz
-#dump		2 all custom 500 dump1.line id type #		c_10[1] c_10[2] c_10[3] c_10[4]
-
-timestep	0.004
-
-compute		1 all erotate/asphere
-compute		2 all ke
-compute		3 all pe
-variable	toteng equal (c_1+c_2+c_3)/atoms
-
-thermo		1000
-thermo_style	custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng
-
-run		10000
-Memory usage per processor = 2.6072 Mbytes
-Step Temp 2 PotEng KinEng 1 2 3 toteng 
-       0            0    1.2780105            0           -0  0.037823677   0.50989511            0   0.54771879 
-    1000            0    1.9896906  -0.13333756           -0   0.12630626   0.72641827  -0.13333756   0.71938697 
-    2000            0    2.0408541  -0.24906647           -0   0.13199238   0.74265938  -0.24906647   0.62558529 
-    3000            0    1.9921323  -0.39759798           -0   0.11671173   0.73705927  -0.39759798   0.45617302 
-    4000            0    2.1392159  -0.36475197           -0   0.11923802    0.7975688  -0.36475197   0.55205485 
-    5000            0     2.139715  -0.52582091           -0   0.15846417   0.75855653  -0.52582091   0.39119979 
-    6000            0    2.1313904  -0.65532027           -0   0.11090422   0.80254883  -0.65532027   0.25813278 
-    7000            0    1.9416614  -0.81322598           -0   0.11722471   0.71491587  -0.81322598  0.018914608 
-    8000            0    1.9388183   -1.0581149           -0   0.10142762   0.72949452   -1.0581149  -0.22719275 
-    9000            0    2.2830265    -1.583347           -0   0.14583927   0.83260066    -1.583347  -0.60490709 
-   10000            0    4.1416666   -2.6034045           -0   0.18839177    1.5866082   -2.6034045  -0.82840455 
-Loop time of 2.84713 on 8 procs for 10000 steps with 350 atoms
-
-Pair  time (%) = 1.26607 (44.4682)
-Neigh time (%) = 0.0163046 (0.572669)
-Comm  time (%) = 0.786148 (27.612)
-Outpt time (%) = 0.000368953 (0.0129588)
-Other time (%) = 0.778241 (27.3342)
-
-Nlocal:    43.75 ave 51 max 39 min
-Histogram: 1 2 0 2 0 1 1 0 0 1
-Nghost:    170.25 ave 180 max 160 min
-Histogram: 2 1 0 0 0 0 2 0 1 2
-Neighs:    963.125 ave 1209 max 767 min
-Histogram: 2 0 2 0 1 0 1 0 1 1
-
-Total # of neighbors = 7705
-Ave neighs/atom = 22.0143
-Neighbor list builds = 987
-Dangerous builds = 0
-
-#undump          1
-#undump          2
-unfix           3
-
-change_box      all triclinic
-  triclinic box = (-6.76616 -6.76616 -0.5) to (6.76616 6.76616 0.5) with tilt (0 0 0)
-
-#dump		1 all custom 500 dump2.atom id type x y z ix iy iz
-#dump		2 all custom 500 dump2.line id type #		c_10[1] c_10[2] c_10[3] c_10[4]
-
-fix		3 all deform 1 xy erate 0.01 units box
-
-run		100000
-Memory usage per processor = 2.75978 Mbytes
-Step Temp 2 PotEng KinEng 1 2 3 toteng 
-   10000            0    4.1416666   -2.6024092           -0   0.18839177    1.5866082   -2.6024092  -0.82740923 
-   11000            0    1.8408319   -3.1031477           -0   0.12073234   0.66819561   -3.1031477   -2.3142198 
-   12000            0    2.0793172   -3.0329681           -0  0.086927592   0.80420833   -3.0329681   -2.1418322 
-   13000            0    2.2022136     -2.99776           -0   0.14309291    0.8007129     -2.99776   -2.0539542 
-   14000            0    1.9510757    -3.094649           -0   0.09482969   0.74134559    -3.094649   -2.2584737 
-   15000            0    1.9874689   -3.1431753           -0    0.1083061    0.7434663   -3.1431753   -2.2914029 
-   16000            0    1.8484778   -2.9491537           -0  0.079102883   0.71310191   -2.9491537   -2.1569489 
-   17000            0    2.1978438   -2.9675694           -0   0.11677634   0.82515673   -2.9675694   -2.0256363 
-   18000            0    2.0293397   -2.9860257           -0    0.1287845    0.7409325   -2.9860257   -2.1163087 
-   19000            0    2.0077219    -3.005622           -0   0.12697603    0.7334762    -3.005622   -2.1451698 
-   20000            0    2.1806369   -3.0622132           -0   0.11066657   0.82389212   -3.0622132   -2.1276545 
-   21000            0    1.8156509   -3.1031481           -0   0.10227614   0.67585994   -3.1031481    -2.325012 
-   22000            0    2.1028516   -3.0861182           -0  0.098877162   0.80234493   -3.0861182   -2.1848961 
-   23000            0    1.8994891   -3.0110243           -0   0.10961187   0.70445488   -3.0110243   -2.1969576 
-   24000            0    1.9305389   -3.0057136           -0   0.11735151    0.7100223   -3.0057136   -2.1783398 
-   25000            0    1.9553918   -3.0848948           -0   0.13217467   0.70585039   -3.0848948   -2.2468697 
-   26000            0    1.8903754   -2.9543658           -0  0.099925113   0.71023579   -2.9543658   -2.1442049 
-   27000            0    2.2624684   -3.2416154           -0   0.11398815   0.85564117   -3.2416154   -2.2719861 
-   28000            0    2.0335234   -3.1795174           -0   0.10291986   0.76859015   -3.1795174   -2.3080074 
-   29000            0    1.7056403   -3.1198739           -0  0.076174496   0.65481419   -3.1198739   -2.3888853 
-   30000            0    2.1203465   -3.0863113           -0   0.11355683   0.79516311   -3.0863113   -2.1775914 
-   31000            0    1.8446708   -3.2764357           -0   0.11006455   0.68050865   -3.2764357   -2.4858625 
-   32000            0    1.7947968    -3.081031           -0  0.087540776   0.68165784    -3.081031   -2.3118324 
-   33000            0    2.2576228   -3.1042222           -0   0.15666855   0.81088407   -3.1042222   -2.1366696 
-   34000            0    1.8522306   -3.0037311           -0   0.08276626   0.71104684   -3.0037311    -2.209918 
-   35000            0    2.0611686   -2.9877406           -0   0.10822003   0.77513794   -2.9877406   -2.1043826 
-   36000            0    2.0739798    -2.981184           -0   0.11784198   0.77100651    -2.981184   -2.0923355 
-   37000            0    2.2120215   -2.8961216           -0   0.13172943    0.8162798   -2.8961216   -1.9481124 
-   38000            0    2.1097357   -2.9746777           -0   0.11881736   0.78535507   -2.9746777   -2.0705053 
-   39000            0    1.8928127   -2.9482169           -0   0.10915752   0.70204792   -2.9482169   -2.1370115 
-   40000            0    1.8515483    -3.003524           -0  0.096981256   0.69653943    -3.003524   -2.2100033 
-   41000            0    1.8569065   -3.0834675           -0   0.10562739    0.6901897   -3.0834675   -2.2876504 
-   42000            0    2.2638459   -3.0577224           -0   0.10896442   0.86125524   -3.0577224   -2.0875027 
-   43000            0    2.0992151   -3.1219185           -0   0.13280434   0.76685929   -3.1219185   -2.2222548 
-   44000            0    2.3479986   -3.0702445           -0   0.14438131   0.86190379   -3.0702445   -2.0639594 
-   45000            0    2.0295235   -2.9619688           -0   0.13726365   0.73253213   -2.9619688    -2.092173 
-   46000            0    2.0597998   -3.1282569           -0   0.10139093    0.7813804   -3.1282569   -2.2454856 
-   47000            0    1.8173541   -3.1122647           -0   0.10380346   0.67506259   -3.1122647   -2.3333986 
-   48000            0    1.9650208     -3.22153           -0   0.10115952   0.74099226     -3.22153   -2.3793782 
-   49000            0    1.8836303   -3.0781944           -0   0.10561306   0.70165705   -3.0781944   -2.2709243 
-   50000            0    1.7799289   -3.1090208           -0   0.10522105   0.65760561   -3.1090208   -2.3461941 
-   51000            0    1.7270244    -2.894789           -0  0.079316066   0.66083727    -2.894789   -2.1546357 
-   52000            0    2.1036512   -3.0708266           -0   0.11762021    0.7839446   -3.0708266   -2.1692618 
-   53000            0    2.1749106    -3.043193           -0   0.11908953   0.81301499    -3.043193   -2.1110885 
-   54000            0    1.7245018   -3.1528646           -0   0.11118993   0.62788226   -3.1528646   -2.4137924 
-   55000            0    1.7599209   -3.0543405           -0  0.098996756   0.65525507   -3.0543405   -2.3000886 
-   56000            0    1.9085953   -3.1072383           -0   0.10931083   0.70865859   -3.1072383   -2.2892689 
-   57000            0    1.9682028    -3.131335           -0  0.094973379   0.74854212    -3.131335   -2.2878195 
-   58000            0    1.7813545    -3.167275           -0  0.085523136    0.6779145    -3.167275   -2.4038374 
-   59000            0    2.0324497   -3.1103534           -0   0.13343285   0.73761703   -3.1103534   -2.2393035 
-   60000            0     1.697349    -3.152831           -0  0.086035815   0.64139945    -3.152831   -2.4253957 
-   61000            0     2.061537   -3.0730484           -0   0.12753143   0.75598441   -3.0730484   -2.1895325 
-   62000            0    1.8186587   -3.1590894           -0  0.096701457   0.68272371   -3.1590894   -2.3796643 
-   63000            0    1.9692063   -3.1053354           -0  0.094864849    0.7490807   -3.1053354   -2.2613899 
-   64000            0    2.0113722   -3.0898117           -0   0.12640828   0.73560838   -3.0898117    -2.227795 
-   65000            0    1.9350085   -3.2290712           -0   0.11850297   0.71078638   -3.2290712   -2.3997819 
-   66000            0    2.0569306   -3.0489252           -0   0.12731012   0.75423156   -3.0489252   -2.1673835 
-   67000            0    2.0119071     -3.10894           -0  0.099142151   0.76310375     -3.10894   -2.2466941 
-   68000            0    2.0615321    -3.167552           -0   0.11066625   0.77284751    -3.167552   -2.2840383 
-   69000            0    1.8731077   -3.1864825           -0   0.12982742     0.672933   -3.1864825   -2.3837221 
-   70000            0     2.109088   -3.1787326           -0   0.13107619   0.77281866   -3.1787326   -2.2748377 
-   71000            0    1.9764202   -3.0731116           -0   0.12035585   0.72668137   -3.0731116   -2.2260744 
-   72000            0    1.6460591   -3.0865952           -0   0.09486718   0.61058673   -3.0865952   -2.3811413 
-   73000            0    1.9756864   -3.0431747           -0    0.1041775   0.74254526   -3.0431747    -2.196452 
-   74000            0    2.0553658   -3.1290715           -0   0.12267262   0.75819842   -3.1290715   -2.2482004 
-   75000            0     1.550997   -2.9813403           -0  0.094350599   0.57036238   -2.9813403   -2.3166273 
-   76000            0    1.9824851   -3.0057088           -0   0.11621875   0.73341774   -3.0057088   -2.1560723 
-   77000            0    1.8451505   -3.0063772           -0   0.12602143   0.66475735   -3.0063772   -2.2155984 
-   78000            0     1.934755   -3.0603773           -0   0.11800375   0.71117696   -3.0603773   -2.2311966 
-   79000            0    2.1982093    -3.095224           -0   0.12840585   0.81368383    -3.095224   -2.1531343 
-   80000            0    1.7547828   -3.0620364           -0  0.092552269   0.65949751   -3.0620364   -2.3099866 
-   81000            0    2.1064588   -3.1631358           -0   0.11415036   0.78861768   -3.1631358   -2.2603677 
-   82000            0    2.0039288   -3.1190532           -0   0.13374009   0.72508654   -3.1190532   -2.2602266 
-   83000            0    1.7749465   -3.2172309           -0   0.11017601   0.65051537   -3.2172309   -2.4565396 
-   84000            0    1.7865147   -3.1433093           -0  0.086859958   0.67878922   -3.1433093   -2.3776602 
-   85000            0    1.4541199   -3.0123872           -0  0.096301993   0.52689225   -3.0123872   -2.3891929 
-   86000            0    2.0345567   -2.9577061           -0   0.11756878    0.7543841   -2.9577061   -2.0857532 
-   87000            0    1.9655671   -3.0235755           -0   0.13068174   0.71170417   -3.0235755   -2.1811896 
-   88000            0    2.1238733   -3.0972095           -0   0.15660293   0.75362848   -3.0972095   -2.1869781 
-   89000            0      1.93413   -3.0018414           -0   0.11736651   0.71154634   -3.0018414   -2.1729285 
-   90000            0    2.0106701   -3.0778989           -0    0.1150105   0.74670527   -3.0778989   -2.2161831 
-   91000            0    1.9700224   -3.0072749           -0    0.1200151   0.72428023   -3.0072749   -2.1629796 
-   92000            0    2.3062898   -3.1245149           -0   0.16045862   0.82795128   -3.1245149    -2.136105 
-   93000            0    1.9977984   -3.1072212           -0  0.098381856   0.75781746   -3.1072212   -2.2510219 
-   94000            0    1.9684844   -3.0923519           -0   0.11228362   0.73135255   -3.0923519   -2.2487157 
-   95000            0    1.8913269   -3.1044766           -0  0.088944817   0.72162386   -3.1044766    -2.293908 
-   96000            0     2.139258   -2.9032081           -0   0.12122357    0.7956013   -2.9032081   -1.9863833 
-   97000            0    2.1549839   -3.0073823           -0   0.14177897   0.78178555   -3.0073823   -2.0838178 
-   98000            0     2.001084   -3.0411655           -0   0.16549603   0.69211139   -3.0411655   -2.1835581 
-   99000            0     2.269108   -3.0749812           -0   0.11370514   0.85876972   -3.0749812   -2.1025064 
-  100000            0    2.0270482   -3.0802101           -0  0.098599302   0.77013563   -3.0802101   -2.2114752 
-  101000            0    1.9412796   -3.1543623           -0   0.11953004   0.71244692   -3.1543623   -2.3223853 
-  102000            0    2.0146461   -3.0140006           -0   0.10152606    0.7618937   -3.0140006   -2.1505808 
-  103000            0    1.7377282   -3.1862597           -0  0.082111131   0.66262952   -3.1862597    -2.441519 
-  104000            0    1.7973897   -3.1055088           -0  0.093370304   0.67693958   -3.1055088   -2.3351989 
-  105000            0    2.2615194   -2.9636424           -0   0.12584102   0.84338157   -2.9636424   -1.9944198 
-  106000            0    1.8974182   -2.9505576           -0  0.085928679   0.72725057   -2.9505576   -2.1373783 
-  107000            0    2.0691161   -3.0804349           -0   0.12411017   0.76265389   -3.0804349   -2.1936708 
-  108000            0    2.0457472    -2.981702           -0   0.09308074   0.78366806    -2.981702   -2.1049532 
-  109000            0    1.6610604   -3.1463569           -0  0.066318676   0.64556436   -3.1463569   -2.4344738 
-  110000            0    1.9606721    -3.080013           -0   0.13164067   0.70864736    -3.080013   -2.2397249 
-Loop time of 62.2251 on 8 procs for 100000 steps with 350 atoms
-
-Pair  time (%) = 43.4946 (69.8987)
-Neigh time (%) = 0.395421 (0.635469)
-Comm  time (%) = 10.3551 (16.6414)
-Outpt time (%) = 0.00358662 (0.00576394)
-Other time (%) = 7.97644 (12.8187)
-
-Nlocal:    43.75 ave 51 max 33 min
-Histogram: 1 0 1 0 0 2 0 1 2 1
-Nghost:    168.375 ave 180 max 155 min
-Histogram: 1 1 0 0 1 0 2 2 0 1
-Neighs:    971 ave 1278 max 631 min
-Histogram: 1 1 0 1 0 1 2 1 0 1
-
-Total # of neighbors = 7768
-Ave neighs/atom = 22.1943
-Neighbor list builds = 7621
-Dangerous builds = 0

examples/ASPHERE/line/log.1Feb14.line.srd.g++.8

@@ -1,244 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Aspherical shear demo - 2d line boxes, solvated by SRD particles
-
-units		lj
-atom_style	line
-atom_modify	first big
-dimension	2
-
-read_data	data.line.srd
-  orthogonal box = (-28.7968 -28.7968 -0.5) to (28.7968 28.7968 0.5)
-  4 by 2 by 1 MPI processor grid
-  reading atoms ...
-  400 atoms
-  400 lines
-
-# add small particles as hi density lattice
-
-lattice		sq 0.4
-Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
-region		plane block INF INF INF INF -0.001 0.001
-lattice		sq 10.0
-Lattice spacing in x,y,z = 0.316228 0.316228 0.316228
-create_atoms	2 region plane
-Created 33489 atoms
-
-group		big type 1
-400 atoms in group big
-group		small type 2
-33489 atoms in group small
-set		group small mass 0.01
-  33489 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
-Deleted 13605 atoms, new total = 20284
-
-# SRD run
-
-reset_timestep	0
-
-velocity	small create 1.44 87287 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule big include big
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style	line/lj 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 400 atoms
-fix	        2 small srd 20 big 1.0 0.25 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip
-
-fix		3 all deform 1 x scale 0.35 y scale 0.35
-fix		4 all enforce2d
-
-# 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		1 big erotate/asphere
-compute		2 all ke
-compute		3 all pe
-variable	toteng equal (c_1+c_2+c_3)/atoms
-
-thermo		1000
-thermo_style	custom step temp c_tsmall f_2[9] c_1 etotal 		v_pebig v_ebig press
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-
-compute		10 big property/atom end1x end1y end2x end2y
-
-#dump		1 all custom 500 dump1.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump1.line.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4]
-
-run		10000
-WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
-SRD info:
-  SRD/big particles = 19884 400
-  big particle diameter max/min = 1.99882 0.503306
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 230 230 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.250407 0.250407 1
-  SRD per actual grid cell = 0.444963
-  SRD viscosity = 4.2356
-  big/SRD mass density ratio = 14.0918
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 15.906 29.1054
-  ave/max big velocity = 0 0
-WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
-Memory usage per processor = 7.79007 Mbytes
-Step Temp tsmall 2[9] 1 TotEng pebig ebig Press 
-       0            0    1.4528554            0            0            0            0            0            0 
-    1000            0    1.1122612    1.1071958 0.00058011072            0            0            0   0.32625408 
-    2000            0    1.0254475    1.0231236 0.00072347646 -2.3144253e-06 -0.00011736451 -0.00011736451   0.44526308 
-    3000            0    1.0089214   0.99966408 0.00061511441 -0.00023298189 -0.011814512 -0.011814512   0.87208025 
-    4000            0    1.0066185   0.99391102 0.00079065587 -0.0021630644  -0.10968899  -0.10968899    1.3901494 
-    5000            0    1.0109003    1.0009124 0.00071588733 -0.0040023493  -0.20295913  -0.20295913    1.2736445 
-    6000            0    1.0119642    1.0105049 0.00080741361 -0.0067908165  -0.34436231  -0.34436231    2.5492857 
-    7000            0    1.0048989   0.98912274 0.00098851463 -0.010933999  -0.55446309  -0.55446309    3.5707613 
-    8000            0    1.0021597   0.99377939 0.0008405671 -0.015690841  -0.79568252  -0.79568252     6.685381 
-    9000            0    1.0197546      1.00114 0.0012645557 -0.021124602   -1.0712286   -1.0712286    18.907993 
-   10000            0    1.0401079    1.0184189 0.0036111452 0.0099395852   0.50403637   0.50403637    96.909257 
-Loop time of 3.93391 on 8 procs for 10000 steps with 20284 atoms
-
-Pair  time (%) = 0.110261 (2.80284)
-Neigh time (%) = 0.32853 (8.35124)
-Comm  time (%) = 0.199613 (5.07416)
-Outpt time (%) = 0.00108692 (0.0276295)
-Other time (%) = 3.29442 (83.7441)
-
-Nlocal:    2535.5 ave 2850 max 2226 min
-Histogram: 1 0 1 1 1 1 1 0 1 1
-Nghost:    109.25 ave 117 max 102 min
-Histogram: 1 0 2 0 1 1 1 1 0 1
-Neighs:    526 ave 665 max 407 min
-Histogram: 1 2 0 1 0 1 1 1 0 1
-
-Total # of neighbors = 4208
-Ave neighs/atom = 0.207454
-Neighbor list builds = 522
-Dangerous builds = 0
-
-#undump          1
-#undump          2
-unfix		3
-
-change_box      all triclinic
-  triclinic box = (-10.0789 -10.0789 -0.5) to (10.0789 10.0789 0.5) with tilt (0 0 0)
-
-fix	        2 small srd 20 big 1.0 0.25 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip tstat yes
-
-#dump		1 all custom 500 dump2.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump2.line.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4]
-
-fix		3 all deform 1 xy erate 0.05 units box remap v
-
-run		40000
-SRD info:
-  SRD/big particles = 19884 400
-  big particle diameter max/min = 1.99882 0.503306
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 81 81 1
-  SRD grid size: request, actual (xyz) = 0.25, 0.248861 0.248861 1
-  SRD per actual grid cell = -11.3331
-  SRD viscosity = -1920.36
-  big/SRD mass density ratio = -0.546468
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
-  # of rescaled SRD velocities = 1
-  ave/max small velocity = 12.724 40
-  ave/max big velocity = 1.54523 5.36901
-Memory usage per processor = 4.23847 Mbytes
-Step Temp tsmall 2[9] 1 TotEng pebig ebig Press 
-   10000            0    1.0277413            0 0.0036111452  0.010135973   0.51399517   0.51399517    60.794865 
-   11000            0    1.0024742            1 0.00040482851 -0.031643325    -1.604633    -1.604633    55.531632 
-   12000            0    1.0036177            1 0.00036416993 -0.030844063   -1.5641024   -1.5641024    56.694788 
-   13000            0    1.0043067            1 0.00068862721 -0.030673787   -1.5554677   -1.5554677    56.852537 
-   14000            0    1.0042533            1 0.00050997053 -0.035967153   -1.8238943   -1.8238943    51.254109 
-   15000            0     1.003956            1 0.00048458218 -0.038060147   -1.9300301   -1.9300301    50.346943 
-   16000            0    1.0059929            1 0.0004740426 -0.037433402   -1.8982478   -1.8982478     49.82532 
-   17000            0    1.0042401            1 0.00039855238 -0.034314446   -1.7400855   -1.7400855    48.430648 
-   18000            0    1.0025952            1 0.00046207703 -0.034166102    -1.732563    -1.732563    53.883613 
-   19000            0    1.0025881            1 0.00034818943 -0.037341367   -1.8935807   -1.8935807     48.90662 
-   20000            0    1.0009932            1 0.00031244041 -0.035274728   -1.7887814   -1.7887814    47.665935 
-   21000            0    1.0025603            1 0.0005514826 -0.034350221   -1.7418997   -1.7418997    63.290704 
-   22000            0    1.0038575            1 0.00034453716  -0.03576596   -1.8136918   -1.8136918    49.805726 
-   23000            0    1.0030321            1 0.00049535709 -0.035873083    -1.819124    -1.819124    48.973244 
-   24000            0    1.0048593            1 0.00034225992  -0.03322158   -1.6846663   -1.6846663    52.557383 
-   25000            0    1.0024423            1 0.00059157362 -0.030152319   -1.5290241   -1.5290241    56.733821 
-   26000            0    1.0022703            1 0.00047512976 -0.029563064    -1.499143    -1.499143    56.271943 
-   27000            0    1.0024537            1 0.00054158319  -0.02957039   -1.4995145   -1.4995145    55.246787 
-   28000            0    1.0023325            1 0.00051129428 -0.035115211   -1.7806924   -1.7806924    49.718172 
-   29000            0     1.002865            1 0.00056728135 -0.035484703   -1.7994293   -1.7994293    48.387401 
-   30000            0    1.0022693            1 0.00040284402 -0.033844303   -1.7162446   -1.7162446    50.486676 
-   31000            0    1.0037106            1 0.00056291948 -0.036529699    -1.852421    -1.852421    52.011803 
-   32000            0    1.0022542            1 0.00041877447 -0.036903458   -1.8713743   -1.8713743    52.712289 
-   33000            0    1.0021364            1 0.00040871451 -0.033616728   -1.7047043   -1.7047043    55.199593 
-   34000            0     1.003779            1 0.00040667148 -0.031745412   -1.6098098   -1.6098098    51.055261 
-   35000            0    1.0015547            1 0.00042509365 -0.033603064   -1.7040114   -1.7040114    53.887389 
-   36000            0    1.0024849            1 0.00040589851 -0.032151258   -1.6303903   -1.6303903    55.673615 
-   37000            0    1.0038204            1 0.00040542177 -0.033643242   -1.7060488   -1.7060488    51.834694 
-   38000            0    1.0031777            1 0.00040237126 -0.034711811   -1.7602359   -1.7602359    56.275778 
-   39000            0     1.002777            1 0.00051021239 -0.034375104   -1.7431615   -1.7431615    48.461145 
-   40000            0    1.0053762            1 0.00041566465 -0.036016384   -1.8263908   -1.8263908    48.937456 
-   41000            0    1.0039078            1 0.00049726673 -0.036481888   -1.8499966   -1.8499966    49.290465 
-   42000            0    1.0033408            1 0.00045236191 -0.034254524   -1.7370469   -1.7370469    52.146603 
-   43000            0    1.0039893            1 0.00048362351 -0.032519474   -1.6490625   -1.6490625    53.320599 
-   44000            0    1.0036667            1 0.00046834006 -0.031099875   -1.5770747   -1.5770747    55.907531 
-   45000            0    1.0035765            1 0.0005195031 -0.029559708   -1.4989728   -1.4989728    56.191165 
-   46000            0     1.004514            1 0.00050134348 -0.028852909    -1.463131    -1.463131    57.547696 
-   47000            0     1.003864            1 0.00038963389 -0.031339229   -1.5892123   -1.5892123    55.775764 
-   48000            0     1.003145            1 0.00035436452 -0.032390682   -1.6425315   -1.6425315    55.233354 
-   49000            0    1.0042615            1 0.00053161075 -0.029960468   -1.5192953   -1.5192953    54.611685 
-   50000            0    1.0037096            1 0.00031191389  -0.02942011   -1.4918938   -1.4918938    58.653762 
-Loop time of 27.1275 on 8 procs for 40000 steps with 20284 atoms
-
-Pair  time (%) = 1.54277 (5.68709)
-Neigh time (%) = 1.26864 (4.67658)
-Comm  time (%) = 1.19871 (4.4188)
-Outpt time (%) = 0.00421953 (0.0155544)
-Other time (%) = 23.1132 (85.202)
-
-Nlocal:    2535.5 ave 2670 max 2406 min
-Histogram: 1 1 1 0 0 2 1 1 0 1
-Nghost:    114.5 ave 124 max 103 min
-Histogram: 1 0 1 0 2 1 0 1 0 2
-Neighs:    521.5 ave 692 max 442 min
-Histogram: 3 1 1 1 0 0 0 1 0 1
-
-Total # of neighbors = 4172
-Ave neighs/atom = 0.205679
-Neighbor list builds = 2002
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

examples/ASPHERE/line/log.21Sep24.line.g++.1

@@ -0,0 +1,189 @@
+LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
+  using 1 OpenMP thread(s) per MPI task
+# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
+
+units           lj
+atom_style      line
+dimension       2
+
+read_data       data.line
+Reading data file ...
+  orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  350 atoms
+  350 lines
+  read_data CPU = 0.003 seconds
+
+velocity        all create 1.44 320984 loop geom
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+neigh_modify    exclude molecule/intra all
+
+pair_style      line/lj 2.5
+pair_coeff      * * 0.25 0.25 1.0 0.25 2.5
+
+fix             2 all rigid molecule langevin 2.0 2.0 1.0 492983
+  100 rigid bodies with 350 atoms
+
+fix             3 all deform 5 x scale 0.8 y scale 0.8
+fix             4 all enforce2d
+
+compute         10 all property/atom end1x end1y end2x end2y
+
+#dump           1 all custom 500 dump1.atom id type x y z ix iy iz
+#dump           2 all custom 500 dump1.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+timestep        0.001
+
+compute         1 all erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+compute_modify  thermo_temp extra/dof -350
+
+thermo          1000
+thermo_style    custom step f_2 pe ke c_1 c_2 c_3 v_toteng
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 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 = 33 33 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, 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) = 4.742 | 4.742 | 4.742 Mbytes
+   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
+         0   1.1872976      0              0.46543528     0.03617212     0.46543528     0              0.5016074    
+      1000   1.9084412     -0.001043719    0.71003395     0.089891202    0.71003395    -0.001043719    0.79888143   
+      2000   2.31668       -0.020711665    0.83611544     0.13062287     0.83611544    -0.020711665    0.94602664   
+      3000   2.3094506     -0.062018072    0.80584123     0.15326943     0.80584123    -0.062018072    0.8970926    
+      4000   2.4383442     -0.053659995    0.86864073     0.14696993     0.86864073    -0.053659995    0.96195067   
+      5000   2.5885917     -0.15612821     0.90351683     0.17156633     0.90351683    -0.15612821     0.91895495   
+      6000   2.1187379     -0.072041135    0.76933527     0.11557939     0.76933527    -0.072041135    0.81287353   
+      7000   2.1407592     -0.057727294    0.75154343     0.13827066     0.75154343    -0.057727294    0.8320868    
+      8000   2.0661844     -0.097529608    0.71093839     0.14547433     0.71093839    -0.097529608    0.75888311   
+      9000   2.1574445     -0.052890857    0.78826145     0.11363136     0.78826145    -0.052890857    0.84900195   
+     10000   2.473097      -0.092376489    0.85756337     0.16861278     0.85756337    -0.092376489    0.93379965   
+Loop time of 1.16704 on 1 procs for 10000 steps with 350 atoms
+
+Performance: 740334.372 tau/day, 8568.685 timesteps/s, 2.999 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    | 0.80757    | 0.80757    | 0.80757    |   0.0 | 69.20
+Neigh   | 0.0090046  | 0.0090046  | 0.0090046  |   0.0 |  0.77
+Comm    | 0.011808   | 0.011808   | 0.011808   |   0.0 |  1.01
+Output  | 0.000194   | 0.000194   | 0.000194   |   0.0 |  0.02
+Modify  | 0.3317     | 0.3317     | 0.3317     |   0.0 | 28.42
+Other   |            | 0.006768   |            |       |  0.58
+
+Nlocal:            350 ave         350 max         350 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            101 ave         101 max         101 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            853 ave         853 max         853 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 853
+Ave neighs/atom = 2.4371429
+Neighbor list builds = 274
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)
+
+#dump           1 all custom 500 dump2.atom id type x y z ix iy iz
+#dump           2 all custom 500 dump2.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+fix             3 all deform 1 xy erate 0.01 units box
+
+run             10000
+Generated 0 of 0 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 = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton/tri
+      stencil: half/bin/2d/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.756 | 4.756 | 4.756 Mbytes
+   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
+     10000   2.473097      -0.092380532    0.85753671     0.16863499     0.85753671    -0.092380532    0.93379117   
+     11000   2.5185915     -0.1015737      0.84230876     0.197573       0.84230876    -0.1015737      0.93830806   
+     12000   2.5971728     -0.13087195     0.90608898     0.17248755     0.90608898    -0.13087195     0.94770458   
+     13000   2.5065714     -0.14666584     0.83804307     0.19683483     0.83804307    -0.14666584     0.88821206   
+     14000   2.1672357     -0.10720878     0.79713452     0.10973398     0.79713452    -0.10720878     0.79965972   
+     15000   2.3444438     -0.14780285     0.81642139     0.15695019     0.81642139    -0.14780285     0.82556873   
+     16000   2.2672973     -0.12590007     0.76672668     0.17081014     0.76672668    -0.12590007     0.81163675   
+     17000   2.3999651     -0.15464102     0.85708567     0.14289234     0.85708567    -0.15464102     0.84533699   
+     18000   2.2024356     -0.14077779     0.76727873     0.14718521     0.76727873    -0.14077779     0.77368615   
+     19000   2.5411572     -0.092014576    0.85750101     0.19297197     0.85750101    -0.092014576    0.95845841   
+     20000   2.2113691     -0.11944862     0.77295445     0.14564597     0.77295445    -0.11944862     0.79915181   
+Loop time of 1.76388 on 1 procs for 10000 steps with 350 atoms
+
+Performance: 489827.896 tau/day, 5669.304 timesteps/s, 1.984 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    | 1.3668     | 1.3668     | 1.3668     |   0.0 | 77.49
+Neigh   | 0.018849   | 0.018849   | 0.018849   |   0.0 |  1.07
+Comm    | 0.013338   | 0.013338   | 0.013338   |   0.0 |  0.76
+Output  | 0.00020434 | 0.00020434 | 0.00020434 |   0.0 |  0.01
+Modify  | 0.35698    | 0.35698    | 0.35698    |   0.0 | 20.24
+Other   |            | 0.007667   |            |       |  0.43
+
+Nlocal:            350 ave         350 max         350 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            119 ave         119 max         119 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            997 ave         997 max         997 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 997
+Ave neighs/atom = 2.8485714
+Neighbor list builds = 283
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/ASPHERE/line/log.21Sep24.line.g++.4

@@ -0,0 +1,189 @@
+LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
+  using 1 OpenMP thread(s) per MPI task
+# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
+
+units           lj
+atom_style      line
+dimension       2
+
+read_data       data.line
+Reading data file ...
+  orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  350 atoms
+  350 lines
+  read_data CPU = 0.003 seconds
+
+velocity        all create 1.44 320984 loop geom
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
+neigh_modify    exclude molecule/intra all
+
+pair_style      line/lj 2.5
+pair_coeff      * * 0.25 0.25 1.0 0.25 2.5
+
+fix             2 all rigid molecule langevin 2.0 2.0 1.0 492983
+  100 rigid bodies with 350 atoms
+
+fix             3 all deform 5 x scale 0.8 y scale 0.8
+fix             4 all enforce2d
+
+compute         10 all property/atom end1x end1y end2x end2y
+
+#dump           1 all custom 500 dump1.atom id type x y z ix iy iz
+#dump           2 all custom 500 dump1.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+timestep        0.001
+
+compute         1 all erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+compute_modify  thermo_temp extra/dof -350
+
+thermo          1000
+thermo_style    custom step f_2 pe ke c_1 c_2 c_3 v_toteng
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 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 = 33 33 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, 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) = 4.736 | 4.736 | 4.736 Mbytes
+   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
+         0   1.1872976      0              0.46543528     0.03617212     0.46543528     0              0.5016074    
+      1000   1.9084412     -0.001043719    0.71003395     0.089891202    0.71003395    -0.001043719    0.79888143   
+      2000   2.31668       -0.020711665    0.83611544     0.13062287     0.83611544    -0.020711665    0.94602664   
+      3000   2.3094506     -0.062018072    0.80584123     0.15326943     0.80584123    -0.062018072    0.8970926    
+      4000   2.4383442     -0.053659995    0.86864073     0.14696993     0.86864073    -0.053659995    0.96195067   
+      5000   2.5885917     -0.15612821     0.90351683     0.17156633     0.90351683    -0.15612821     0.91895494   
+      6000   2.118738      -0.072041141    0.76933528     0.1155794      0.76933528    -0.072041141    0.81287354   
+      7000   2.1407609     -0.057727453    0.75154404     0.13827078     0.75154404    -0.057727453    0.83208737   
+      8000   2.066348      -0.097639137    0.71096217     0.14551295     0.71096217    -0.097639137    0.75883597   
+      9000   2.1969096     -0.050133795    0.8028133      0.11559948     0.8028133     -0.050133795    0.86827899   
+     10000   2.3932442     -0.098008752    0.83753779     0.15678193     0.83753779    -0.098008752    0.89631097   
+Loop time of 0.596624 on 4 procs for 10000 steps with 350 atoms
+
+Performance: 1448149.372 tau/day, 16760.988 timesteps/s, 5.866 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    | 0.17419    | 0.21073    | 0.27006    |   7.8 | 35.32
+Neigh   | 0.0015899  | 0.0018079  | 0.0020932  |   0.5 |  0.30
+Comm    | 0.041688   | 0.101      | 0.13805    |  11.3 | 16.93
+Output  | 0.00011945 | 0.0001262  | 0.000143   |   0.0 |  0.02
+Modify  | 0.26906    | 0.27183    | 0.27467    |   0.4 | 45.56
+Other   |            | 0.01113    |            |       |  1.87
+
+Nlocal:           87.5 ave          94 max          80 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:           54.5 ave          67 max          42 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:         212.75 ave         286 max         122 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 851
+Ave neighs/atom = 2.4314286
+Neighbor list builds = 273
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)
+
+#dump           1 all custom 500 dump2.atom id type x y z ix iy iz
+#dump           2 all custom 500 dump2.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+fix             3 all deform 1 xy erate 0.01 units box
+
+run             10000
+Generated 0 of 0 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 = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton/tri
+      stencil: half/bin/2d/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
+   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
+     10000   2.3932442     -0.098029446    0.83751359     0.1568021      0.83751359    -0.098029446    0.89628624   
+     11000   2.4541893     -0.15538223     0.82053681     0.19271549     0.82053681    -0.15538223     0.85787007   
+     12000   2.4124449     -0.14024177     0.84559598     0.15692416     0.84559598    -0.14024177     0.86227837   
+     13000   2.2095814     -0.10822636     0.73930104     0.173052       0.73930104    -0.10822636     0.80412668   
+     14000   2.0946831     -0.087303541    0.77743494     0.10023865     0.77743494    -0.087303541    0.79037005   
+     15000   2.0911016     -0.11524594     0.74044758     0.12978235     0.74044758    -0.11524594     0.75498398   
+     16000   1.9736428     -0.17259563     0.67852978     0.13943094     0.67852978    -0.17259563     0.64536509   
+     17000   2.3284367     -0.17673537     0.77018991     0.1897596      0.77018991    -0.17673537     0.78321414   
+     18000   2.3178564     -0.16634746     0.81488323     0.1487365      0.81488323    -0.16634746     0.79727227   
+     19000   2.7497251     -0.18254513     1.0041125      0.14528424     1.0041125     -0.18254513     0.96685165   
+     20000   2.3897059     -0.12664177     0.8390411      0.15426546     0.8390411     -0.12664177     0.86666479   
+Loop time of 0.79519 on 4 procs for 10000 steps with 350 atoms
+
+Performance: 1086533.223 tau/day, 12575.616 timesteps/s, 4.401 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    | 0.26601    | 0.35051    | 0.443      |  12.3 | 44.08
+Neigh   | 0.0029891  | 0.0036725  | 0.0040631  |   0.7 |  0.46
+Comm    | 0.049744   | 0.14268    | 0.22734    |  19.3 | 17.94
+Output  | 0.00013783 | 0.00014503 | 0.00016304 |   0.0 |  0.02
+Modify  | 0.27963    | 0.28446    | 0.29049    |   0.8 | 35.77
+Other   |            | 0.01372    |            |       |  1.73
+
+Nlocal:           87.5 ave         101 max          75 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:           61.5 ave          67 max          50 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:         244.75 ave         268 max         198 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 979
+Ave neighs/atom = 2.7971429
+Neighbor list builds = 289
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/ASPHERE/line/log.21Sep24.line.srd.g++.1

@@ -0,0 +1,363 @@
+LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
+  using 1 OpenMP thread(s) per MPI task
+# Aspherical shear demo - 2d line boxes, solvated by SRD particles
+
+units           lj
+atom_style      line
+atom_modify     first big
+dimension       2
+
+read_data       data.line.srd
+Reading data file ...
+  orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  400 atoms
+  400 lines
+  read_data CPU = 0.003 seconds
+
+# add small particles as hi density lattice
+
+lattice         sq 0.4
+Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
+region          plane block INF INF INF INF -0.001 0.001
+lattice         sq 10.0
+Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
+create_atoms    2 region plane
+Created 33489 atoms
+  using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  create_atoms CPU = 0.003 seconds
+
+group           big type 1
+400 atoms in group big
+group           small type 2
+33489 atoms in group small
+set             group small mass 0.01
+Setting atom values ...
+  33489 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 1.0 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 = 64 64 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:313)
+Deleted 13605 atoms, new total = 20284
+
+# SRD run
+
+reset_timestep  0
+
+velocity        small create 1.44 87287 loop geom
+
+neighbor        0.8 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      line/lj 2.5
+pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
+pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
+pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 400 atoms
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip
+
+fix             3 all deform 1 x scale 1.25 y scale 1.25
+fix             4 all enforce2d
+
+# 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 -350
+
+compute         1 big erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+thermo          1000
+thermo_style    custom step c_tsmall f_2[9] c_1 etotal                 v_pebig v_ebig press
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
+
+compute         10 big property/atom end1x end1y end2x end2y
+
+#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump1.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+- 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 = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.02
+  SRD max distance & max velocity = 0.08 40
+  SRD grid counts: 230 230 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
+  SRD per actual grid cell = 0.45503978
+  SRD viscosity = 0.92062623
+  big/SRD mass density ratio = 12.298053
+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)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 15.906001 29.105426
+  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 = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 35 35 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, 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) = 43.18 | 43.18 | 43.18 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+         0   1.6084386      0              0              0              0              0              0            
+      1000   1.4566787      1.2042825      0.00015900089  0.0011955837   0              0.060628048    0.75322967   
+      2000   1.3561018      1.2092936      0.00026739313  0.0020783306   0              0.10539215     0.53247025   
+      3000   1.3327447      1.1696777      0.0003215116   0.0024935719   0              0.12644903     0.32024668   
+      4000   1.3031273      1.1385596      0.00037337107  0.0031214473   0              0.15828859     0.64066244   
+      5000   1.28204        1.0983763      0.00047966362  0.0033295434   0              0.16884114     0.32103666   
+      6000   1.2654396      1.0969562      0.00049917373  0.0037382387   0              0.18956609     0.16211614   
+      7000   1.2401503      1.1232046      0.00045137168  0.0037522201   0              0.19027508     0.014071672  
+      8000   1.2349025      1.059008       0.00056648801  0.0039664742   0              0.20113991     0.24483817   
+      9000   1.2272907      1.0371006      0.00056271544  0.0037847074   0              0.19192251     0.032968056  
+     10000   1.2153817      1.0209113      0.00053291164  0.0037197691   0              0.18862949     0.3237698    
+Loop time of 6.0346 on 1 procs for 10000 steps with 20284 atoms
+
+Performance: 14317.424 tau/day, 1657.109 timesteps/s, 33.613 Matom-step/s
+96.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10636    | 0.10636    | 0.10636    |   0.0 |  1.76
+Neigh   | 0.01905    | 0.01905    | 0.01905    |   0.0 |  0.32
+Comm    | 0.041223   | 0.041223   | 0.041223   |   0.0 |  0.68
+Output  | 0.0017015  | 0.0017015  | 0.0017015  |   0.0 |  0.03
+Modify  | 5.8165     | 5.8165     | 5.8165     |   0.0 | 96.39
+Other   |            | 0.04976    |            |       |  0.82
+
+Nlocal:          20284 ave       20284 max       20284 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             84 ave          84 max          84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 500
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
+
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip #tstat yes
+
+#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump2.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+fix             3 all deform 1 xy erate 0.0002 units box remap v
+
+run             30000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.02
+  SRD max distance & max velocity = 0.08 40
+  SRD grid counts: 288 288 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
+  SRD per actual grid cell = 0.26976265
+  SRD viscosity = 1.0312189
+  big/SRD mass density ratio = 20.672578
+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)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 12.805429 40
+  ave/max big velocity = 0.50400801 2.1697856
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 44 44 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton/tri
+      stencil: half/multi/2d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 58.85 | 58.85 | 58.85 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+     10000   1.0423767      0              0.00053289774  0.0037197858   0              0.18863034     0.014558088  
+     11000   1.0333923      1.0309908      0.00058283908  0.0042336078   0              0.21468625     0.13036048   
+     12000   1.0268543      1.0290122      0.00055294944  0.0044278861   0              0.2245381      0.53275676   
+     13000   1.0257856      1.0140434      0.00051520803  0.0042888387   0              0.21748701     0.2066835    
+     14000   1.0239497      1.0321558      0.00054742053  0.004259664    0              0.21600756     0.24430097   
+     15000   1.0194475      1.0119806      0.00053619565  0.0041113765   0              0.2084879      0.18420434   
+     16000   1.016421       1.0309991      0.00049553642  0.0041338645   0              0.20962827     0.18298406   
+     17000   1.0088527      0.99723694     0.00049824173  0.0044777581   0              0.22706711     0.65557023   
+     18000   1.0073877      1.0136962      0.00058327835  0.0045355884   0              0.22999969     0.13700737   
+     19000   1.0026916      1.0253129      0.00056760151  0.0045138437   0              0.22889701     0.16443344   
+     20000   1.0024042      0.98988084     0.00057568118  0.0048644983   0              0.24667871     0.060864322  
+     21000   0.99500641     0.99075324     0.00062187543  0.0050480594   0              0.25598709     0.18428384   
+     22000   0.99286446     0.98642266     0.00061024492  0.0050497174   0              0.25607117     0.18499738   
+     23000   0.99204086     0.98869005     0.00064013575  0.0052921112   0              0.26836296     0.046987646  
+     24000   0.98768375     1.0110613      0.00065868636  0.0049285304   0              0.24992578     0.22623751   
+     25000   0.98763308     0.98752678     0.00067070463  0.0049364253   0              0.25032613     0.022819382  
+     26000   0.9844889      1.0059918      0.00075364589  0.0053381778   0              0.270699       0.089735771  
+     27000   0.98574608     0.99094039     0.00080711088  0.0054137233   0              0.27452991     0.14477885   
+     28000   0.98139419     0.97487219     0.00071242405  0.0053315389   0              0.27036234    -0.016357088  
+     29000   0.98458705     0.98600894     0.00068355573  0.0050157315   0              0.25434775     0.015749835  
+     30000   0.98440759     1.0010793      0.00067594666  0.0048121267   0              0.24402295     0.20422918   
+     31000   0.98060632     0.9825933      0.00069529947  0.0050649881  -0.00010700206  0.25684555     0.0014601267 
+     32000   0.97616624     0.94976641     0.00067682494  0.0052111319  -0.00013230279  0.2642565      0.013738873  
+     33000   0.97926122     0.95756794     0.00071774059  0.0053716513  -0.00024804252  0.27239644     0.10643895   
+     34000   0.97227771     0.94365547     0.00080885359  0.0055744144  -0.00063217879  0.28267856     0.12472959   
+     35000   0.97295679     0.98103625     0.0008130852   0.0057598371  -0.00097218501  0.29208134     0.88422099   
+     36000   0.97131919     0.97164636     0.0008345433   0.0062212675  -0.001543055    0.31548048     0.22389401   
+     37000   0.96988732     0.98589058     0.00083271625  0.0062999411  -0.0026064482   0.31947001     0.11797226   
+     38000   0.97135512     0.96486494     0.00076943974  0.0057397763  -0.0041174109   0.29106406     0.072790492  
+     39000   0.97386738     0.95218062     0.00079594844  0.0056308358  -0.0069006312   0.28553968     0.12417837   
+     40000   0.97914045     1.0033941      0.000830798    0.0055952714  -0.0086705514   0.28373621     0.1976663    
+Loop time of 15.944 on 1 procs for 30000 steps with 20284 atoms
+
+Performance: 16256.931 tau/day, 1881.589 timesteps/s, 38.166 Matom-step/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.31871    | 0.31871    | 0.31871    |   0.0 |  2.00
+Neigh   | 0.082974   | 0.082974   | 0.082974   |   0.0 |  0.52
+Comm    | 0.16092    | 0.16092    | 0.16092    |   0.0 |  1.01
+Output  | 0.0047257  | 0.0047257  | 0.0047257  |   0.0 |  0.03
+Modify  | 15.189     | 15.189     | 15.189     |   0.0 | 95.27
+Other   |            | 0.1871     |            |       |  1.17
+
+Nlocal:          20284 ave       20284 max       20284 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             76 ave          76 max          76 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             38 ave          38 max          38 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 38
+Ave neighs/atom = 0.0018733978
+Neighbor list builds = 1500
+Dangerous builds = 0
+Total wall time: 0:00:22

examples/ASPHERE/line/log.21Sep24.line.srd.g++.4

@@ -0,0 +1,363 @@
+LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
+  using 1 OpenMP thread(s) per MPI task
+# Aspherical shear demo - 2d line boxes, solvated by SRD particles
+
+units           lj
+atom_style      line
+atom_modify     first big
+dimension       2
+
+read_data       data.line.srd
+Reading data file ...
+  orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  400 atoms
+  400 lines
+  read_data CPU = 0.003 seconds
+
+# add small particles as hi density lattice
+
+lattice         sq 0.4
+Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
+region          plane block INF INF INF INF -0.001 0.001
+lattice         sq 10.0
+Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
+create_atoms    2 region plane
+Created 33489 atoms
+  using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  create_atoms CPU = 0.001 seconds
+
+group           big type 1
+400 atoms in group big
+group           small type 2
+33489 atoms in group small
+set             group small mass 0.01
+Setting atom values ...
+  33489 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 1.0 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 = 64 64 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:313)
+Deleted 13605 atoms, new total = 20284
+
+# SRD run
+
+reset_timestep  0
+
+velocity        small create 1.44 87287 loop geom
+
+neighbor        0.8 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      line/lj 2.5
+pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
+pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
+pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0001
+
+fix             1 big rigid molecule
+  100 rigid bodies with 400 atoms
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip
+
+fix             3 all deform 1 x scale 1.25 y scale 1.25
+fix             4 all enforce2d
+
+# 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 -350
+
+compute         1 big erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+thermo          1000
+thermo_style    custom step c_tsmall f_2[9] c_1 etotal                 v_pebig v_ebig press
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
+
+compute         10 big property/atom end1x end1y end2x end2y
+
+#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump1.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+- 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 = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.02
+  SRD max distance & max velocity = 0.08 40
+  SRD grid counts: 230 230 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
+  SRD per actual grid cell = 0.45503978
+  SRD viscosity = 0.92062623
+  big/SRD mass density ratio = 12.298053
+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)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 15.906001 29.105426
+  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 = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 35 35 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, 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) = 13.44 | 13.45 | 13.47 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+         0   1.6084386      0              0              0              0              0              0            
+      1000   1.4539924      1.2578325      0.0001679809   0.0010497614   0              0.053233399    0.69841607   
+      2000   1.3516746      1.1693535      0.00031932331  0.0021450754   0              0.10877677     0.058141137  
+      3000   1.3294093      1.1539986      0.00032558495  0.0022345521   0              0.11331414     0.085892255  
+      4000   1.3049311      1.1174444      0.00039637116  0.0026520968   0              0.13448783     0.10574422   
+      5000   1.2790124      1.1209176      0.0004519172   0.0032635257   0              0.16549339     0.59225702   
+      6000   1.2631214      1.0868777      0.00052274216  0.003527049    0              0.17885666     0.26093936   
+      7000   1.2520054      1.0780954      0.00051683183  0.0038111141   0              0.1932616     -0.0014733978 
+      8000   1.2412037      1.0587149      0.00056620143  0.0038329297   0              0.19436786     0.31576462   
+      9000   1.2242125      1.0699712      0.00065335672  0.0039948578   0              0.20257924     0.19755012   
+     10000   1.2155758      1.0279682      0.00059730828  0.004142635    0              0.21007302     0.30022953   
+Loop time of 1.92412 on 4 procs for 10000 steps with 20284 atoms
+
+Performance: 44903.607 tau/day, 5197.177 timesteps/s, 105.420 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    | 0.026855   | 0.027529   | 0.028377   |   0.4 |  1.43
+Neigh   | 0.0073723  | 0.007433   | 0.0075693  |   0.1 |  0.39
+Comm    | 0.062837   | 0.065574   | 0.066747   |   0.6 |  3.41
+Output  | 0.00072894 | 0.00076558 | 0.00083361 |   0.0 |  0.04
+Modify  | 1.7861     | 1.7926     | 1.8        |   0.4 | 93.16
+Other   |            | 0.03026    |            |       |  1.57
+
+Nlocal:           5071 ave        5096 max        5051 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost:             44 ave          51 max          40 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 500
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
+
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip #tstat yes
+
+#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump2.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+fix             3 all deform 1 xy erate 0.0002 units box remap v
+
+run             30000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.02
+  SRD max distance & max velocity = 0.08 40
+  SRD grid counts: 288 288 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
+  SRD per actual grid cell = 0.26976265
+  SRD viscosity = 1.0312189
+  big/SRD mass density ratio = 20.672578
+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)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 12.826666 40
+  ave/max big velocity = 0.53469722 1.7415554
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 44 44 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton/tri
+      stencil: half/multi/2d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 17.6 | 17.6 | 17.61 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+     10000   1.0416233      0              0.0005972922   0.0041426543   0              0.210074       0.016213064  
+     11000   1.0366852      1.0236717      0.00066926382  0.004404743    0              0.22336452     0.097686059  
+     12000   1.028695       1.0023004      0.00065323121  0.0043971164   0              0.22297777     0.30007875   
+     13000   1.0223214      1.0296267      0.00060201395  0.0041815724   0              0.21204754     0.17307062   
+     14000   1.0210601      1.0092227      0.00057020066  0.0041936718   0              0.2126611      0.13379405   
+     15000   1.0169223      1.003359       0.00060818329  0.0046120335   0              0.23387622     0.39144341   
+     16000   1.012222       0.99937463     0.00060471571  0.004533278    0              0.22988253     0.16026051   
+     17000   1.0087993      0.98937449     0.00061843646  0.0048888197   0              0.24791205     0.095507016  
+     18000   1.0030288      0.94092316     0.00054252694  0.0046740839   0              0.2370228     -0.070838649  
+     19000   1.0010739      0.99759814     0.00054041829  0.0045481798   0              0.2306382      0.1944996    
+     20000   1.004189       1.0157285      0.00053330893  0.0044999261   0              0.22819125     0.14452619   
+     21000   0.99601133     1.003771       0.00053282188  0.0048954851   0              0.24825005     0.20196263   
+     22000   0.99445408     1.0163465      0.00059954941  0.0051668276   0              0.26200983     0.21332194   
+     23000   0.99663947     0.94920707     0.00057729723  0.0051052499   0              0.25888722     0.19282224   
+     24000   0.99500015     1.0021742      0.00064312956  0.0053430656   0              0.27094686     0.18044164   
+     25000   0.99388189     0.98446723     0.00060150964  0.0054017824   0              0.27392438     0.18844037   
+     26000   0.99632932     0.94670024     0.00052479857  0.004905147    0              0.24874        0.17961314   
+     27000   0.99112962     1.0247118      0.00053159824  0.004752248    0              0.2409865      0.12037737   
+     28000   0.98887153     0.97734068     0.00052255365  0.0050199491   0              0.25456162     0.29110866   
+     29000   0.98938025     0.99467239     0.00053095044  0.0050303107   0              0.25508706     0.59776339   
+     30000   0.99081592     0.98822122     0.00056693985  0.0052452228   0              0.26598525     0.0150843    
+     31000   0.99050903     1.0184912      0.00056742049  0.0056515686   0              0.28659104     0.07877756   
+     32000   0.98929926     0.99257634     0.00058111732  0.005740055    0              0.29107819     0.19146041   
+     33000   0.98698723     0.94872564     0.00056547335  0.0057628447   0              0.29223385     0.076755599  
+     34000   0.98967998     0.98777081     0.00056045905  0.0055645603   0              0.28217885     0.095025284  
+     35000   0.98777734     0.95746323     0.00050104756  0.0055630681  -4.7847642e-05  0.28210318     0.25667997   
+     36000   0.98661597     0.98801246     0.00047074618  0.0054500805  -5.8956193e-05  0.27637358     0.18221607   
+     37000   0.98390111     0.9837894      0.00044581144  0.0054703357  -7.4197741e-05  0.27740072     0.11959303   
+     38000   0.98092646     1.0142057      0.0004945556   0.0056372628  -8.6736668e-05  0.2858656      0.017325263  
+     39000   0.98125957     0.94219822     0.00059691168  0.0060914156  -9.9726556e-05  0.30889569     0.0081217281 
+     40000   0.98362942     0.9649582      0.00062286697  0.0063736358  -0.00010700337  0.32320707     0.293121     
+Loop time of 5.08621 on 4 procs for 30000 steps with 20284 atoms
+
+Performance: 50961.296 tau/day, 5898.298 timesteps/s, 119.641 Matom-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    | 0.084321   | 0.084948   | 0.086233   |   0.3 |  1.67
+Neigh   | 0.027521   | 0.029247   | 0.030632   |   0.7 |  0.58
+Comm    | 0.19101    | 0.20262    | 0.2068     |   1.5 |  3.98
+Output  | 0.0019581  | 0.0020369  | 0.0022544  |   0.3 |  0.04
+Modify  | 4.681      | 4.6884     | 4.7051     |   0.4 | 92.18
+Other   |            | 0.07891    |            |       |  1.55
+
+Nlocal:           5071 ave        5197 max        4951 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:             44 ave          50 max          41 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Neighs:           5.75 ave          12 max           0 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 23
+Ave neighs/atom = 0.0011338986
+Neighbor list builds = 1500
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/ASPHERE/line/log.21Sep24.line.srd.g++.8

@@ -0,0 +1,323 @@
+LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
+  using 1 OpenMP thread(s) per MPI task
+# Aspherical shear demo - 2d line boxes, solvated by SRD particles
+
+units           lj
+atom_style      line
+atom_modify     first big
+dimension       2
+
+read_data       data.line.srd
+Reading data file ...
+  orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  4 by 2 by 1 MPI processor grid
+  reading atoms ...
+  400 atoms
+  400 lines
+  read_data CPU = 0.002 seconds
+
+# add small particles as hi density lattice
+
+lattice         sq 0.4
+Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
+region          plane block INF INF INF INF -0.001 0.001
+lattice         sq 10.0
+Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
+create_atoms    2 region plane
+Created 33489 atoms
+  using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
+  create_atoms CPU = 0.001 seconds
+
+group           big type 1
+400 atoms in group big
+group           small type 2
+33489 atoms in group small
+set             group small mass 0.01
+Setting atom values ...
+  33489 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 1.0 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 = 64 64 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:313)
+Deleted 13605 atoms, new total = 20284
+
+# SRD run
+
+reset_timestep  0
+
+velocity        small create 1.44 87287 loop geom
+
+neighbor        0.8 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      line/lj 2.5
+pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
+pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
+pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep        0.0002
+
+fix             1 big rigid molecule
+  100 rigid bodies with 400 atoms
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip
+
+fix             3 all deform 1 x scale 1.25 y scale 1.25
+fix             4 all enforce2d
+
+# 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 -350
+
+compute         1 big erotate/asphere
+compute         2 all ke
+compute         3 all pe
+variable        toteng equal (c_1+c_2+c_3)/atoms
+
+thermo          1000
+thermo_style    custom step c_tsmall f_2[9] c_1 etotal                 v_pebig v_ebig press
+thermo_modify   temp tbig
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
+
+compute         10 big property/atom end1x end1y end2x end2y
+
+#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump1.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+run             10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282–-3297}
+}
+
+- 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 = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.04
+  SRD max distance & max velocity = 0.16 40
+  SRD grid counts: 230 230 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
+  SRD per actual grid cell = 0.45503978
+  SRD viscosity = 1.0732692
+  big/SRD mass density ratio = 12.298053
+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)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 15.906001 29.105426
+  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 = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 35 35 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, 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) = 9.752 | 9.762 | 9.781 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+         0   1.4809886      0              0              0              0              0              0            
+      1000   1.2265081      1.1522909      0.00027866069  0.0022427232   0              0.1137285      0.58262976   
+      2000   1.1757141      1.1251323      0.00040597152  0.003287261    0              0.16669701     0.27109853   
+      3000   1.126304       1.0646585      0.00050542958  0.0040748897   0              0.20663766     0.36959653   
+      4000   1.1140297      1.0761435      0.00060430927  0.0052863645   0              0.26807154     0.35099205   
+      5000   1.0823307      1.0256814      0.00066557681  0.0051213284   0              0.25970256     0.28491631   
+      6000   1.0656188      1.0387091      0.00066454105  0.005213537    0              0.26437846     0.2150581    
+      7000   1.0600108      1.0099931      0.0007238719   0.005470459    0              0.27740698     0.21846568   
+      8000   1.0464374      1.0049819      0.00061068366  0.0053702582   0              0.27232579     0.1326171    
+      9000   1.0381097      1.0126049      0.00057318728  0.0055976321   0              0.28385592     0.16797796   
+     10000   1.0312982      1.0018962      0.00050597007  0.0051153126   0              0.2593975      0.15281043   
+Loop time of 1.2997 on 8 procs for 10000 steps with 20284 atoms
+
+Performance: 132953.355 tau/day, 7694.060 timesteps/s, 156.066 Matom-step/s
+96.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.01406    | 0.014495   | 0.01532    |   0.3 |  1.12
+Neigh   | 0.0051916  | 0.0053424  | 0.0054386  |   0.1 |  0.41
+Comm    | 0.062053   | 0.065305   | 0.069014   |   0.9 |  5.02
+Output  | 0.00062289 | 0.00065254 | 0.00077243 |   0.0 |  0.05
+Modify  | 1.169      | 1.178      | 1.1905     |   0.6 | 90.64
+Other   |            | 0.03589    |            |       |  2.76
+
+Nlocal:         2535.5 ave        2637 max        2476 min
+Histogram: 1 3 1 1 0 0 0 0 1 1
+Nghost:         31.125 ave          42 max          25 min
+Histogram: 3 0 1 2 0 0 0 0 1 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 500
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix           3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
+
+fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip #tstat yes
+
+#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump           2 all custom 500 dump2.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]
+
+fix             3 all deform 1 xy erate 0.0002 units box remap v
+
+run             40000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 19884 400
+  big particle diameter max/min = 1.9988171 0.50330564
+  SRD temperature & lamda = 1 0.04
+  SRD max distance & max velocity = 0.16 40
+  SRD grid counts: 288 288 1
+  SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
+  SRD per actual grid cell = 0.26976265
+  SRD viscosity = 1.5799049
+  big/SRD mass density ratio = 20.672578
+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)
+  # of rescaled SRD velocities = 1
+  ave/max small velocity = 12.481632 40
+  ave/max big velocity = 0.58815233 1.5489134
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 44 44 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair line/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/atomonly/newton/tri
+      stencil: half/multi/2d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 11.95 | 11.95 | 11.95 Mbytes
+   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
+     10000   0.98889306     0              0.00050595647  0.0051153289   0              0.25939833     0.020019811  
+     11000   0.98995417     0.99721412     0.0005166709   0.0054320552   0              0.27545952     0.03376188   
+     12000   0.99401168     0.95502319     0.00053659416  0.0054974426   0              0.27877531     0.056856034  
+     13000   0.98790692     0.96488357     0.00061076364  0.0053196554   0              0.26975972     0.2677228    
+     14000   0.98939233     0.98809694     0.00052317779  0.0050536922   0              0.25627273     0.20381427   
+     15000   0.99046365     0.97048828     0.00056914402  0.0053274908   0              0.27015706     0.082163088  
+     16000   0.99743447     1.0111983      0.00053706165  0.0048068384   0              0.24375478     0.06429569   
+     17000   0.99622359     1.0124982      0.0005905197   0.0055966416  -7.4541903e-05  0.2838057      0.25418037   
+     18000   0.99283929     0.99581721     0.00061730878  0.0059098964  -0.00014754106  0.29969084     0.12701702   
+     19000   0.99175517     1.0115581      0.0005128714   0.0059214809  -0.00046203987  0.30027829     0.2640506    
+     20000   0.98895811     0.97731528     0.00052294314  0.0055670021  -0.0016029702   0.28230268     0.26239209   
+     21000   0.98904093     0.98120258     0.00054169978  0.0052762731  -0.0026834879   0.26755981     0.15432481   
+     22000   0.98773149     0.99217218     0.00056091602  0.0052754729  -0.0044093345   0.26751923     0.2208051    
+     23000   0.98802862     0.96564549     0.00062226338  0.0053263454  -0.008790914    0.27009898     0.18058977   
+     24000   0.98754002     1.024015       0.00057178953  0.0054083382  -0.0094859317   0.27425683     0.01598147   
+     25000   0.98656341     0.94647246     0.00066215791  0.0053555849  -0.014877058    0.27158171     0.28794628   
+     26000   0.98750471     1.0077626      0.00058955769  0.0057081639  -0.013151869    0.28946099     0.20814911   
+     27

examples/COUPLE/plugin/liblammpsplugin.c

@@ -81,6 +81,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(python_finalize);
 
   ADDSYM(error);
+  ADDSYM(expand);
 
   ADDSYM(file);
   ADDSYM(command);

examples/COUPLE/plugin/liblammpsplugin.h

@@ -126,6 +126,7 @@ struct _liblammpsplugin {
   void (*python_finalize)();
 
   void (*error)(void *, int, const char *);
+  char *(*expand)(void *, const char *);
 
   void (*file)(void *, const char *);
   char *(*command)(void *, const char *);

examples/bpm/impact/in.bpm.impact.rotational

@@ -45,7 +45,7 @@ thermo          100
 thermo_modify   lost ignore lost/bond ignore
 #dump            1 all custom 100 atomDump id radius x y z c_nbond
 
-dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+#dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
-dump_modify     2 header no
+#dump_modify     2 header no
 
 run             7500

examples/bpm/impact/in.bpm.impact.spring

@@ -47,7 +47,7 @@ thermo          100
 thermo_modify   lost ignore lost/bond ignore
 #dump            1 all custom 100 atomDump id x y z c_nbond
 
-dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+#dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
-dump_modify     2 header no
+#dump_modify     2 header no
 
 run             7500

examples/granregion/log.16Mar23.granregion.box.g++.1

@@ -1,484 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-# pouring spheres into container box
-
-units		lj
-atom_style      sphere
-boundary        f f f
-dimension	3
-comm_modify     vel yes
-
-region          box block -10 10 -10 10 -10 10 units box
-create_box      2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff	* * gran/hooke
-
-region          container block -6 6 -6 6 -6 6 units box
-fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix             2 all nve/sphere
-fix		3 all gravity 1.0 vector 0 0 -1
-
-region          slab block -2 2 -2 2 -2 2 units box
-fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep	0.005
-
-compute         1 all temp
-compute_modify  1 dynamic/dof yes
-
-compute         2 all temp/sphere
-compute_modify  2 dynamic/dof yes
-
-thermo		100
-thermo_style	custom step atoms temp c_1 c_2 press
-thermo_modify   lost ignore
-compute_modify  thermo_temp dynamic/dof yes
-
-#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify	2 pad 5
-
-run	        5000
-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 = 1.3
-  ghost atom cutoff = 1.3
-  binsize = 0.65, bins = 31 31 31
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke, perpetual
-      attributes: half, newton on, size
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-         0           0   0              0              0              0            
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-       100          30   0.803783       0.803783       0.39507978     0.0029137134 
-       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
-       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
-       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
-       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
-       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
-       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
-       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
-      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
-      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
-      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
-      1400          99   0.35615284     0.35615284     0.19785725     0.0046170772 
-      1500          99   0.31486693     0.31486693     0.17429055     0.0064903432 
-      1600          99   0.26369001     0.26369001     0.15095266     0.0045226847 
-      1700         100   0.1925923      0.1925923      0.11308104     0.007362313  
-      1800         100   0.13724978     0.13724978     0.083276845    0.0058136373 
-      1900         100   0.077212636    0.077212636    0.053159386    0.0016509598 
-      2000         100   0.065294031    0.065294031    0.04372752     0.0020346467 
-      2100         100   0.057431398    0.057431398    0.037977068    0.0012681098 
-      2200         100   0.059093045    0.059093045    0.037435193    0.00096610799
-      2300         100   0.03422338     0.03422338     0.025491304    0.00069886052
-      2400         100   0.020558284    0.020558284    0.016163009    0.0017260663 
-      2500         100   0.015339709    0.015339709    0.012329236    0.00041308031
-      2600         100   0.012891354    0.012891354    0.009766054    0.00030356722
-      2700         100   0.0092634449   0.0092634449   0.0073580108   0.00077723051
-      2800         100   0.0073925841   0.0073925841   0.0059932218   0.00016466767
-      2900         100   0.0081228267   0.0081228267   0.006281761    0.00013828388
-      3000         100   0.0041833223   0.0041833223   0.0035147096   0.00013160599
-      3100         100   0.0035930775   0.0035930775   0.0030039922   0.00060639771
-      3200         100   0.0030824465   0.0030824465   0.0026541293   0.00047391014
-      3300         100   0.0035087522   0.0035087522   0.0027664508   0.00014080317
-      3400         100   0.0018537868   0.0018537868   0.0017099705   6.3326674e-05
-      3500         100   0.0015371228   0.0015371228   0.0014155433   0.00021612522
-      3600         100   0.001708556    0.001708556    0.0014369892   8.1034202e-05
-      3700         100   0.00095948652  0.00095948652  0.0009788528   3.4694023e-05
-      3800         100   0.00091875668  0.00091875668  0.00086805146  3.9373686e-05
-      3900         100   0.001557068    0.001557068    0.001159526    2.5178607e-05
-      4000         100   0.00062012451  0.00062012451  0.00066806922  5.6680551e-06
-      4100         100   0.00060940771  0.00060940771  0.00065614741  1.0137901e-05
-      4200         100   0.00059538437  0.00059538437  0.00064501521  7.3679744e-06
-      4300         100   0.00052946048  0.00052946048  0.00059353641  5.9225081e-06
-      4400         100   0.00051202281  0.00051202281  0.00057524772  3.6198435e-05
-      4500         100   0.00049986632  0.00049986632  0.00055754521  2.2275519e-05
-      4600         100   0.00048187334  0.00048187334  0.00053988815  2.2015243e-05
-      4700         100   0.00045261491  0.00045261491  0.00050298355  8.9681339e-05
-      4800         100   0.00034965427  0.00034965427  0.0004278781   1.0983535e-05
-      4900         100   0.00033555621  0.00033555621  0.00041435167  2.9266598e-05
-      5000         100   0.00031387148  0.00031387148  0.00039605781  2.5628425e-05
-Loop time of 0.073938 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 29213677.752 tau/day, 67624.254 timesteps/s, 6.762 Matom-step/s
-98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0084547  | 0.0084547  | 0.0084547  |   0.0 | 11.43
-Neigh   | 0.011399   | 0.011399   | 0.011399   |   0.0 | 15.42
-Comm    | 0.00077205 | 0.00077205 | 0.00077205 |   0.0 |  1.04
-Output  | 0.00042663 | 0.00042663 | 0.00042663 |   0.0 |  0.58
-Modify  | 0.049692   | 0.049692   | 0.049692   |   0.0 | 67.21
-Other   |            | 0.003194   |            |       |  4.32
-
-Nlocal:            100 ave         100 max         100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            164 ave         164 max         164 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 164
-Ave neighs/atom = 1.64
-Neighbor list builds = 281
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-5000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
-run	        5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
-Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-      5000         100   0.00031387148  0.00031387148  0.00039605781  2.6174978e-05
-      5100         100   0.54537023     0.54537023     0.30042175     0.0087427352 
-      5200         100   0.57210852     0.57210852     0.3192468      0.0098134067 
-      5300         100   0.7168108      0.7168108      0.38577893     0.011004584  
-      5400         100   0.78895524     0.78895524     0.41889428     0.013555713  
-      5500         100   0.87797874     0.87797874     0.45689223     0.01565356   
-      5600         100   0.95424379     0.95424379     0.48830429     0.014707858  
-      5700         100   1.0046012      1.0046012      0.51054927     0.01469179   
-      5800         100   1.0371453      1.0371453      0.5262568      0.015576788  
-      5900         100   1.0545743      1.0545743      0.5361173      0.01589889   
-      6000         100   1.0932949      1.0932949      0.55402214     0.017484573  
-      6100         100   1.1148364      1.1148364      0.56241126     0.01721788   
-      6200         100   1.1315267      1.1315267      0.57050887     0.017961246  
-      6300         100   1.1506124      1.1506124      0.58009471     0.017159062  
-      6400         100   1.1663328      1.1663328      0.5876586      0.017935311  
-      6500         100   1.1821086      1.1821086      0.59595161     0.018005316  
-      6600         100   1.2039397      1.2039397      0.60567523     0.021604661  
-      6700         100   1.2269912      1.2269912      0.61770225     0.018907995  
-      6800         100   1.2447034      1.2447034      0.62576519     0.020537655  
-      6900         100   1.2625323      1.2625323      0.63486698     0.02010613   
-      7000         100   1.2617127      1.2617127      0.63318163     0.019670429  
-      7100         100   1.260715       1.260715       0.63311254     0.01981063   
-      7200         100   1.2790404      1.2790404      0.64079        0.020218912  
-      7300         100   1.2760228      1.2760228      0.6395331      0.021749952  
-      7400         100   1.2799657      1.2799657      0.64139078     0.020472917  
-      7500         100   1.2846472      1.2846472      0.64343076     0.020610029  
-      7600         100   1.2883963      1.2883963      0.6449186      0.020748906  
-      7700         100   1.2926891      1.2926891      0.64684538     0.020599574  
-      7800         100   1.3033565      1.3033565      0.65126214     0.021822145  
-      7900         100   1.3025797      1.3025797      0.65069472     0.02121384   
-      8000         100   1.3052551      1.3052551      0.65209898     0.021398725  
-      8100         100   1.3069868      1.3069868      0.65304899     0.021246465  
-      8200         100   1.3091964      1.3091964      0.65438143     0.021222398  
-      8300         100   1.3101277      1.3101277      0.65518554     0.021329556  
-      8400         100   1.3117162      1.3117162      0.65551056     0.021468306  
-      8500         100   1.3143892      1.3143892      0.65683087     0.021610874  
-      8600         100   1.3164123      1.3164123      0.65789423     0.021564818  
-      8700         100   1.3186854      1.3186854      0.65914031     0.021745193  
-      8800         100   1.3216944      1.3216944      0.66041385     0.022178553  
-      8900         100   1.3207558      1.3207558      0.65988071     0.021810027  
-      9000         100   1.3213131      1.3213131      0.66020938     0.021890893  
-      9100         100   1.3224905      1.3224905      0.66088289     0.021824994  
-      9200         100   1.3240681      1.3240681      0.66183168     0.021784616  
-      9300         100   1.3254174      1.3254174      0.66279883     0.021664485  
-      9400         100   1.3326916      1.3326916      0.66633358     0.021979709  
-      9500         100   1.3405062      1.3405062      0.66975745     0.022238702  
-      9600         100   1.3363695      1.3363695      0.66742377     0.022104646  
-      9700         100   1.3363391      1.3363391      0.6673032      0.022066628  
-      9800         100   1.334875       1.334875       0.6665532      0.021902669  
-      9900         100   1.3339805      1.3339805      0.66614358     0.022018971  
-     10000         100   1.3337897      1.3337897      0.66609803     0.022184385  
-Loop time of 0.213875 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 10099379.673 tau/day, 23378.194 timesteps/s, 2.338 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    | 0.031863   | 0.031863   | 0.031863   |   0.0 | 14.90
-Neigh   | 0.026844   | 0.026844   | 0.026844   |   0.0 | 12.55
-Comm    | 0.0011059  | 0.0011059  | 0.0011059  |   0.0 |  0.52
-Output  | 0.00072907 | 0.00072907 | 0.00072907 |   0.0 |  0.34
-Modify  | 0.14874    | 0.14874    | 0.14874    |   0.0 | 69.54
-Other   |            | 0.004595   |            |       |  2.15
-
-Nlocal:            100 ave         100 max         100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            186 ave         186 max         186 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 186
-Ave neighs/atom = 1.86
-Neighbor list builds = 626
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     10000         100   1.3337897      1.3337897      0.66609803     0.022303323  
-     10100         100   0.29960521     0.29960521     0.17535846     0.0099382421 
-     10200         100   0.15737069     0.15737069     0.1024212      0.0045555648 
-     10300         100   0.087501771    0.087501771    0.070895975    0.00093482858
-     10400         100   0.069967301    0.069967301    0.059253397    0.0008760803 
-     10500         100   0.056137153    0.056137153    0.047810947    0.0009202993 
-     10600         100   0.046835352    0.046835352    0.039400006    0.0011343063 
-     10700         100   0.035422167    0.035422167    0.030746587    0.00081816474
-     10800         100   0.029180739    0.029180739    0.02627693     0.00039292712
-     10900         100   0.025094915    0.025094915    0.023244435    0.00044742245
-     11000         100   0.018014893    0.018014893    0.016862375    0.00017018411
-     11100         100   0.014549072    0.014549072    0.014551468    0.00020988549
-     11200         100   0.012586232    0.012586232    0.012569333    0.00019035396
-     11300         100   0.01003586     0.01003586     0.010253286    0.0004598214 
-     11400         100   0.0067515743   0.0067515743   0.0069569741   0.00040592883
-     11500         100   0.0057834612   0.0057834612   0.0060790719   0.00013993531
-     11600         100   0.005496335    0.005496335    0.0056855922   0.00013419698
-     11700         100   0.0051524178   0.0051524178   0.0053354591   7.4388594e-05
-     11800         100   0.004911096    0.004911096    0.0051415984   0.00010665621
-     11900         100   0.004687138    0.004687138    0.0049520306   6.7492552e-05
-     12000         100   0.0041516495   0.0041516495   0.0044351666   4.3841199e-05
-     12100         100   0.0033948026   0.0033948026   0.0036851466   4.2010682e-05
-     12200         100   0.0029584231   0.0029584231   0.0031151054   5.1583068e-05
-     12300         100   0.0028401114   0.0028401114   0.0030094644   4.5499489e-05
-     12400         100   0.002650861    0.002650861    0.0027699066   0.00015370263
-     12500         100   0.0026018053   0.0026018053   0.0027178583   3.219734e-05 
-     12600         100   0.0025788693   0.0025788693   0.0026939358   3.6615314e-05
-     12700         100   0.0024798907   0.0024798907   0.0026181033   3.0688648e-05
-     12800         100   0.0023930719   0.0023930719   0.0025491721   7.5200629e-05
-     12900         100   0.0022100795   0.0022100795   0.0024231125   2.3210159e-05
-     13000         100   0.0021267492   0.0021267492   0.0023312893   2.463758e-05 
-     13100         100   0.0020732193   0.0020732193   0.0022673707   2.5656089e-05
-     13200         100   0.0020010659   0.0020010659   0.0021834293   2.4913608e-05
-     13300         100   0.0019645929   0.0019645929   0.0021311636   6.8209063e-05
-     13400         100   0.0019236711   0.0019236711   0.0020928899   2.3805429e-05
-     13500         100   0.001857137    0.001857137    0.0020387354   3.1316165e-05
-     13600         100   0.0018399111   0.0018399111   0.0020204586   2.27689e-05  
-     13700         100   0.0016240252   0.0016240252   0.0017492695   0.00023180963
-     13800         100   0.0015856393   0.0015856393   0.0017164012   4.2480373e-05
-     13900         100   0.0014770352   0.0014770352   0.001571278    2.3192512e-05
-     14000         100   0.0013712974   0.0013712974   0.0014839763   4.7410142e-05
-     14100         100   0.0012396318   0.0012396318   0.0013778109   1.3867692e-05
-     14200         100   0.0011502319   0.0011502319   0.0012780584   0.00018410725
-     14300         100   0.0011020896   0.0011020896   0.0012348357   7.8122446e-05
-     14400         100   0.0010486644   0.0010486644   0.0011483239   0.00015074963
-     14500         100   0.00094167471  0.00094167471  0.0010033809   1.9550083e-05
-     14600         100   0.00080775791  0.00080775791  0.00087434944  4.6043659e-05
-     14700         100   0.00076176039  0.00076176039  0.00083462461  8.1916038e-05
-     14800         100   0.00073637901  0.00073637901  0.00081306941  9.1126903e-06
-     14900         100   0.00072682383  0.00072682383  0.00079396231  8.9944449e-06
-     15000         100   0.00070207518  0.00070207518  0.00077168127  2.2155171e-05
-Loop time of 0.0756704 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 28544845.995 tau/day, 66076.032 timesteps/s, 6.608 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    | 0.0079484  | 0.0079484  | 0.0079484  |   0.0 | 10.50
-Neigh   | 0.0043035  | 0.0043035  | 0.0043035  |   0.0 |  5.69
-Comm    | 0.00064796 | 0.00064796 | 0.00064796 |   0.0 |  0.86
-Output  | 0.00044137 | 0.00044137 | 0.00044137 |   0.0 |  0.58
-Modify  | 0.059329   | 0.059329   | 0.059329   |   0.0 | 78.40
-Other   |            | 0.003      |            |       |  3.97
-
-Nlocal:            100 ave         100 max         100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            165 ave         165 max         165 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 165
-Ave neighs/atom = 1.65
-Neighbor list builds = 101
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-15000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
-run	        5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     15000         100   0.00070207518  0.00070207518  0.00077168127  2.0192237e-05
-     15100         100   1.1160127      1.1160127      0.69939857     0.01822663   
-     15200         100   1.2546016      1.2546016      0.78819474     0.017013321  
-     15300         100   1.1930613      1.1930613      0.77429911     0.015607175  
-     15400         100   1.3791371      1.3791371      0.87875984     0.018478669  
-     15500         100   1.6063158      1.6063158      0.98587325     0.027330546  
-     15600         100   1.7719925      1.7719925      1.0773314      0.025651867  
-     15700         100   1.8053439      1.8053439      1.0934572      0.033790716  
-     15800         100   1.959016       1.959016       1.1465659      0.033715025  
-     15900         100   2.1365654      2.1365654      1.2217718      0.03009529   
-     16000         100   2.2883378      2.2883378      1.2768504      0.030582689  
-     16100         100   2.4384012      2.4384012      1.3513708      0.031435936  
-     16200         100   2.3571308      2.3571308      1.29989        0.034824253  
-     16300         100   2.4671092      2.4671092      1.3516798      0.032364282  
-     16400         100   2.4411936      2.4411936      1.3385743      0.031890134  
-     16500         100   2.4930545      2.4930545      1.3635435      0.032601452  
-     16600         100   2.5771906      2.5771906      1.4113993      0.034547128  
-     16700         100   2.723199       2.723199       1.4769168      0.036582811  
-     16800         100   2.8616886      2.8616886      1.5379462      0.036224198  
-     16900         100   2.9517942      2.9517942      1.5872824      0.038757052  
-     17000         100   3.0150335      3.0150335      1.6337001      0.044031411  
-     17100         100   3.2211536      3.2211536      1.7374532      0.041483093  
-     17200         100   3.2509982      3.2509982      1.7512835      0.042718835  
-     17300         100   3.262348       3.262348       1.7648674      0.049291835  
-     17400         100   3.4050702      3.4050702      1.8352043      0.04435958   
-     17500         100   3.5236051      3.5236051      1.9003369      0.045640904  
-     17600         100   3.4005287      3.4005287      1.8404347      0.044832295  
-     17700         100   3.3190992      3.3190992      1.8154147      0.046365998  
-     17800         100   3.2981138      3.2981138      1.811389       0.04607132   
-     17900         100   3.2839466      3.2839466      1.7863773      0.045628167  
-     18000         100   3.1519747      3.1519747      1.7382103      0.041739193  
-     18100         100   3.1205305      3.1205305      1.7101547      0.043511342  
-     18200         100   3.2014874      3.2014874      1.746745       0.04452173   
-     18300         100   3.2739622      3.2739622      1.7796276      0.041345823  
-     18400         100   3.3157359      3.3157359      1.8158932      0.047414     
-     18500         100   3.5592096      3.5592096      1.9307695      0.046458132  
-     18600         100   3.6594352      3.6594352      1.9851626      0.046396953  
-     18700         100   3.6392917      3.6392917      1.9701361      0.047272883  
-     18800         100   3.8490892      3.8490892      2.0832481      0.052344106  
-     18900         100   3.8465732      3.8465732      2.0790411      0.054203126  
-     19000         100   4.010008       4.010008       2.1620722      0.054242542  
-     19100         100   4.0417392      4.0417392      2.168506       0.066484948  
-     19200         100   3.8791541      3.8791541      2.0791914      0.060788142  
-     19300         100   4.1023603      4.1023603      2.1944127      0.056461298  
-     19400         100   4.1294375      4.1294375      2.2009649      0.061099665  
-     19500         100   3.9274112      3.9274112      2.0877398      0.066068401  
-     19600         100   4.066229       4.066229       2.1678487      0.055961003  
-     19700         100   3.9829257      3.9829257      2.1184329      0.061961838  
-     19800         100   4.0303258      4.0303258      2.14544        0.053667616  
-     19900         100   3.9385166      3.9385166      2.1074364      0.060804382  
-     20000         100   3.8534401      3.8534401      2.0796496      0.057588336  
-Loop time of 0.167801 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 12872385.064 tau/day, 29797.188 timesteps/s, 2.980 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    | 0.013849   | 0.013849   | 0.013849   |   0.0 |  8.25
-Neigh   | 0.038108   | 0.038108   | 0.038108   |   0.0 | 22.71
-Comm    | 0.0011352  | 0.0011352  | 0.0011352  |   0.0 |  0.68
-Output  | 0.00073125 | 0.00073125 | 0.00073125 |   0.0 |  0.44
-Modify  | 0.10927    | 0.10927    | 0.10927    |   0.0 | 65.12
-Other   |            | 0.004703   |            |       |  2.80
-
-Nlocal:            100 ave         100 max         100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            157 ave         157 max         157 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 157
-Ave neighs/atom = 1.57
-Neighbor list builds = 914
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     20000         100   3.8534401      3.8534401      2.0796496      0.057176513  
-     20100         100   1.2993548      1.2993548      0.81360425     0.016153186  
-     20200         100   1.0761427      1.0761427      0.68479926     0.014383682  
-     20300         100   0.95889127     0.95889127     0.61193887     0.01314653   
-     20400         100   0.89684043     0.89684043     0.57475851     0.011106613  
-     20500         100   0.85901565     0.85901565     0.54372093     0.015717834  
-     20600         100   0.98438384     0.98438384     0.6079212      0.013965815  
-     20700         100   1.1061789      1.1061789      0.66511277     0.013698526  
-     20800         100   1.0615292      1.0615292      0.6269413      0.014496973  
-     20900         100   0.92980037     0.92980037     0.54727184     0.014568574  
-     21000         100   0.71248123     0.71248123     0.41945517     0.01199152   
-     21100         100   0.34785801     0.34785801     0.21699877     0.0062324631 
-     21200         100   0.2452514      0.2452514      0.15265503     0.0041094159 
-     21300         100   0.22937209     0.22937209     0.13988978     0.0034016589 
-     21400         100   0.17765021     0.17765021     0.11334596     0.0024169343 
-     21500         100   0.11484505     0.11484505     0.078119393    0.0020987046 
-     21600         100   0.077564645    0.077564645    0.056175123    0.002107237  
-     21700         100   0.049571519    0.049571519    0.039920177    0.00099127481
-     21800         100   0.0403125      0.0403125      0.032827882    0.00074671903
-     21900         100   0.02735168     0.02735168     0.023877339    0.0018186225 
-     22000         100   0.02218474     0.02218474     0.01893178     0.00061438633
-     22100         100   0.021701103    0.021701103    0.0179008      0.00068071664
-     22200         100   0.01777321     0.01777321     0.014521817    0.00045296506
-     22300         100   0.016056338    0.016056338    0.01280709     0.00038192299
-     22400         100   0.013344054    0.013344054    0.010788852    0.0002617289 
-     22500         100   0.011625836    0.011625836    0.0094362641   0.00045947089
-     22600         100   0.0068875777   0.0068875777   0.0058858647   0.00028566999
-     22700         100   0.0054081662   0.0054081662   0.0049545239   0.00029291503
-     22800         100   0.0045080107   0.0045080107   0.0042362636   0.00015217816
-     22900         100   0.0038090552   0.0038090552   0.0036905284   0.00049430003
-     23000         100   0.003551951    0.003551951    0.0033639677   0.00022478393
-     23100         100   0.0033854012   0.0033854012   0.00317485     0.00015179604
-     23200         100   0.0032951003   0.0032951003   0.0029760374   0.00015363208
-     23300         100   0.0022995179   0.0022995179   0.0023224311   0.00018791799
-     23400         100   0.0020834178   0.0020834178   0.0021434342   0.00020683744
-     23500         100   0.0019221303   0.0019221303   0.0020227484   0.00018960984
-     23600         100   0.0018393381   0.0018393381   0.0019560681   0.00021375486
-     23700         100   0.0019027035   0.0019027035   0.0020047598   0.00010932204
-     23800         100   0.0023612063   0.0023612063   0.0021895633   6.7671176e-05
-     23900         100   0.0019570853   0.0019570853   0.0018847178   5.6761457e-05
-     24000         100   0.0013011744   0.0013011744   0.0013899106   3.8847148e-05
-     24100         100   0.001281115    0.001281115    0.0013737259   3.7559904e-05
-     24200         100   0.0012136262   0.0012136262   0.0013002937   6.8727546e-05
-     24300         100   0.0011789934   0.0011789934   0.0012399341   3.7633632e-05
-     24400         100   0.0011601514   0.0011601514   0.0012186534   4.0077907e-05
-     24500         100   0.0010660295   0.0010660295   0.0011419405   0.00015757237
-     24600         100   0.00098862453  0.00098862453  0.0010869455   4.5714503e-05
-     24700         100   0.00087647136  0.00087647136  0.00091405278  3.3129869e-05
-     24800         100   0.00063913046  0.00063913046  0.00072298864  3.5424308e-05
-     24900         100   0.00062195456  0.00062195456  0.00070527087  2.6201396e-05
-     25000         100   0.00057599538  0.00057599538  0.00065623226  2.0096103e-05
-Loop time of 0.0771328 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 28003659.560 tau/day, 64823.286 timesteps/s, 6.482 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    | 0.0090635  | 0.0090635  | 0.0090635  |   0.0 | 11.75
-Neigh   | 0.012028   | 0.012028   | 0.012028   |   0.0 | 15.59
-Comm    | 0.0008345  | 0.0008345  | 0.0008345  |   0.0 |  1.08
-Output  | 0.00038777 | 0.00038777 | 0.00038777 |   0.0 |  0.50
-Modify  | 0.051619   | 0.051619   | 0.051619   |   0.0 | 66.92
-Other   |            | 0.0032     |            |       |  4.15
-
-Nlocal:            100 ave         100 max         100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            158 ave         158 max         158 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 158
-Ave neighs/atom = 1.58
-Neighbor list builds = 310
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.16Mar23.granregion.box.g++.4

@@ -1,484 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-# pouring spheres into container box
-
-units		lj
-atom_style      sphere
-boundary        f f f
-dimension	3
-comm_modify     vel yes
-
-region          box block -10 10 -10 10 -10 10 units box
-create_box      2 box
-Created orthogonal box = (-10 -10 -10) to (10 10 10)
-  1 by 2 by 2 MPI processor grid
-
-pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
-pair_coeff	* * gran/hooke
-
-region          container block -6 6 -6 6 -6 6 units box
-fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix             2 all nve/sphere
-fix		3 all gravity 1.0 vector 0 0 -1
-
-region          slab block -2 2 -2 2 -2 2 units box
-fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
-Particle insertion: 48 every 566 steps, 100 by step 1133
-
-timestep	0.005
-
-compute         1 all temp
-compute_modify  1 dynamic/dof yes
-
-compute         2 all temp/sphere
-compute_modify  2 dynamic/dof yes
-
-thermo		100
-thermo_style	custom step atoms temp c_1 c_2 press
-thermo_modify   lost ignore
-compute_modify  thermo_temp dynamic/dof yes
-
-#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
-#dump_modify	2 pad 5
-
-run	        5000
-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 = 1.3
-  ghost atom cutoff = 1.3
-  binsize = 0.65, bins = 31 31 31
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke, perpetual
-      attributes: half, newton on, size
-      pair build: half/size/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-         0           0   0              0              0              0            
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-       100          30   0.803783       0.803783       0.39507978     0.0029137134 
-       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
-       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
-       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
-       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
-       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
-       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
-       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
-      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
-      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
-WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
-      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
-      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
-      1400          99   0.35615284     0.35615284     0.19785725     0.0046170772 
-      1500          99   0.31486693     0.31486693     0.17429055     0.0064903432 
-      1600          99   0.26369001     0.26369001     0.15095266     0.0045226847 
-      1700         100   0.1925923      0.1925923      0.11308104     0.007362313  
-      1800         100   0.13724978     0.13724978     0.083276845    0.0058136373 
-      1900         100   0.077212636    0.077212636    0.053159386    0.0016509598 
-      2000         100   0.065294031    0.065294031    0.04372752     0.0020346467 
-      2100         100   0.057431398    0.057431398    0.037977068    0.0012681098 
-      2200         100   0.059093046    0.059093046    0.037435194    0.00096610935
-      2300         100   0.034223376    0.034223376    0.025491303    0.00069886041
-      2400         100   0.020558283    0.020558283    0.016163008    0.0017260646 
-      2500         100   0.015339698    0.015339698    0.012329233    0.00041312351
-      2600         100   0.012891357    0.012891357    0.0097660566   0.00030356702
-      2700         100   0.0092631621   0.0092631621   0.0073576327   0.00077729311
-      2800         100   0.0073866488   0.0073866488   0.0060126175   0.00018677664
-      2900         100   0.0081122362   0.0081122362   0.0062557089   0.00013749542
-      3000         100   0.0042333757   0.0042333757   0.0035407672   0.00016515787
-      3100         100   0.0035433278   0.0035433278   0.0029683167   0.00033693479
-      3200         100   0.0030692964   0.0030692964   0.0026495167   0.00043739373
-      3300         100   0.0033703684   0.0033703684   0.0026931948   0.00014857157
-      3400         100   0.0018405709   0.0018405709   0.0016990035   6.0202278e-05
-      3500         100   0.0014788087   0.0014788087   0.0013889916   0.00016730937
-      3600         100   0.0015932961   0.0015932961   0.0013807898   0.0001418157 
-      3700         100   0.00096238915  0.00096238915  0.00097931829  6.7974535e-05
-      3800         100   0.00093087985  0.00093087985  0.00087659377  0.0001504142 
-      3900         100   0.0015825065   0.0015825065   0.0011708936   1.9583518e-05
-      4000         100   0.00062295367  0.00062295367  0.00067129665  3.9455653e-05
-      4100         100   0.00061259406  0.00061259406  0.00065710963  1.8540759e-05
-      4200         100   0.00059619666  0.00059619666  0.00064365219  7.3779336e-06
-      4300         100   0.00051191641  0.00051191641  0.00057870947  6.3349656e-06
-      4400         100   0.00050668587  0.00050668587  0.00057057233  6.2702376e-06
-      4500         100   0.00049474942  0.00049474942  0.00055151343  1.5746831e-05
-      4600         100   0.00049309932  0.00049309932  0.00054086323  6.1021041e-06
-      4700         100   0.00049263883  0.00049263883  0.00052677244  6.0964056e-06
-      4800         100   0.00041885021  0.00041885021  0.00047389202  9.5350789e-05
-      4900         100   0.00035596444  0.00035596444  0.00042522549  5.8036712e-05
-      5000         100   0.00032946897  0.00032946897  0.00040320773  6.5350005e-06
-Loop time of 0.0763179 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 28302682.620 tau/day, 65515.469 timesteps/s, 6.552 Matom-step/s
-96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0010572  | 0.0039588  | 0.0074661  |   4.6 |  5.19
-Neigh   | 0.0025868  | 0.0049885  | 0.0075283  |   3.4 |  6.54
-Comm    | 0.011862   | 0.014631   | 0.018383   |   2.0 | 19.17
-Output  | 0.0009702  | 0.0012326  | 0.0014234  |   0.5 |  1.62
-Modify  | 0.0019843  | 0.018558   | 0.036592   |  12.2 | 24.32
-Other   |            | 0.03295    |            |       | 43.17
-
-Nlocal:             25 ave          54 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:            4.5 ave          10 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:           40.5 ave          94 max           0 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 162
-Ave neighs/atom = 1.62
-Neighbor list builds = 281
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-5000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
-run	        5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
-Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-      5000         100   0.00032946897  0.00032946897  0.00040320773  6.050219e-06 
-      5100         100   0.54371575     0.54371575     0.29836301     0.008148168  
-      5200         100   0.60281896     0.60281896     0.33161676     0.0083772071 
-      5300         100   0.70823011     0.70823011     0.38289657     0.0099694209 
-      5400         100   0.78467127     0.78467127     0.4133495      0.010119104  
-      5500         100   0.85741178     0.85741178     0.44761254     0.013013239  
-      5600         100   0.93241573     0.93241573     0.47879351     0.017769592  
-      5700         100   1.019104       1.019104       0.51644461     0.015312937  
-      5800         100   1.0550014      1.0550014      0.53450507     0.017227797  
-      5900         100   1.0910946      1.0910946      0.55272891     0.017469625  
-      6000         100   1.1275288      1.1275288      0.56906788     0.018958103  
-      6100         100   1.1545017      1.1545017      0.58324166     0.019220208  
-      6200         100   1.1815817      1.1815817      0.59552677     0.019397271  
-      6300         100   1.1963931      1.1963931      0.60251664     0.018382058  
-      6400         100   1.2084652      1.2084652      0.60776713     0.020027986  
-      6500         100   1.2217215      1.2217215      0.61406339     0.021750945  
-      6600         100   1.2364016      1.2364016      0.62124174     0.021701243  
-      6700         100   1.2739954      1.2739954      0.63930766     0.02025277   
-      6800         100   1.3032733      1.3032733      0.65268105     0.021684843  
-      6900         100   1.3226653      1.3226653      0.66168772     0.021187963  
-      7000         100   1.3464995      1.3464995      0.67431153     0.022066117  
-      7100         100   1.3250485      1.3250485      0.66342366     0.02109487   
-      7200         100   1.3384316      1.3384316      0.67035095     0.021554113  
-      7300         100   1.3280234      1.3280234      0.66553439     0.020829435  
-      7400         100   1.3218971      1.3218971      0.66186263     0.020882591  
-      7500         100   1.3293858      1.3293858      0.66506462     0.020897778  
-      7600         100   1.3386019      1.3386019      0.66909392     0.020754479  
-      7700         100   1.3465327      1.3465327      0.67316081     0.021231547  
-      7800         100   1.3510586      1.3510586      0.67531764     0.021053475  
-      7900         100   1.3508987      1.3508987      0.67535907     0.020769633  
-      8000         100   1.3575635      1.3575635      0.67875993     0.022020776  
-      8100         100   1.3655144      1.3655144      0.68258066     0.021016999  
-      8200         100   1.375187       1.375187       0.68732222     0.021385146  
-      8300         100   1.3799568      1.3799568      0.69000134     0.02114428   
-      8400         100   1.3755871      1.3755871      0.68757909     0.022395102  
-      8500         100   1.3708345      1.3708345      0.68509834     0.021603853  
-      8600         100   1.3689806      1.3689806      0.68388935     0.022127839  
-      8700         100   1.3697516      1.3697516      0.68411868     0.02165119   
-      8800         100   1.3700522      1.3700522      0.68423671     0.021554001  
-      8900         100   1.3705045      1.3705045      0.68451935     0.021470392  
-      9000         100   1.3715107      1.3715107      0.68506443     0.021789844  
-      9100         100   1.3707806      1.3707806      0.68467539     0.021451331  
-      9200         100   1.371112       1.371112       0.68485975     0.021479203  
-      9300         100   1.3716851      1.3716851      0.68516034     0.021515076  
-      9400         100   1.3719031      1.3719031      0.68529221     0.021502802  
-      9500         100   1.3726759      1.3726759      0.68544012     0.021585119  
-      9600         100   1.3746583      1.3746583      0.68636924     0.02206073   
-      9700         100   1.3761662      1.3761662      0.68716579     0.021533719  
-      9800         100   1.3760157      1.3760157      0.687092       0.02163129   
-      9900         100   1.3762626      1.3762626      0.68726404     0.021707045  
-     10000         100   1.376303       1.376303       0.68735031     0.022306557  
-Loop time of 0.128472 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 16812995.511 tau/day, 38918.971 timesteps/s, 3.892 Matom-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    | 0.0012241  | 0.0085024  | 0.016023   |   7.8 |  6.62
-Neigh   | 0.0051137  | 0.0079745  | 0.011012   |   3.2 |  6.21
-Comm    | 0.0050448  | 0.009504   | 0.015048   |   4.6 |  7.40
-Output  | 0.00090309 | 0.0014765  | 0.0019648  |   1.2 |  1.15
-Modify  | 0.0072253  | 0.041211   | 0.076226   |  16.7 | 32.08
-Other   |            | 0.0598     |            |       | 46.55
-
-Nlocal:             25 ave          51 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:           3.25 ave           7 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:             46 ave         101 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 184
-Ave neighs/atom = 1.84
-Neighbor list builds = 628
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     10000         100   1.376303       1.376303       0.68735031     0.022411506  
-     10100         100   0.28192752     0.28192752     0.16298909     0.0041760951 
-     10200         100   0.14576408     0.14576408     0.10117889     0.0058653094 
-     10300         100   0.10070361     0.10070361     0.078060938    0.0041432979 
-     10400         100   0.07455595     0.07455595     0.061163197    0.0029733745 
-     10500         100   0.063531027    0.063531027    0.052515707    0.0015731241 
-     10600         100   0.049259626    0.049259626    0.041321284    0.00073083104
-     10700         100   0.037377957    0.037377957    0.032017729    0.0022631642 
-     10800         100   0.031849901    0.031849901    0.027079116    0.0014148618 
-     10900         100   0.02795233     0.02795233     0.02461403     0.00037567522
-     11000         100   0.02597858     0.02597858     0.022516094    0.00054992645
-     11100         100   0.021812043    0.021812043    0.019276946    0.00043233309
-     11200         100   0.019318956    0.019318956    0.017224213    0.00035792964
-     11300         100   0.017760494    0.017760494    0.01578407     0.00056959435
-     11400         100   0.015485043    0.015485043    0.013703       0.00061308169
-     11500         100   0.015051781    0.015051781    0.012994991    0.00040607387
-     11600         100   0.012204953    0.012204953    0.01079191     0.00059482171
-     11700         100   0.011242847    0.011242847    0.0096811013   0.00018299476
-     11800         100   0.0089605707   0.0089605707   0.0075086629   0.0012779422 
-     11900         100   0.0065544011   0.0065544011   0.0056480432   0.00039599272
-     12000         100   0.0048068901   0.0048068901   0.004185961    0.00022434097
-     12100         100   0.0045272524   0.0045272524   0.0039084556   7.8443821e-05
-     12200         100   0.0038926209   0.0038926209   0.0033949999   0.00011203445
-     12300         100   0.0034653      0.0034653      0.0030246557   0.00014999893
-     12400         100   0.0034031041   0.0034031041   0.0029879474   7.9628343e-05
-     12500         100   0.0032219984   0.0032219984   0.0028369239   6.1651251e-05
-     12600         100   0.0031148659   0.0031148659   0.0027543848   5.7332789e-05
-     12700         100   0.0027407824   0.0027407824   0.0024822578   5.150993e-05 
-     12800         100   0.0026205294   0.0026205294   0.0023576698   8.896122e-05 
-     12900         100   0.0025633289   0.0025633289   0.0023134486   7.0525939e-05
-     13000         100   0.0025434711   0.0025434711   0.0022833007   5.5638668e-05
-     13100         100   0.0025046562   0.0025046562   0.002227265    5.2772716e-05
-     13200         100   0.0023544645   0.0023544645   0.0021086805   0.00030775943
-     13300         100   0.0022163971   0.0022163971   0.0020107508   4.9204292e-05
-     13400         100   0.0021307794   0.0021307794   0.0019334987   4.8144132e-05
-     13500         100   0.0019891796   0.0019891796   0.0018128084   4.8532374e-05
-     13600         100   0.0018591538   0.0018591538   0.0016721703   4.4781385e-05
-     13700         100   0.001768055    0.001768055    0.001597222    1.6800418e-05
-     13800         100   0.001569014    0.001569014    0.0014331265   4.2982654e-05
-     13900         100   0.0013700893   0.0013700893   0.0012782771   4.8209662e-05
-     14000         100   0.0012398662   0.0012398662   0.0011606486   5.5766702e-05
-     14100         100   0.0011707267   0.0011707267   0.0010811523   3.4913501e-05
-     14200         100   0.0010483984   0.0010483984   0.0009831881   3.4742894e-05
-     14300         100   0.0010043196   0.0010043196   0.00092474592  3.4196115e-05
-     14400         100   0.00094238924  0.00094238924  0.00087181843  8.1414071e-05
-     14500         100   0.00093341457  0.00093341457  0.00086429224  3.3276909e-05
-     14600         100   0.00086042474  0.00086042474  0.00079524877  3.2260019e-05
-     14700         100   0.00080525469  0.00080525469  0.00075380989  2.8374703e-05
-     14800         100   0.00070848512  0.00070848512  0.0006762901   2.9937591e-05
-     14900         100   0.00060414588  0.00060414588  0.00058494979  2.5684401e-05
-     15000         100   0.00054251571  0.00054251571  0.00053643753  4.5496354e-05
-Loop time of 0.0553238 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 39042861.362 tau/day, 90376.994 timesteps/s, 9.038 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    | 0.00085556 | 0.0028667  | 0.0052429  |   3.6 |  5.18
-Neigh   | 0.00076731 | 0.0012173  | 0.0016987  |   1.3 |  2.20
-Comm    | 0.0016497  | 0.0060965  | 0.010792   |   5.7 | 11.02
-Output  | 0.00072675 | 0.00099509 | 0.0011615  |   0.0 |  1.80
-Modify  | 0.00064371 | 0.014719   | 0.030427   |  11.6 | 26.61
-Other   |            | 0.02943    |            |       | 53.19
-
-Nlocal:             25 ave          54 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:              5 ave          11 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:             40 ave          88 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 160
-Ave neighs/atom = 1.6
-Neighbor list builds = 97
-Dangerous builds = 0
-
-region          container delete
-variable        theta equal (step-15000)*(4.0*PI/5000)
-region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
-run	        5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     15000         100   0.00054251571  0.00054251571  0.00053643753  4.3506263e-05
-     15100         100   1.1164435      1.1164435      0.7163854      0.017358175  
-     15200         100   1.0384203      1.0384203      0.66790042     0.016095459  
-     15300         100   1.0829984      1.0829984      0.712381       0.015915015  
-     15400         100   1.4187366      1.4187366      0.89537718     0.023771032  
-     15500         100   1.5397547      1.5397547      0.97895571     0.025145916  
-     15600         100   1.7993339      1.7993339      1.1003794      0.026783317  
-     15700         100   1.8858073      1.8858073      1.1481696      0.030802833  
-     15800         100   1.9368129      1.9368129      1.1450129      0.032144729  
-     15900         100   2.0379823      2.0379823      1.1738926      0.031969116  
-     16000         100   2.0655671      2.0655671      1.187038       0.032395513  
-     16100         100   2.1199141      2.1199141      1.2102937      0.028830059  
-     16200         100   2.1819656      2.1819656      1.245147       0.029493813  
-     16300         100   2.2451204      2.2451204      1.2726968      0.029915554  
-     16400         100   2.1697892      2.1697892      1.2342734      0.027495983  
-     16500         100   2.2689358      2.2689358      1.2710223      0.029516621  
-     16600         100   2.3901976      2.3901976      1.3328992      0.030049751  
-     16700         100   2.4731258      2.4731258      1.3763126      0.032663365  
-     16800         100   2.5708338      2.5708338      1.4255635      0.032731991  
-     16900         100   2.7232422      2.7232422      1.5006931      0.036649645  
-     17000         100   2.901986       2.901986       1.5886643      0.037333791  
-     17100         100   2.8787369      2.8787369      1.5752504      0.03582313   
-     17200         100   3.1137189      3.1137189      1.6974538      0.041245422  
-     17300         100   3.1805823      3.1805823      1.7370013      0.040766564  
-     17400         100   3.3215703      3.3215703      1.8109954      0.044269306  
-     17500         100   3.3767256      3.3767256      1.813696       0.048012575  
-     17600         100   3.3618731      3.3618731      1.8004834      0.06103562   
-     17700         100   3.2288285      3.2288285      1.7447885      0.042875761  
-     17800         100   3.2545435      3.2545435      1.7617642      0.04661949   
-     17900         100   3.1162969      3.1162969      1.6850561      0.040086156  
-     18000         100   3.2053719      3.2053719      1.7132296      0.040657811  
-     18100         100   3.2924625      3.2924625      1.7709303      0.048407939  
-     18200         100   3.1682076      3.1682076      1.7136129      0.040996326  
-     18300         100   3.2244534      3.2244534      1.7401102      0.043957312  
-     18400         100   3.1470903      3.1470903      1.7171698      0.043123438  
-     18500         100   3.2690021      3.2690021      1.7803818      0.042693323  
-     18600         100   3.2566233      3.2566233      1.7670476      0.04776305   
-     18700         100   3.384347       3.384347       1.8334885      0.04441225   
-     18800         100   3.6479797      3.6479797      1.9565845      0.047454733  
-     18900         100   3.6894531      3.6894531      1.9767079      0.053222159  
-     19000         100   3.7867788      3.7867788      2.0265223      0.055923793  
-     19100         100   3.9120999      3.9120999      2.0850815      0.053591707  
-     19200         100   3.8255419      3.8255419      2.0517931      0.061034295  
-     19300         100   3.764721       3.764721       2.0089969      0.068118255  
-     19400         100   3.8604884      3.8604884      2.0640292      0.052825172  
-     19500         100   3.7763823      3.7763823      2.0223758      0.054529616  
-     19600         100   3.9158781      3.9158781      2.0873723      0.053130512  
-     19700         100   3.6394071      3.6394071      1.9735106      0.047466529  
-     19800         100   3.5409741      3.5409741      1.9335311      0.047317029  
-     19900         100   3.5961407      3.5961407      1.954696       0.048093129  
-     20000         100   3.4355899      3.4355899      1.8679902      0.0486077    
-Loop time of 0.107854 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 20026986.271 tau/day, 46358.765 timesteps/s, 4.636 Matom-step/s
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0025992  | 0.0042158  | 0.0061269  |   1.9 |  3.91
-Neigh   | 0.0089595  | 0.011254   | 0.012853   |   1.3 | 10.43
-Comm    | 0.020408   | 0.022579   | 0.024669   |   1.4 | 20.94
-Output  | 0.0010271  | 0.0011457  | 0.0012268  |   0.2 |  1.06
-Modify  | 0.019454   | 0.032696   | 0.040003   |   4.4 | 30.31
-Other   |            | 0.03596    |            |       | 33.34
-
-Nlocal:             25 ave          36 max          16 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Nghost:            5.5 ave           8 max           2 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-Neighs:          34.25 ave          48 max          19 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 137
-Ave neighs/atom = 1.37
-Neighbor list builds = 908
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
-   Step        Atoms         Temp           c_1            c_2           Press     
-     20000         100   3.4355899      3.4355899      1.8679902      0.047866781  
-     20100         100   1.1677914      1.1677914      0.70763342     0.015645481  
-     20200         100   0.99137326     0.99137326     0.61064707     0.012080974  
-     20300         100   0.84603548     0.84603548     0.52093267     0.012501649  
-     20400         100   0.82813609     0.82813609     0.50585936     0.010248184  
-     20500         100   0.86524293     0.86524293     0.5210492      0.011145216  
-     20600         100   0.92229302     0.92229302     0.54567614     0.012838894  
-     20700         100   0.93499886     0.93499886     0.55161401     0.011618713  
-     20800         100   0.95831407     0.95831407     0.56173113     0.014502297  
-     20900         100   0.88486451     0.88486451     0.51926962     0.013847246  
-     21000         100   0.66876325     0.66876325     0.39313901     0.010224296  
-     21100         100   0.46578708     0.46578708     0.28086455     0.0089121873 
-     21200         100   0.21445902     0.21445902     0.14749113     0.0033665892 
-     21300         100   0.12935011     0.12935011     0.09319765     0.002811107  
-     21400         100   0.10572326     0.10572326     0.075154962    0.0034728629 
-     21500         100   0.10952604     0.10952604     0.073864376    0.0017411404 
-     21600         100   0.074321422    0.074321422    0.051368858    0.0037915268 
-     21700         100   0.043324694    0.043324694    0.032954769    0.00092476658
-     21800         100   0.034911155    0.034911155    0.026843877    0.00061350592
-     21900         100   0.02261818     0.02261818     0.018357224    0.00049800957
-     22000         100   0.015096211    0.015096211    0.01390442     0.00059260194
-     22100         100   0.016119209    0.016119209    0.013990821    0.00038431756
-     22200         100   0.012184692    0.012184692    0.011062653    0.00030466184
-     22300         100   0.0090526001   0.0090526001   0.0080893293   0.00082507232
-     22400         100   0.007155528    0.007155528    0.0067365227   0.00094740021
-     22500         100   0.0057433117   0.0057433117   0.0057438575   0.00016706605
-     22600         100   0.0053029734   0.0053029734   0.0050429137   0.00018457156
-     22700         100   0.0041888319   0.0041888319   0.0039979907   0.00029467329
-     22800         100   0.0046486843   0.0046486843   0.0042259456   0.00019395675
-     22900         100   0.0046414295   0.0046414295   0.0040659744   0.00016025205
-     23000         100   0.0033983576   0.0033983576   0.0033431909   0.00039998961
-     23100         100   0.0031212625   0.0031212625   0.0031113361   0.00024783655
-     23200         100   0.0026724347   0.0026724347   0.0026905233   0.00026001445
-     23300         100   0.0029222876   0.0029222876   0.002946198    0.00012385327
-     23400         100   0.0023944825   0.0023944825   0.0021829995   0.00016185776
-     23500         100   0.0020384082   0.0020384082   0.0019106613   9.2139544e-05
-     23600         100   0.0019773679   0.0019773679   0.0018577006   8.9169073e-05
-     23700         100   0.0018850072   0.0018850072   0.0017715658   9.1301463e-05
-     23800         100   0.0020857322   0.0020857322   0.001864009    7.4633597e-05
-     23900         100   0.0017616498   0.0017616498   0.001680563    4.8547939e-05
-     24000         100   0.0017183254   0.0017183254   0.0016568629   6.56741e-05  
-     24100         100   0.0014311732   0.0014311732   0.0013829993   6.0743962e-05
-     24200         100   0.0013434756   0.0013434756   0.001315682    0.00025727478
-     24300         100   0.0012855885   0.0012855885   0.0012558467   9.0130585e-05
-     24400         100   0.0012731213   0.0012731213   0.0012408428   8.2008231e-05
-     24500         100   0.0011333063   0.0011333063   0.001045815    8.8391061e-05
-     24600         100   0.0010560932   0.0010560932   0.00098304208  5.6725938e-05
-     24700         100   0.00097698038  0.00097698038  0.00092381967  7.1771848e-05
-     24800         100   0.00094316799  0.00094316799  0.00089343119  5.5558578e-05
-     24900         100   0.00082812377  0.00082812377  0.00076615512  5.8668812e-05
-     25000         100   0.00076097781  0.00076097781  0.00069462801  6.5742694e-05
-Loop time of 0.0523621 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 41251226.669 tau/day, 95488.951 timesteps/s, 9.549 Matom-step/s
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0011166  | 0.0029573  | 0.0049613  |   3.3 |  5.65
-Neigh   | 0.0026276  | 0.0033989  | 0.0041666  |   1.1 |  6.49
-Comm    | 0.0054479  | 0.0084136  | 0.01182    |   2.9 | 16.07
-Output  | 0.00070658 | 0.00092447 | 0.0010421  |   0.0 |  1.77
-Modify  | 0.0015069  | 0.012796   | 0.025273   |   9.9 | 24.44
-Other   |            | 0.02387    |            |       | 45.59
-
-Nlocal:             25 ave          55 max           0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:              6 ave          14 max           0 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs:          39.25 ave          88 max           0 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 157
-Ave neighs/atom = 1.57
-Neighbor list builds = 280
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.16Mar23.granregion.funnel.g++.1

@@ -1,635 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable	name string funnel_pour
-
-thermo_modify	flush yes
-units 		si
-variable	PI equal 3.141592653589
-variable	seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	xlo equal 10
-variable	xhi equal 40
-variable	ylo equal 10
-variable	yhi equal 40
-variable	zlo equal -20
-variable	zhi equal 50
-
-variable	xc equal 25
-variable	yc equal 25
-
-variable	zconehi equal 50
-variable	zconelo equal 10
-variable	zcyllo equal 0
-variable	radconelo equal 2
-variable	radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable 	skin equal ${rhi}
-variable 	skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	density equal 1.0
-variable	EYoung equal 10^5
-variable 	Poisson equal 2.0/7.0
-variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+0.285714285714286))
-
-variable	gravity equal 1.0
-
-variable	reff equal 0.5*(${rhi}+${rlo})
-variable	reff equal 0.5*(0.5+${rlo})
-variable	reff equal 0.5*(0.5+0.25)
-variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable        kt equal 4.0*${GShear}/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable	a equal (-2.0*log(${coeffRes})/${PI})^2
-variable	a equal (-2.0*log(0.1)/${PI})^2
-variable	a equal (-2.0*log(0.1)/3.141592653589)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 903.503751814138*0.5
-
-variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable	dt equal ${tcol}*0.05
-variable	dt equal 0.00210943016014969*0.05
-timestep	${dt}
-timestep	0.000105471508007485
-
-###############################################
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		off
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 -20 ${zhi}
-region		boxreg block 10 40 10 40 -20 50
-create_box	1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} multi
-neighbor        0.5 multi
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Balancing ...
-Generated 0 of 0 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 = 0
-  ghost atom cutoff = 0
-  binsize = 30, bins = 1 1 3
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/multi/newtoff
-      stencil: full/multi/3d
-      bin: multi
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
-
-region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
-region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
-
-region		hopreg union 2 conereg cylreg
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-
-fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-
-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}
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
-   Step          CPU          Atoms        KinEng    
-         0   0                      0  -0            
-      1000   0.52844331          2000  -0            
-      2000   0.76085445          2000  -0            
-      3000   0.99183068          2000  -0            
-      4000   1.2193085           2000  -0            
-      5000   1.4439617           2000  -0            
-      6000   1.6703511           2000  -0            
-      7000   1.9053408           2000  -0            
-      8000   2.1323525           2000  -0            
-      9000   2.3566342           2000  -0            
-     10000   2.5829638           2000  -0            
-     11000   2.8106202           2000  -0            
-     12000   3.0371473           2000  -0            
-     13000   3.2621782           2000  -0            
-     14000   3.4860689           2000  -0            
-     15000   3.7138322           2000  -0            
-     16000   3.9424002           2000  -0            
-     17000   4.1703584           2000  -0            
-     18000   4.3973348           2000  -0            
-     19000   4.6213358           2000  -0            
-     20000   4.8547603           2000  -0            
-Loop time of 4.85478 on 1 procs for 20000 steps with 2000 atoms
-
-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    | 0.52375    | 0.52375    | 0.52375    |   0.0 | 10.79
-Neigh   | 0.070018   | 0.070018   | 0.070018   |   0.0 |  1.44
-Comm    | 0.011077   | 0.011077   | 0.011077   |   0.0 |  0.23
-Output  | 0.00071321 | 0.00071321 | 0.00071321 |   0.0 |  0.01
-Modify  | 4.1233     | 4.1233     | 4.1233     |   0.0 | 84.93
-Other   |            | 0.126      |            |       |  2.59
-
-Nlocal:           2000 ave        2000 max        2000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:           1607 ave        1607 max        1607 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1607
-Ave neighs/atom = 0.8035
-Neighbor list builds = 71
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
-   Step          CPU          Atoms        KinEng    
-     20000   0                   2000   6652.2957    
-     21000   0.22761741          2000   6807.2201    
-     22000   0.45508977          2000   6973.9359    
-     23000   0.68132308          2000   7142.3648    
-     24000   0.91084802          2000   7276.9717    
-     25000   1.1397154           2000   7369.4191    
-     26000   1.3724974           2000   7497.6526    
-     27000   1.6037436           2000   7638.946     
-     28000   1.8381254           2000   7780.0339    
-     29000   2.0763695           2000   7881.8177    
-     30000   2.3169444           2000   7967.2641    
-     31000   2.5544704           2000   7994.9273    
-     32000   2.7981688           2000   7937.0671    
-     33000   3.0486439           2000   7774.0508    
-     34000   3.3065315           2000   7591.1491    
-     35000   3.5712927           2000   7357.5176    
-     36000   3.8415508           2000   7147.2024    
-     37000   4.1137466           2000   6979.1604    
-     38000   4.3946186           2000   6813.2152    
-     39000   4.6737386           2000   6660.2701    
-     40000   4.9654287           2000   6502.8957    
-     41000   5.2606376           2000   6324.3951    
-     42000   5.5633065           2000   6132.7516    
-     43000   5.8692745           2000   5913.1841    
-     44000   6.1757115           2000   5732.2095    
-     45000   6.4896845           2000   5508.8322    
-     46000   6.8170163           2000   5306.8932    
-     47000   7.1514543           2000   5152.0521    
-     48000   7.4863157           2000   5028.2274    
-     49000   7.8214974           2000   4896.102     
-     50000   8.1600826           2000   4723.5189    
-     51000   8.4984004           2000   4583.7526    
-     52000   8.8500924           2000   4447.0187    
-     53000   9.2046999           2000   4303.2307    
-     54000   9.5724785           2000   4168.5251    
-     55000   9.9479954           2000   4036.9704    
-     56000   10.324666           2000   3901.1183    
-     57000   10.708944           2000   3716.7071    
-     58000   11.108887           2000   3473.5422    
-     59000   11.515057           2000   3245.1223    
-     60000   11.922119           2000   3039.7845    
-     61000   12.331146           2000   2780.0187    
-     62000   12.745147           2000   2577.3345    
-     63000   13.169644           2000   2346.2488    
-     64000   13.602869           2000   2116.7298    
-     65000   14.044828           2000   1903.7828    
-     66000   14.49159            2000   1631.1676    
-     67000   14.953127           2000   1431.0198    
-     68000   15.428874           2000   1212.875     
-     69000   15.981012           2000   995.45046    
-     70000   16.458356           2000   811.54766    
-     71000   16.936094           2000   624.08622    
-     72000   17.432306           2000   471.00862    
-     73000   17.949423           2000   358.33486    
-     74000   18.467878           2000   284.39416    
-     75000   18.970599           2000   234.26671    
-     76000   19.45957            2000   185.61836    
-     77000   19.959792           2000   152.95918    
-     78000   20.455734           2000   122.49023    
-     79000   20.93849            2000   102.29396    
-     80000   21.430632           2000   86.284684    
-     81000   21.925932           2000   73.984781    
-     82000   22.428573           2000   63.042918    
-     83000   22.945552           2000   53.338428    
-     84000   23.467102           2000   45.89585     
-     85000   23.992243           2000   40.412826    
-     86000   24.512956           2000   34.183381    
-     87000   25.037944           2000   29.671524    
-     88000   25.56622            2000   26.90414     
-     89000   26.102251           2000   24.362631    
-     90000   26.638165           2000   21.887341    
-     91000   27.17863            2000   19.985662    
-     92000   27.72662            2000   18.728162    
-     93000   28.276842           2000   16.99941     
-     94000   28.830281           2000   15.71941     
-     95000   29.389744           2000   14.744057    
-     96000   29.972451           2000   14.214918    
-     97000   30.575245           2000   13.450182    
-     98000   31.141552           2000   12.79222     
-     99000   31.711177           2000   12.10595     
-    100000   32.286609           2000   11.281863    
-    101000   32.879692           2000   10.025419    
-    102000   33.460265           2000   9.9574468    
-    103000   34.040002           2000   9.4078117    
-    104000   34.619096           2000   8.9079161    
-    105000   35.199384           2000   8.6269302    
-    106000   35.784782           2000   8.5512649    
-    107000   36.37489            2000   8.4703948    
-    108000   36.963891           2000   8.2747542    
-    109000   37.551549           2000   8.2895118    
-    110000   38.154561           2000   8.1785613    
-    111000   38.749306           2000   7.8443234    
-    112000   39.344241           2000   7.7436124    
-    113000   39.938878           2000   7.8118604    
-    114000   40.531935           2000   7.3806177    
-    115000   41.130022           2000   7.0857235    
-    116000   41.726772           2000   7.1346752    
-    117000   42.322611           2000   7.0653751    
-    118000   42.927287           2000   6.6314104    
-    119000   43.524125           2000   6.2169614    
-    120000   44.127912           2000   5.8988829    
-    121000   44.724988           2000   5.4197277    
-    122000   45.328051           2000   4.6381303    
-    123000   45.93285            2000   4.4949206    
-    124000   46.54149            2000   4.4261118    
-    125000   47.301723           2000   4.4223703    
-    126000   48.071689           2000   4.4858898    
-    127000   48.834286           2000   4.3312536    
-    128000   49.448737           2000   3.7124973    
-    129000   50.169622           2000   3.5467396    
-    130000   50.867494           2000   3.5104139    
-    131000   51.585563           2000   3.5725612    
-    132000   52.240372           2000   3.669455     
-    133000   52.892134           2000   3.6168912    
-    134000   53.50594            2000   3.3598517    
-    135000   54.114565           2000   3.3743407    
-    136000   54.725082           2000   3.1109764    
-    137000   55.358218           2000   3.0720146    
-    138000   55.977314           2000   3.1303776    
-    139000   56.589791           2000   3.2052806    
-    140000   57.212518           2000   2.8958882    
-    141000   57.867102           2000   2.9931572    
-    142000   58.690342           2000   3.0967832    
-    143000   59.418639           2000   3.0576365    
-    144000   60.035852           2000   3.2016943    
-    145000   60.666569           2000   3.3817709    
-    146000   61.368878           2000   3.4527239    
-    147000   62.159309           2000   3.5928733    
-    148000   62.879677           2000   3.7784682    
-    149000   63.50784            2000   3.6587944    
-    150000   64.129366           2000   3.7945669    
-    151000   64.74324            2000   3.5551557    
-    152000   65.360802           2000   3.6248848    
-    153000   65.979475           2000   3.7361463    
-    154000   66.593554           2000   3.8534319    
-    155000   67.30899            2000   4.0101408    
-    156000   68.295637           2000   3.7670652    
-    157000   69.257704           2000   3.1487676    
-    158000   70.085566           2000   2.980076     
-    159000   70.914218           2000   3.0350592    
-    160000   71.734553           2000   3.125389     
-    161000   72.423913           2000   2.7516115    
-    162000   73.264994           2000   2.413911     
-    163000   74.126424           2000   2.297713     
-    164000   75.050891           2000   2.3190806    
-    165000   75.917063           2000   2.2868879    
-    166000   76.783267           2000   2.1658547    
-    167000   77.516683           2000   1.7511071    
-    168000   78.319102           2000   1.4112478    
-    169000   78.961239           2000   1.3623558    
-    170000   79.578448           2000   1.3701579    
-Loop time of 79.5785 on 1 procs for 150000 steps with 2000 atoms
-
-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    | 40.78      | 40.78      | 40.78      |   0.0 | 51.25
-Neigh   | 0.6504     | 0.6504     | 0.6504     |   0.0 |  0.82
-Comm    | 0.090848   | 0.090848   | 0.090848   |   0.0 |  0.11
-Output  | 0.0059597  | 0.0059597  | 0.0059597  |   0.0 |  0.01
-Modify  | 36.939     | 36.939     | 36.939     |   0.0 | 46.42
-Other   |            | 1.112      |            |       |  1.40
-
-Nlocal:           2000 ave        2000 max        2000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          15308 ave       15308 max       15308 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15308
-Ave neighs/atom = 7.654
-Neighbor list builds = 367
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region	  	cylreg delete
-region		hopreg delete
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
-
-region		hopreg union 2 cylreg conereg
-
-unfix		hopper3
-fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run		100000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
-   Step          CPU          Atoms        KinEng    
-    170000   0                   2000   1.3701579    
-    171000   0.71457906          2000   2.3724823    
-    172000   1.4067557           2000   3.5881441    
-    173000   2.0500352           2000   5.3771633    
-    174000   2.8020081           2000   7.5896471    
-    175000   3.467807            2000   10.77251     
-    176000   4.064748            2000   14.806868    
-    177000   4.6769962           2000   19.607624    
-    178000   5.26259             2000   25.426227    
-    179000   5.8424937           2000   32.23584     
-    180000   6.4222206           2000   39.930468    
-    181000   6.9910375           2000   47.686304    
-    182000   7.5601562           2000   56.506806    
-    183000   8.1243537           2000   66.514326    
-    184000   8.6871123           2000   77.554644    
-    185000   9.3749051           2000   89.224002    
-    186000   10.008412           2000   102.07846    
-    187000   10.668269           2000   116.08141    
-    188000   11.26663            2000   130.97964    
-    189000   11.874542           2000   146.77806    
-    190000   12.436262           2000   162.79858    
-    191000   12.973297           2000   179.02052    
-    192000   13.532286           2000   196.26683    
-    193000   14.056018           2000   214.38928    
-    194000   14.593726           2000   232.32068    
-    195000   15.115478           2000   251.74644    
-    196000   15.637308           2000   272.25231    
-    197000   16.159144           2000   294.64075    
-    198000   16.676958           2000   318.32895    
-    199000   17.186114           2000   342.44005    
-    200000   17.706244           2000   368.35469    
-    201000   18.221731           2000   395.2465     
-    202000   18.739505           2000   422.63599    
-    203000   19.259645           2000   450.45248    
-    204000   19.769875           2000   479.60812    
-    205000   20.293972           2000   510.44155    
-    206000   20.806658           2000   543.25751    
-    207000   21.348998           2000   577.35928    
-    208000   21.888691           2000   612.29718    
-    209000   22.421596           2000   647.8951     
-    210000   22.922782           2000   683.79409    
-    211000   23.473165           2000   720.36556    
-    212000   24.008952           2000   759.27331    
-    213000   24.56155            2000   798.27302    
-    214000   25.062386           2000   837.93849    
-    215000   25.563743           2000   877.92945    
-    216000   26.066188           2000   919.62532    
-    217000   26.584605           2000   962.83509    
-    218000   27.15076            2000   1008.5243    
-    219000   27.651387           2000   1054.5769    
-    220000   28.146147           2000   1103.1843    
-    221000   28.644239           2000   1153.0349    
-    222000   29.141899           2000   1204.5599    
-    223000   29.636644           2000   1257.1367    
-    224000   30.13786            2000   1308.6735    
-WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
-    225000   30.638093           1999   1360.1205    
-    226000   31.127956           1998   1404.8405    
-    227000   31.620394           1996   1448.4869    
-    228000   32.108597           1992   1491.8112    
-    229000   32.592048           1985   1518.7013    
-    230000   33.067462           1971   1507.6699    
-    231000   33.552874           1965   1533.5096    
-    232000   34.037763           1948   1489.4128    
-    233000   34.531058           1933   1477.4536    
-    234000   35.01451            1915   1425.8398    
-    235000   35.495081           1904   1410.1451    
-    236000   35.963357           1892   1401.7595    
-    237000   36.428382           1880   1368.893     
-    238000   36.890459           1868   1341.8885    
-    239000   37.358838           1850   1286.7968    
-    240000   37.828549           1833   1219.5123    
-    241000   38.29428            1820   1173.3608    
-    242000   38.750021           1806   1106.0727    
-    243000   39.206425           1788   1035.912     
-    244000   39.690492           1779   1021.6147    
-    245000   40.138287           1767   969.40032    
-    246000   40.582591           1757   939.12022    
-    247000   41.02378            1739   840.9396     
-    248000   41.472154           1730   822.06575    
-    249000   41.916625           1719   762.11057    
-    250000   42.365019           1707   708.50308    
-    251000   42.804617           1700   692.12647    
-    252000   43.257666           1697   694.5812     
-    253000   43.777656           1686   652.36951    
-    254000   44.244131           1682   662.95256    
-    255000   44.667759           1677   637.34619    
-    256000   45.111967           1672   630.71277    
-    257000   45.550194           1669   641.87365    
-    258000   45.985106           1665   635.862      
-    259000   46.42582            1664   658.5339     
-    260000   46.860965           1662   669.95468    
-    261000   47.298309           1660   676.93495    
-    262000   47.748236           1657   681.72646    
-    263000   48.215018           1655   687.4078     
-    264000   48.657973           1651   681.61352    
-    265000   49.076584           1647   673.20622    
-    266000   49.497823           1644   677.30073    
-    267000   49.917789           1641   671.05897    
-    268000   50.347112           1639   689.55776    
-    269000   50.778062           1637   711.98809    
-    270000   51.226034           1633   705.29974    
-Loop time of 51.2261 on 1 procs for 100000 steps with 1633 atoms
-
-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    | 27.462     | 27.462     | 27.462     |   0.0 | 53.61
-Neigh   | 0.47887    | 0.47887    | 0.47887    |   0.0 |  0.93
-Comm    | 0.058496   | 0.058496   | 0.058496   |   0.0 |  0.11
-Output  | 0.0039167  | 0.0039167  | 0.0039167  |   0.0 |  0.01
-Modify  | 22.566     | 22.566     | 22.566     |   0.0 | 44.05
-Other   |            | 0.6567     |            |       |  1.28
-
-Nlocal:           1633 ave        1633 max        1633 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          11358 ave       11358 max       11358 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 11358
-Ave neighs/atom = 6.955297
-Neighbor list builds = 244
-Dangerous builds = 0
-Total wall time: 0:02:15

examples/granregion/log.16Mar23.granregion.funnel.g++.4

@@ -1,635 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-# pour particles into cone-shaped funnel, settle them, let them run out bottom
-
-variable	name string funnel_pour
-
-thermo_modify	flush yes
-units 		si
-variable	PI equal 3.141592653589
-variable	seed equal 14314
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	xlo equal 10
-variable	xhi equal 40
-variable	ylo equal 10
-variable	yhi equal 40
-variable	zlo equal -20
-variable	zhi equal 50
-
-variable	xc equal 25
-variable	yc equal 25
-
-variable	zconehi equal 50
-variable	zconelo equal 10
-variable	zcyllo equal 0
-variable	radconelo equal 2
-variable	radconehi equal 20
-
-################################################
-# Particle sizes
-################################################
-
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable 	skin equal ${rhi}
-variable 	skin equal 0.5
-
-###############################################
-# Granular contact parameters
-###############################################
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	density equal 1.0
-variable	EYoung equal 10^5
-variable 	Poisson equal 2.0/7.0
-variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+${Poisson}))
-variable	GShear equal 100000/(2*(1+0.285714285714286))
-
-variable	gravity equal 1.0
-
-variable	reff equal 0.5*(${rhi}+${rlo})
-variable	reff equal 0.5*(0.5+${rlo})
-variable	reff equal 0.5*(0.5+0.25)
-variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
-variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
-variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
-variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
-variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
-variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
-
-## Typical way to set kn, kt, etc.:
-variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
-variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
-variable        kt equal 4.0*${GShear}/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
-variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
-
-variable	a equal (-2.0*log(${coeffRes})/${PI})^2
-variable	a equal (-2.0*log(0.1)/${PI})^2
-variable	a equal (-2.0*log(0.1)/3.141592653589)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 903.503751814138*0.5
-
-variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
-variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
-
-variable	dt equal ${tcol}*0.05
-variable	dt equal 0.00210943016014969*0.05
-timestep	${dt}
-timestep	0.000105471508007485
-
-###############################################
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		off
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 ${zlo} ${zhi}
-region		boxreg block 10 40 10 40 -20 ${zhi}
-region		boxreg block 10 40 10 40 -20 50
-create_box	1 boxreg
-Created orthogonal box = (10 10 -20) to (40 40 50)
-  1 by 1 by 4 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
-pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} multi
-neighbor        0.5 multi
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Balancing ...
-Generated 0 of 0 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 = 0
-  ghost atom cutoff = 0
-  binsize = 30, bins = 1 1 3
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/multi/newtoff
-      stencil: full/multi/3d
-      bin: multi
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-# insertion region for fix/pour
-
-region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
-region	     	insreg cylinder z 25 25 10 30 50 side in units box
-
-# define cone and cylinder regions - see lammps doc on region command
-# note new open options
-
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
-
-region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
-region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
-region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
-
-region		hopreg union 2 conereg cylreg
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-
-fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
-fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
-Particle insertion: 3000 every 59965 steps, 2000 by step 1
-
-#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-
-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}
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
-   Step          CPU          Atoms        KinEng    
-         0   0                      0  -0            
-      1000   0.55467905          2000  -0            
-      2000   0.77825615          2000  -0            
-      3000   0.99338813          2000  -0            
-      4000   1.2048904           2000  -0            
-      5000   1.4073987           2000  -0            
-      6000   1.6070452           2000  -0            
-      7000   1.8056594           2000  -0            
-      8000   1.9907326           2000  -0            
-      9000   2.1732359           2000  -0            
-     10000   2.3525506           2000  -0            
-     11000   2.4202338           2000  -0            
-     12000   2.4883928           2000  -0            
-     13000   2.5587335           2000  -0            
-     14000   2.6327822           2000  -0            
-     15000   2.7095893           2000  -0            
-     16000   2.7909032           2000  -0            
-     17000   2.8763781           2000  -0            
-     18000   2.9671807           2000  -0            
-     19000   3.05783             2000  -0            
-     20000   3.1546642           2000  -0            
-Loop time of 3.1547 on 4 procs for 20000 steps with 2000 atoms
-
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.045592   | 0.12271    | 0.29398    |  28.5 |  3.89
-Neigh   | 0.011353   | 0.019401   | 0.032667   |   5.7 |  0.61
-Comm    | 0.043342   | 0.09899    | 0.1539     |  14.6 |  3.14
-Output  | 0.00097884 | 0.0019761  | 0.0024333  |   1.3 |  0.06
-Modify  | 0.8096     | 1.2822     | 2.26       |  50.7 | 40.65
-Other   |            | 1.629      |            |       | 51.65
-
-Nlocal:            500 ave         510 max         493 min
-Histogram: 1 1 0 0 0 1 0 0 0 1
-Nghost:            154 ave         227 max          79 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:          415.5 ave         610 max         258 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 1662
-Ave neighs/atom = 0.831
-Neighbor list builds = 71
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
-   Step          CPU          Atoms        KinEng    
-     20000   0                   2000   6652.2957    
-     21000   0.068149031         2000   6807.2201    
-     22000   0.13906682          2000   6973.9359    
-     23000   0.21167896          2000   7142.3648    
-     24000   0.28828482          2000   7276.9717    
-     25000   0.36895294          2000   7369.4191    
-     26000   0.45705665          2000   7497.6526    
-     27000   0.55283141          2000   7638.946     
-     28000   0.65163553          2000   7780.0339    
-     29000   0.75208427          2000   7881.8177    
-     30000   0.85956458          2000   7967.2641    
-     31000   0.94177635          2000   7994.9273    
-     32000   1.0345834           2000   7937.0672    
-     33000   1.1315152           2000   7774.0508    
-     34000   1.2426423           2000   7591.1511    
-     35000   1.3578344           2000   7357.5032    
-     36000   1.4893311           2000   7147.3776    
-     37000   1.6240315           2000   6980.0719    
-     38000   1.7664339           2000   6813.0872    
-     39000   1.91857             2000   6657.0694    
-     40000   2.0835393           2000   6505.1356    
-     41000   2.2038908           2000   6330.3106    
-     42000   2.330345            2000   6148.0635    
-     43000   2.4596185           2000   5933.4808    
-     44000   2.5912876           2000   5759.5507    
-     45000   2.7316375           2000   5510.4729    
-     46000   2.8777238           2000   5332.8673    
-     47000   3.0357893           2000   5164.4197    
-     48000   3.1931582           2000   5027.4099    
-     49000   3.341993            2000   4904.6999    
-     50000   3.4914327           2000   4712.0967    
-     51000   3.6880787           2000   4575.8693    
-     52000   3.8868278           2000   4443.4894    
-     53000   4.0538325           2000   4272.1666    
-     54000   4.2275386           2000   4113.2811    
-     55000   4.3935565           2000   3974.5981    
-     56000   4.6008319           2000   3863.5272    
-     57000   4.8305792           2000   3676.8918    
-     58000   5.1085757           2000   3446.5177    
-     59000   5.3025239           2000   3227.8857    
-     60000   5.5061134           2000   2997.8151    
-     61000   5.6771065           2000   2745.5998    
-     62000   5.8533046           2000   2530.2536    
-     63000   6.0266287           2000   2352.9283    
-     64000   6.1975348           2000   2102.4916    
-     65000   6.375875            2000   1906.3034    
-     66000   6.6008814           2000   1683.179     
-     67000   6.8728018           2000   1440.0663    
-     68000   7.1104699           2000   1220.2743    
-     69000   7.3660591           2000   1012.4596    
-     70000   7.6208232           2000   796.99913    
-     71000   7.8459169           2000   631.28788    
-     72000   8.0433916           2000   459.93641    
-     73000   8.2225178           2000   359.28959    
-     74000   8.3982201           2000   286.19292    
-     75000   8.5769976           2000   235.53259    
-     76000   8.7541865           2000   187.55737    
-     77000   9.0010462           2000   144.42323    
-     78000   9.2721615           2000   116.12613    
-     79000   9.4992863           2000   95.625301    
-     80000   9.7368141           2000   82.645629    
-     81000   9.9462546           2000   72.124657    
-     82000   10.15281            2000   64.266704    
-     83000   10.365519           2000   56.7285      
-     84000   10.55069            2000   49.44393     
-     85000   10.764107           2000   42.434733    
-     86000   10.993211           2000   37.816266    
-     87000   11.243268           2000   33.892006    
-     88000   11.487204           2000   29.898596    
-     89000   11.684173           2000   26.4401      
-     90000   11.880908           2000   23.329056    
-     91000   12.078366           2000   21.291141    
-     92000   12.347446           2000   19.494401    
-     93000   12.582632           2000   18.157646    
-     94000   12.833491           2000   17.176709    
-     95000   13.109452           2000   16.059418    
-     96000   13.34541            2000   15.524934    
-     97000   13.604566           2000   13.887097    
-     98000   13.816696           2000   12.98846     
-     99000   14.043128           2000   12.325347    
-    100000   14.35998            2000   11.567779    
-    101000   14.584033           2000   11.097346    
-    102000   14.793606           2000   10.981696    
-    103000   15.011832           2000   10.914661    
-    104000   15.223053           2000   10.183009    
-    105000   15.435892           2000   9.9825606    
-    106000   15.651946           2000   9.5164341    
-    107000   15.870696           2000   9.4270389    
-    108000   16.237826           2000   9.2752131    
-    109000   16.525601           2000   8.580319     
-    110000   16.74452            2000   8.3138082    
-    111000   16.991527           2000   7.826454     
-    112000   17.322972           2000   7.5958866    
-    113000   17.649386           2000   7.2760339    
-    114000   17.967676           2000   7.2879075    
-    115000   18.27941            2000   6.8298855    
-    116000   18.619507           2000   6.6964815    
-    117000   18.979092           2000   6.490952     
-    118000   19.303215           2000   6.0204595    
-    119000   19.683409           2000   5.9293145    
-    120000   20.034873           2000   5.7244854    
-    121000   20.329374           2000   5.4221021    
-    122000   20.670529           2000   4.8227757    
-    123000   20.970073           2000   4.7914829    
-    124000   21.297132           2000   4.6895984    
-    125000   21.524346           2000   4.4951309    
-    126000   21.742931           2000   4.5186107    
-    127000   21.983039           2000   4.5989696    
-    128000   22.203881           2000   4.5578225    
-    129000   22.428553           2000   4.2667783    
-    130000   22.662049           2000   4.0855202    
-    131000   22.893977           2000   4.129346     
-    132000   23.134398           2000   4.1720282    
-    133000   23.367561           2000   4.3178701    
-    134000   23.614361           2000   4.1047803    
-    135000   23.840139           2000   3.856834     
-    136000   24.095293           2000   4.0099605    
-    137000   24.320746           2000   4.1104868    
-    138000   24.555868           2000   4.1538456    
-    139000   24.798604           2000   4.3079797    
-    140000   25.125474           2000   4.0655486    
-    141000   25.360498           2000   4.1257388    
-    142000   25.597535           2000   4.1180413    
-    143000   25.824173           2000   4.2764691    
-    144000   26.082826           2000   4.3992832    
-    145000   26.307002           2000   4.0978942    
-    146000   26.532413           2000   4.1776805    
-    147000   26.759469           2000   4.2261665    
-    148000   26.989405           2000   4.4049886    
-    149000   27.215826           2000   4.5559941    
-    150000   27.443235           2000   4.7449947    
-    151000   27.670397           2000   4.962558     
-    152000   27.901368           2000   4.8517188    
-    153000   28.148201           2000   4.9263912    
-    154000   28.379071           2000   4.6200149    
-    155000   28.621063           2000   4.8289752    
-    156000   28.870192           2000   5.043235     
-    157000   29.105614           2000   5.2399981    
-    158000   29.330537           2000   5.494424     
-    159000   29.558095           2000   4.9215021    
-    160000   29.785841           2000   4.8938104    
-    161000   30.011182           2000   5.0832139    
-    162000   30.23825            2000   5.2281894    
-    163000   30.464829           2000   5.4710487    
-    164000   30.719854           2000   5.7311326    
-    165000   31.038065           2000   5.9048483    
-    166000   31.340672           2000   6.1177544    
-    167000   31.649901           2000   4.0749212    
-    168000   31.928746           2000   4.0087545    
-    169000   32.153717           2000   2.8333927    
-    170000   32.380796           2000   2.6131424    
-Loop time of 32.3808 on 4 procs for 150000 steps with 2000 atoms
-
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.997      | 12.251     | 14.992     |  89.3 | 37.83
-Neigh   | 0.1358     | 0.20191    | 0.24331    |   9.0 |  0.62
-Comm    | 1.2102     | 2.0432     | 2.4992     |  36.1 |  6.31
-Output  | 0.0079578  | 0.012222   | 0.020149   |   4.4 |  0.04
-Modify  | 7.1333     | 9.974      | 12.03      |  56.2 | 30.80
-Other   |            | 7.899      |            |       | 24.39
-
-Nlocal:            500 ave         547 max         414 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:          447.5 ave         678 max         201 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:        4478.75 ave        5715 max        3358 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 17915
-Ave neighs/atom = 8.9575
-Neighbor list builds = 375
-Dangerous builds = 0
-
-# remove "plug" - need to redefine cylinder region & union
-
-region	  	cylreg delete
-region		hopreg delete
-region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
-region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
-region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
-
-region		hopreg union 2 cylreg conereg
-
-unfix		hopper3
-fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
-fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
-
-run		100000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
-   Step          CPU          Atoms        KinEng    
-    170000   0                   2000   2.6131424    
-    171000   0.22601136          2000   3.529459     
-    172000   0.45221016          2000   4.7071494    
-    173000   0.68427839          2000   6.3480095    
-    174000   0.91114205          2000   8.8055429    
-    175000   1.1431874           2000   12.020148    
-    176000   1.3732197           2000   16.079961    
-    177000   1.6051751           2000   20.911155    
-    178000   1.8346523           2000   26.447901    
-    179000   2.0762403           2000   32.277607    
-    180000   2.3420473           2000   39.374754    
-    181000   2.6328957           2000   46.824434    
-    182000   2.8669203           2000   54.755937    
-    183000   3.1047916           2000   63.957816    
-    184000   3.3310346           2000   74.217343    
-    185000   3.5685015           2000   85.472859    
-    186000   3.7955114           2000   97.586962    
-    187000   4.0326183           2000   110.39658    
-    188000   4.267244            2000   123.54524    
-    189000   4.4987867           2000   137.45798    
-    190000   4.7358838           2000   151.81094    
-    191000   4.9494874           2000   166.91945    
-    192000   5.1552044           2000   182.93379    
-    193000   5.3547002           2000   200.32195    
-    194000   5.5590208           2000   218.31863    
-    195000   5.7575332           2000   237.22122    
-    196000   5.9520759           2000   255.12936    
-    197000   6.1457469           2000   273.87347    
-    198000   6.341216            2000   293.82126    
-    199000   6.5397944           2000   315.13067    
-    200000   6.7418645           2000   337.18517    
-    201000   6.9368245           2000   359.48438    
-    202000   7.1538903           2000   382.76229    
-    203000   7.3864641           2000   408.60338    
-    204000   7.6731476           2000   435.15421    
-    205000   7.9053649           2000   462.53542    
-    206000   8.1480905           2000   490.85791    
-    207000   8.3856692           2000   519.80878    
-    208000   8.6034715           2000   550.44978    
-    209000   8.8046602           2000   581.78594    
-    210000   9.0044136           2000   615.02491    
-    211000   9.2216638           2000   649.34564    
-    212000   9.4269046           2000   684.24357    
-    213000   9.6587854           2000   720.72627    
-    214000   9.8596293           2000   757.96901    
-    215000   10.05877            2000   796.8493     
-    216000   10.256066           2000   836.58839    
-    217000   10.48718            2000   877.81823    
-    218000   10.694787           2000   920.81077    
-    219000   10.891455           2000   963.77552    
-    220000   11.147269           2000   1007.6868    
-    221000   11.400829           2000   1054.0654    
-    222000   11.65238            2000   1102.4934    
-    223000   11.846807           2000   1151.1348    
-    224000   12.040148           2000   1200.6622    
-    225000   12.229259           2000   1251.5126    
-WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
-    226000   12.420863           1999   1299.6349    
-    227000   12.635492           1997   1338.1126    
-    228000   12.827738           1987   1354.6661    
-    229000   13.016127           1980   1369.1412    
-    230000   13.211511           1970   1369.1776    
-    231000   13.404909           1963   1377.7863    
-    232000   13.602332           1950   1362.1028    
-    233000   13.796103           1938   1344.4535    
-    234000   13.988442           1924   1318.1397    
-    235000   14.185813           1907   1269.3181    
-    236000   14.378388           1895   1242.269     
-    237000   14.568867           1881   1188.0729    
-    238000   14.75676            1868   1162.8778    
-    239000   14.947894           1854   1111.9974    
-    240000   15.160004           1840   1050.2813    
-    241000   15.340495           1831   1024.5782    
-    242000   15.523597           1816   980.07203    
-    243000   15.725193           1807   973.84606    
-    244000   15.902549           1796   936.95947    
-    245000   16.081382           1790   916.53685    
-    246000   16.261081           1780   893.82891    
-    247000   16.451727           1770   853.09944    
-    248000   16.628641           1755   804.73429    
-    249000   16.804105           1749   773.19378    
-    250000   16.978354           1738   734.78084    
-    251000   17.152527           1725   668.92528    
-    252000   17.328291           1717   651.36038    
-    253000   17.512786           1706   595.48412    
-    254000   17.695931           1699   564.79829    
-    255000   17.874221           1695   558.19897    
-    256000   18.050516           1693   568.02459    
-    257000   18.228697           1692   584.97166    
-    258000   18.400925           1689   574.19701    
-    259000   18.576449           1687   583.36332    
-    260000   18.754006           1684   577.56927    
-    261000   18.946091           1681   582.0375     
-    262000   19.182957           1679   583.29644    
-    263000   19.394795           1676   575.09831    
-    264000   19.604668           1673   575.78272    
-    265000   19.81517            1672   595.66572    
-    266000   20.046658           1670   610.84262    
-    267000   20.332684           1665   588.36505    
-    268000   20.573691           1662   593.44831    
-    269000   20.800574           1660   600.31964    
-    270000   21.058624           1656   588.46212    
-Loop time of 21.0587 on 4 procs for 100000 steps with 1656 atoms
-
-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    | 3.8632     | 8.4037     | 11.541     |  97.3 | 39.91
-Neigh   | 0.13431    | 0.15665    | 0.17248    |   3.8 |  0.74
-Comm    | 0.70516    | 1.4552     | 1.9637     |  40.7 |  6.91
-Output  | 0.0030904  | 0.0079543  | 0.016722   |   5.9 |  0.04
-Modify  | 5.3661     | 6.1781     | 6.8249     |  22.0 | 29.34
-Other   |            | 4.857      |            |       | 23.06
-
-Nlocal:            414 ave         426 max         385 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost:            408 ave         634 max         183 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs:           3463 ave        4360 max        2354 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-
-Total # of neighbors = 13852
-Ave neighs/atom = 8.3647343
-Neighbor list builds = 255
-Dangerous builds = 0
-Total wall time: 0:00:56

examples/granregion/log.16Mar23.granregion.mixer.g++.1

@@ -1,634 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-variable	name string mixer
-
-thermo_modify	flush yes
-variable	seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable	rlo equal 0.3
-variable	rhi equal 0.6
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.3
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.6
-variable 	skin equal ${rhi}
-variable 	skin equal 0.6
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	kn equal 10^5
-variable	kt equal 0.2*${kn}
-variable	kt equal 0.2*100000
-
-variable	gravity equal 1.0
-variable	density equal 1.0
-
-variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable	a equal (-2.0*log(${coeffRes})/PI)^2
-variable	a equal (-2.0*log(0.1)/PI)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 806.699778405191*0.5
-
-variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable	dt equal ${tcol}*0.02
-variable	dt equal 0.00236257621510454*0.02
-timestep	${dt}
-timestep	4.72515243020908e-05
-
-###############################################
-
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		on
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block 0 20 0 20 0 20
-create_box	1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
-  1 by 1 by 1 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} multi
-neighbor        0.6 multi
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Balancing ...
-Generated 0 of 0 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 = 0
-  ghost atom cutoff = 0
-  binsize = 20, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/multi/newton
-      stencil: half/multi/3d
-      bin: multi
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region	     	insreg cylinder z 10 10 8 10 18 side in units box
-region	    	cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable	theta equal (step/400000)*2*PI
-
-region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
-region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
-
-region		mixer intersect 3 cylreg b1 b2 side in
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
-thermo_modify	flush yes lost warn
-
-run		200000
-
-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}
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
-   Step          CPU          Atoms        KinEng        v_theta    
-         0   0                      0  -0              0            
-      1000   0.11477344           444  -0              0.015707963  
-      2000   0.21604269           444  -0              0.031415927  
-      3000   0.31421365           444  -0              0.04712389   
-      4000   0.41095902           444  -0              0.062831853  
-      5000   0.50703042           444  -0              0.078539816  
-      6000   0.60585007           444  -0              0.09424778   
-      7000   0.70232419           444  -0              0.10995574   
-      8000   0.80002622           444  -0              0.12566371   
-      9000   0.89464008           444  -0              0.14137167   
-     10000   0.99260726           444  -0              0.15707963   
-     11000   1.090675             444  -0              0.1727876    
-     12000   1.1878107            444  -0              0.18849556   
-     13000   1.2860401            444  -0              0.20420352   
-     14000   1.3830433            444  -0              0.21991149   
-     15000   1.4834023            444  -0              0.23561945   
-     16000   1.5799984            444  -0              0.25132741   
-     17000   1.6758091            444  -0              0.26703538   
-     18000   1.7713554            444  -0              0.28274334   
-     19000   1.8684734            444  -0              0.2984513    
-     20000   1.9661563            444  -0              0.31415927   
-     21000   2.0629748            444  -0              0.32986723   
-     22000   2.1575594            444  -0              0.34557519   
-     23000   2.2530422            444  -0              0.36128316   
-     24000   2.3525179            444  -0              0.37699112   
-     25000   2.4494323            444  -0              0.39269908   
-     26000   2.5454666            444  -0              0.40840704   
-     27000   2.6402269            444  -0              0.42411501   
-     28000   2.7364338            444  -0              0.43982297   
-     29000   2.8349               444  -0              0.45553093   
-     30000   2.9327959            444  -0              0.4712389    
-     31000   3.0304534            444  -0              0.48694686   
-     32000   3.1315005            444  -0              0.50265482   
-     33000   3.2290307            444  -0              0.51836279   
-     34000   3.3243787            444  -0              0.53407075   
-     35000   3.4232964            444  -0              0.54977871   
-     36000   3.5235978            444  -0              0.56548668   
-     37000   3.6214101            444  -0              0.58119464   
-     38000   3.7179412            444  -0              0.5969026    
-     39000   3.8159856            444  -0              0.61261057   
-     40000   3.9121916            444  -0              0.62831853   
-     41000   4.0080794            444  -0              0.64402649   
-     42000   4.1087349            444  -0              0.65973446   
-     43000   4.2059697            444  -0              0.67544242   
-     44000   4.3043867            444  -0              0.69115038   
-     45000   4.4014253            444  -0              0.70685835   
-     46000   4.5000241            444  -0              0.72256631   
-     47000   4.5970258            444  -0              0.73827427   
-     48000   4.6929243            444  -0              0.75398224   
-     49000   4.7894702            444  -0              0.7696902    
-     50000   4.8858098            444  -0              0.78539816   
-     51000   4.985063             444  -0              0.80110613   
-     52000   5.0863877            444  -0              0.81681409   
-     53000   5.181301             444  -0              0.83252205   
-     54000   5.2819523            444  -0              0.84823002   
-     55000   5.3895357            444  -0              0.86393798   
-     56000   5.5225568            444  -0              0.87964594   
-     57000   5.6473901            444  -0              0.89535391   
-     58000   5.7786123            444  -0              0.91106187   
-     59000   5.8932617            444  -0              0.92676983   
-     60000   6.004952             444  -0              0.9424778    
-     61000   6.1168028            444  -0              0.95818576   
-     62000   6.2274784            444  -0              0.97389372   
-     63000   6.341172             444  -0              0.98960169   
-     64000   6.4565154            444  -0              1.0053096    
-     65000   6.5684785            444  -0              1.0210176    
-     66000   6.6836542            444  -0              1.0367256    
-     67000   6.797745             444  -0              1.0524335    
-     68000   6.9091592            444  -0              1.0681415    
-     69000   7.0230958            444  -0              1.0838495    
-     70000   7.140508             444  -0              1.0995574    
-     71000   7.2547153            444  -0              1.1152654    
-     72000   7.3698096            444  -0              1.1309734    
-     73000   7.4846587            444  -0              1.1466813    
-     74000   7.6005538            444  -0              1.1623893    
-     75000   7.715498             444  -0              1.1780972    
-     76000   7.8306339            444  -0              1.1938052    
-     77000   7.9458861            444  -0              1.2095132    
-     78000   8.0608796            444  -0              1.2252211    
-     79000   8.1819612            444  -0              1.2409291    
-     80000   8.3017939            444  -0              1.2566371    
-     81000   8.4206794            444  -0              1.272345     
-     82000   8.5396045            444  -0              1.288053     
-     83000   8.6588178            444  -0              1.303761     
-     84000   8.7939815            444  -0              1.3194689    
-     85000   8.9999511            888  -0              1.3351769    
-     86000   9.2762515            888  -0              1.3508848    
-     87000   9.5497189            888  -0              1.3665928    
-     88000   9.8025426            888  -0              1.3823008    
-     89000   10.063005            888  -0              1.3980087    
-     90000   10.343956            888  -0              1.4137167    
-     91000   10.630004            888  -0              1.4294247    
-     92000   10.865437            888  -0              1.4451326    
-     93000   11.090302            888  -0              1.4608406    
-     94000   11.306921            888  -0              1.4765485    
-     95000   11.525442            888  -0              1.4922565    
-     96000   11.786482            888  -0              1.5079645    
-     97000   12.033336            888  -0              1.5236724    
-     98000   12.258224            888  -0              1.5393804    
-     99000   12.486583            888  -0              1.5550884    
-    100000   12.70566             888  -0              1.5707963    
-    101000   12.934051            888  -0              1.5865043    
-    102000   13.194977            888  -0              1.6022123    
-    103000   13.503561            888  -0              1.6179202    
-    104000   13.737785            888  -0              1.6336282    
-    105000   13.96388             888  -0              1.6493361    
-    106000   14.190156            888  -0              1.6650441    
-    107000   14.416346            888  -0              1.6807521    
-    108000   14.642321            888  -0              1.69646      
-    109000   14.877668            888  -0              1.712168     
-    110000   15.114644            888  -0              1.727876     
-    111000   15.354762            888  -0              1.7435839    
-    112000   15.615795            888  -0              1.7592919    
-    113000   15.854301            888  -0              1.7749998    
-    114000   16.099855            888  -0              1.7907078    
-    115000   16.344044            888  -0              1.8064158    
-    116000   16.60829             888  -0              1.8221237    
-    117000   16.847146            888  -0              1.8378317    
-    118000   17.086787            888  -0              1.8535397    
-    119000   17.324264            888  -0              1.8692476    
-    120000   17.563913            888  -0              1.8849556    
-    121000   17.798333            888  -0              1.9006636    
-    122000   18.033339            888  -0              1.9163715    
-    123000   18.275883            888  -0              1.9320795    
-    124000   18.542879            888  -0              1.9477874    
-    125000   18.790098            888  -0              1.9634954    
-    126000   19.034113            888  -0              1.9792034    
-    127000   19.286183            888  -0              1.9949113    
-    128000   19.574764            888  -0              2.0106193    
-    129000   19.832536            888  -0              2.0263273    
-    130000   20.085705            888  -0              2.0420352    
-    131000   20.327805            888  -0              2.0577432    
-    132000   20.576476            888  -0              2.0734512    
-    133000   20.82021             888  -0              2.0891591    
-    134000   21.063425            888  -0              2.1048671    
-    135000   21.304848            888  -0              2.120575     
-    136000   21.554936            888  -0              2.136283     
-    137000   21.797949            888  -0              2.151991     
-    138000   22.041181            888  -0              2.1676989    
-    139000   22.288509            888  -0              2.1834069    
-    140000   22.539512            888  -0              2.1991149    
-    141000   22.786046            888  -0              2.2148228    
-    142000   23.052553            888  -0              2.2305308    
-    143000   23.321282            888  -0              2.2462387    
-    144000   23.619171            888  -0              2.2619467    
-    145000   23.918581            888  -0              2.2776547    
-    146000   24.200849            888  -0              2.2933626    
-    147000   24.500127            888  -0              2.3090706    
-    148000   24.756357            888  -0              2.3247786    
-    149000   25.015262            888  -0              2.3404865    
-    150000   25.271136            888  -0              2.3561945    
-    151000   25.519846            888  -0              2.3719025    
-    152000   25.780481            888  -0              2.3876104    
-    153000   26.027917            888  -0              2.4033184    
-    154000   26.277021            888  -0              2.4190263    
-    155000   26.54158             888  -0              2.4347343    
-    156000   26.828357            888  -0              2.4504423    
-    157000   27.172993            888  -0              2.4661502    
-    158000   27.454171            888  -0              2.4818582    
-    159000   27.72964             888  -0              2.4975662    
-    160000   28.007464            888  -0              2.5132741    
-    161000   28.28268             888  -0              2.5289821    
-    162000   28.561094            888  -0              2.54469      
-    163000   28.839295            888  -0              2.560398     
-    164000   29.117588            888  -0              2.576106     
-    165000   29.394126            888  -0              2.5918139    
-    166000   29.675102            888  -0              2.6075219    
-    167000   29.951524            888  -0              2.6232299    
-    168000   30.233181            888  -0              2.6389378    
-    169000   30.516798            888  -0              2.6546458    
-    170000   30.818897           1000  -0              2.6703538    
-    171000   31.215403           1000  -0              2.6860617    
-    172000   31.528362           1000  -0              2.7017697    
-    173000   31.844759           1000  -0              2.7174776    
-    174000   32.159787           1000  -0              2.7331856    
-    175000   32.482605           1000  -0              2.7488936    
-    176000   32.798004           1000  -0              2.7646015    
-    177000   33.112668           1000  -0              2.7803095    
-    178000   33.429501           1000  -0              2.7960175    
-    179000   33.74646            1000  -0              2.8117254    
-    180000   34.059172           1000  -0              2.8274334    
-    181000   34.381226           1000  -0              2.8431414    
-    182000   34.697465           1000  -0              2.8588493    
-    183000   35.008892           1000  -0              2.8745573    
-    184000   35.332856           1000  -0              2.8902652    
-    185000   35.650733           1000  -0              2.9059732    
-    186000   35.971328           1000  -0              2.9216812    
-    187000   36.298046           1000  -0              2.9373891    
-    188000   36.622634           1000  -0              2.9530971    
-    189000   36.945728           1000  -0              2.9688051    
-    190000   37.268801           1000  -0              2.984513     
-    191000   37.592615           1000  -0              3.000221     
-    192000   37.915197           1000  -0              3.0159289    
-    193000   38.226138           1000  -0              3.0316369    
-    194000   38.534735           1000  -0              3.0473449    
-    195000   38.844711           1000  -0              3.0630528    
-    196000   39.159518           1000  -0              3.0787608    
-    197000   39.474235           1000  -0              3.0944688    
-    198000   39.786609           1000  -0              3.1101767    
-    199000   40.10213            1000  -0              3.1258847    
-    200000   40.421226           1000  -0              3.1415927    
-Loop time of 40.4213 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 20199.903 tau/day, 4947.886 timesteps/s, 4.948 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    | 3.6681     | 3.6681     | 3.6681     |   0.0 |  9.07
-Neigh   | 0.050194   | 0.050194   | 0.050194   |   0.0 |  0.12
-Comm    | 0.53308    | 0.53308    | 0.53308    |   0.0 |  1.32
-Output  | 0.0071363  | 0.0071363  | 0.0071363  |   0.0 |  0.02
-Modify  | 35.563     | 35.563     | 35.563     |   0.0 | 87.98
-Other   |            | 0.5999     |            |       |  1.48
-
-Nlocal:           1000 ave        1000 max        1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:            197 ave         197 max         197 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:           3812 ave        3812 max        3812 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3812
-Ave neighs/atom = 3.812
-Neighbor list builds = 205
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
-   Step          CPU          Atoms        KinEng        v_theta    
-    200000   0                   1000   1.0188213      3.1415927    
-    201000   0.31745969          1000   1.0237918      3.1573006    
-    202000   0.6315036           1000   1.0177231      3.1730086    
-    203000   0.9480314           1000   1.0127096      3.1887165    
-    204000   1.2572431           1000   1.0084386      3.2044245    
-    205000   1.5683429           1000   0.9957528      3.2201325    
-    206000   1.8801922           1000   1.0003921      3.2358404    
-    207000   2.1905883           1000   0.99358387     3.2515484    
-    208000   2.4948426           1000   0.99103748     3.2672564    
-    209000   2.8195665           1000   0.98488628     3.2829643    
-    210000   3.1420952           1000   0.98305824     3.2986723    
-    211000   3.4618849           1000   0.97185818     3.3143802    
-    212000   3.7910078           1000   0.96191966     3.3300882    
-    213000   4.1184009           1000   0.95953159     3.3457962    
-    214000   4.4491355           1000   0.95307268     3.3615041    
-    215000   4.7782398           1000   0.95612155     3.3772121    
-    216000   5.1088177           1000   0.96582166     3.3929201    
-    217000   5.4376503           1000   0.96124408     3.408628     
-    218000   5.7707229           1000   0.95705813     3.424336     
-    219000   6.1055922           1000   0.9660222      3.440044     
-    220000   6.4418056           1000   0.97539486     3.4557519    
-    221000   6.7755181           1000   0.97919396     3.4714599    
-    222000   7.104521            1000   0.97448171     3.4871678    
-    223000   7.4368025           1000   0.95742917     3.5028758    
-    224000   7.7623405           1000   0.94218245     3.5185838    
-    225000   8.0932682           1000   0.93056484     3.5342917    
-    226000   8.4217598           1000   0.92009109     3.5499997    
-    227000   8.747426            1000   0.90684871     3.5657077    
-    228000   9.0818038           1000   0.91719046     3.5814156    
-    229000   9.4125504           1000   0.92681746     3.5971236    
-    230000   9.7439963           1000   0.9195493      3.6128316    
-    231000   10.075499           1000   0.93275667     3.6285395    
-    232000   10.404017           1000   0.9494565      3.6442475    
-    233000   10.774786           1000   0.95036607     3.6599554    
-    234000   11.158713           1000   0.9596283      3.6756634    
-    235000   11.566878           1000   0.98314341     3.6913714    
-    236000   11.977294           1000   0.98115865     3.7070793    
-    237000   12.347191           1000   0.9723466      3.7227873    
-    238000   12.686388           1000   0.95267817     3.7384953    
-    239000   13.031631           1000   0.92661956     3.7542032    
-    240000   13.451121           1000   0.92237207     3.7699112    
-    241000   13.855031           1000   0.91301732     3.7856191    
-    242000   14.272001           1000   0.90488754     3.8013271    
-    243000   14.632631           1000   0.90430417     3.8170351    
-    244000   14.97608            1000   0.90179051     3.832743     
-    245000   15.419173           1000   0.89658897     3.848451     
-    246000   15.903699           1000   0.89583335     3.864159     
-    247000   16.312374           1000   0.89409138     3.8798669    
-    248000   16.660472           1000   0.89948364     3.8955749    
-    249000   17.063147           1000   0.90196936     3.9112829    
-    250000   17.423622           1000   0.89616943     3.9269908    
-    251000   17.76439            1000   0.87816303     3.9426988    
-    252000   18.103828           1000   0.86705341     3.9584067    
-    253000   18.454644           1000   0.84494344     3.9741147    
-    254000   18.876297           1000   0.81541663     3.9898227    
-    255000   19.264851           1000   0.80071805     4.0055306    
-    256000   19.669757           1000   0.80290754     4.0212386    
-    257000   20.066097           1000   0.80000385     4.0369466    
-    258000   20.481516           1000   0.80379277     4.0526545    
-    259000   20.851537           1000   0.81091684     4.0683625    
-    260000   21.246226           1000   0.80124855     4.0840704    
-    261000   21.586832           1000   0.79581606     4.0997784    
-    262000   21.968726           1000   0.78415946     4.1154864    
-    263000   22.388474           1000   0.78837276     4.1311943    
-    264000   22.76238            1000   0.78962435     4.1469023    
-    265000   23.13787            1000   0.79388706     4.1626103    
-    266000   23.470742           1000   0.80484385     4.1783182    
-    267000   23.801402           1000   0.79505699     4.1940262    
-    268000   24.14266            1000   0.78663829     4.2097342    
-    269000   24.545281           1000   0.77557297     4.2254421    
-    270000   24.886776           1000   0.76992342     4.2411501    
-    271000   25.218744           1000   0.75955867     4.256858     
-    272000   25.549898           1000   0.76207709     4.272566     
-    273000   25.882738           1000   0.76891185     4.288274     
-    274000   26.212384           1000   0.77380617     4.3039819    
-    275000   26.540612           1000   0.77349795     4.3196899    
-    276000   26.869636           1000   0.77559636     4.3353979    
-    277000   27.200449           1000   0.76806972     4.3511058    
-    278000   27.548549           1000   0.76223861     4.3668138    
-    279000   27.883681           1000   0.76306533     4.3825218    
-    280000   28.221552           1000   0.76369569     4.3982297    
-    281000   28.558479           1000   0.75945303     4.4139377    
-    282000   28.892758           1000   0.75872312     4.4296456    
-    283000   29.224927           1000   0.75354345     4.4453536    
-    284000   29.565477           1000   0.74433058     4.4610616    
-    285000   29.914679           1000   0.7349005      4.4767695    
-    286000   30.265305           1000   0.73182808     4.4924775    
-    287000   30.607982           1000   0.73334122     4.5081855    
-    288000   30.94168            1000   0.73308623     4.5238934    
-    289000   31.276062           1000   0.73620818     4.5396014    
-    290000   31.614934           1000   0.73906492     4.5553093    
-    291000   31.959782           1000   0.73921306     4.5710173    
-    292000   32.296279           1000   0.73919766     4.5867253    
-    293000   32.615262           1000   0.75148875     4.6024332    
-    294000   32.93925            1000   0.76390126     4.6181412    
-    295000   33.266316           1000   0.76421084     4.6338492    
-    296000   33.591115           1000   0.78124272     4.6495571    
-    297000   33.924279           1000   0.78526224     4.6652651    
-    298000   34.256265           1000   0.78279226     4.6809731    
-    299000   34.584382           1000   0.78390001     4.696681     
-    300000   34.910629           1000   0.78017239     4.712389     
-    301000   35.233205           1000   0.77432653     4.7280969    
-    302000   35.55956            1000   0.7627792      4.7438049    
-    303000   35.885484           1000   0.75222273     4.7595129    
-    304000   36.205453           1000   0.73765921     4.7752208    
-    305000   36.525101           1000   0.72338298     4.7909288    
-    306000   36.845236           1000   0.71944975     4.8066368    
-    307000   37.168044           1000   0.71547274     4.8223447    
-    308000   37.491196           1000   0.71267737     4.8380527    
-    309000   37.827079           1000   0.70506173     4.8537606    
-    310000   38.168049           1000   0.70685173     4.8694686    
-    311000   38.504282           1000   0.70327488     4.8851766    
-    312000   38.846152           1000   0.69732519     4.9008845    
-    313000   39.191958           1000   0.70137823     4.9165925    
-    314000   39.532177           1000   0.70613806     4.9323005    
-    315000   39.876728           1000   0.70981591     4.9480084    
-    316000   40.225244           1000   0.72246602     4.9637164    
-    317000   40.573681           1000   0.71946499     4.9794244    
-    318000   40.918134           1000   0.73275857     4.9951323    
-    319000   41.261914           1000   0.74357547     5.0108403    
-    320000   41.607984           1000   0.74138038     5.0265482    
-    321000   41.957822           1000   0.73285846     5.0422562    
-    322000   42.30176            1000   0.72990718     5.0579642    
-    323000   42.644077           1000   0.72024459     5.0736721    
-    324000   42.985509           1000   0.71052943     5.0893801    
-    325000   43.323921           1000   0.69560261     5.1050881    
-    326000   43.664945           1000   0.69939398     5.120796     
-    327000   44.004741           1000   0.71331291     5.136504     
-    328000   44.347204           1000   0.72181082     5.152212     
-    329000   44.689866           1000   0.72534262     5.1679199    
-    330000   45.055673           1000   0.73874292     5.1836279    
-    331000   45.400501           1000   0.74135464     5.1993358    
-    332000   45.743289           1000   0.73578005     5.2150438    
-    333000   46.087061           1000   0.72662516     5.2307518    
-    334000   46.427231           1000   0.72030125     5.2464597    
-    335000   46.767813           1000   0.72801784     5.2621677    
-    336000   47.108619           1000   0.73020974     5.2778757    
-    337000   47.44666            1000   0.7344527      5.2935836    
-    338000   47.784653           1000   0.73826638     5.3092916    
-    339000   48.124114           1000   0.74079395     5.3249995    
-    340000   48.463953           1000   0.74030413     5.3407075    
-    341000   48.804616           1000   0.74815855     5.3564155    
-    342000   49.143226           1000   0.75762011     5.3721234    
-    343000   49.482788           1000   0.76311094     5.3878314    
-    344000   49.822597           1000   0.76394459     5.4035394    
-    345000   50.162186           1000   0.75550163     5.4192473    
-    346000   50.496689           1000   0.7594991      5.4349553    
-    347000   50.831695           1000   0.76650932     5.4506633    
-    348000   51.167201           1000   0.76750437     5.4663712    
-    349000   51.501847           1000   0.77084248     5.4820792    
-    350000   51.841805           1000   0.76487701     5.4977871    
-    351000   52.179907           1000   0.76870148     5.5134951    
-    352000   52.517605           1000   0.77597853     5.5292031    
-    353000   52.850047           1000   0.77929348     5.544911     
-    354000   53.182408           1000   0.7744937      5.560619     
-    355000   53.512931           1000   0.76114616     5.576327     
-    356000   53.845782           1000   0.75392687     5.5920349    
-    357000   54.178336           1000   0.74858889     5.6077429    
-    358000   54.514517           1000   0.75630978     5.6234508    
-    359000   54.850783           1000   0.75781107     5.6391588    
-    360000   55.183323           1000   0.75613713     5.6548668    
-    361000   55.518704           1000   0.75250391     5.6705747    
-    362000   55.851425           1000   0.75790051     5.6862827    
-    363000   56.212376           1000   0.75283475     5.7019907    
-    364000   56.542027           1000   0.7431151      5.7176986    
-    365000   56.874325           1000   0.73274509     5.7334066    
-    366000   57.208926           1000   0.72261631     5.7491146    
-    367000   57.596495           1000   0.71279773     5.7648225    
-    368000   58.007863           1000   0.70452113     5.7805305    
-    369000   58.346944           1000   0.69777381     5.7962384    
-    370000   58.686215           1000   0.69698007     5.8119464    
-    371000   59.030366           1000   0.69322062     5.8276544    
-    372000   59.368607           1000   0.67728454     5.8433623    
-    373000   59.704376           1000   0.67335006     5.8590703    
-    374000   60.044772           1000   0.66920493     5.8747783    
-    375000   60.382875           1000   0.65614401     5.8904862    
-    376000   60.72002            1000   0.65874131     5.9061942    
-    377000   61.058554           1000   0.67072465     5.9219022    
-    378000   61.400078           1000   0.68118419     5.9376101    
-    379000   61.748931           1000   0.68481865     5.9533181    
-    380000   62.098203           1000   0.68840839     5.969026     
-    381000   62.444961           1000   0.69447162     5.984734     
-    382000   62.797286           1000   0.69881397     6.000442     
-    383000   63.154921           1000   0.69610171     6.0161499    
-    384000   63.508448           1000   0.70059329     6.0318579    
-    385000   63.857115           1000   0.71085103     6.0475659    
-    386000   64.207915           1000   0.71532684     6.0632738    
-    387000   64.561127           1000   0.72968624     6.0789818    
-    388000   64.939826           1000   0.74729894     6.0946897    
-    389000   65.284635           1000   0.76268063     6.1103977    
-    390000   65.631752           1000   0.77170089     6.1261057    
-    391000   65.981566           1000   0.77212462     6.1418136    
-    392000   66.328406           1000   0.773784       6.1575216    
-    393000   66.655905           1000   0.7731096      6.1732296    
-    394000   66.993751           1000   0.77245259     6.1889375    
-    395000   67.322842           1000   0.76912533     6.2046455    
-    396000   67.647532           1000   0.76397972     6.2203535    
-    397000   67.977448           1000   0.75736166     6.2360614    
-    398000   68.310064           1000   0.75287599     6.2517694    
-    399000   68.635966           1000   0.75354368     6.2674773    
-    400000   68.963492           1000   0.75582397     6.2831853    
-Loop time of 68.9635 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 11839.683 tau/day, 2900.084 timesteps/s, 2.900 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    | 11.238     | 11.238     | 11.238     |   0.0 | 16.30
-Neigh   | 0.077817   | 0.077817   | 0.077817   |   0.0 |  0.11
-Comm    | 1.5441     | 1.5441     | 1.5441     |   0.0 |  2.24
-Output  | 0.0082341  | 0.0082341  | 0.0082341  |   0.0 |  0.01
-Modify  | 55.304     | 55.304     | 55.304     |   0.0 | 80.19
-Other   |            | 0.7909     |            |       |  1.15
-
-Nlocal:           1000 ave        1000 max        1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:            278 ave         278 max         278 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:           5072 ave        5072 max        5072 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5072
-Ave neighs/atom = 5.072
-Neighbor list builds = 166
-Dangerous builds = 0
-Total wall time: 0:01:49

examples/granregion/log.16Mar23.granregion.mixer.g++.4

@@ -1,634 +0,0 @@
-LAMMPS (8 Feb 2023)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-  using 1 OpenMP thread(s) per MPI task
-variable	name string mixer
-
-thermo_modify	flush yes
-variable	seed equal 14314
-
-###############################################
-# Particle parameters
-################################################
-
-variable	rlo equal 0.3
-variable	rhi equal 0.6
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.3
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.6
-variable 	skin equal ${rhi}
-variable 	skin equal 0.6
-
-variable	coeffRes equal 0.1
-variable	coeffFric equal 0.5
-
-variable	kn equal 10^5
-variable	kt equal 0.2*${kn}
-variable	kt equal 0.2*100000
-
-variable	gravity equal 1.0
-variable	density equal 1.0
-
-variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
-variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
-variable	a equal (-2.0*log(${coeffRes})/PI)^2
-variable	a equal (-2.0*log(0.1)/PI)^2
-variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
-variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
-variable        gamma_t equal ${gamma_n}*0.5
-variable        gamma_t equal 806.699778405191*0.5
-
-variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
-variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
-
-variable	dt equal ${tcol}*0.02
-variable	dt equal 0.00236257621510454*0.02
-timestep	${dt}
-timestep	4.72515243020908e-05
-
-###############################################
-
-variable	dumpfreq equal 1000
-variable	logfreq equal 1000
-
-newton 		on
-atom_style	sphere
-
-boundary	p p f
-
-region		boxreg block 0 20 0 20 0 20
-create_box	1 boxreg
-Created orthogonal box = (0 0 0) to (20 20 20)
-  1 by 2 by 2 MPI processor grid
-
-pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
-pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
-pair_coeff	* *
-
-neighbor        ${skin} multi
-neighbor        0.6 multi
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Balancing ...
-Generated 0 of 0 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 = 0
-  ghost atom cutoff = 0
-  binsize = 20, bins = 1 1 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hertz/history, perpetual
-      attributes: half, newton on, size, history
-      pair build: half/size/multi/newton
-      stencil: half/multi/3d
-      bin: multi
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
-fix		bal all balance 10000 1.1 shift xyz 20 1.01
-
-####################### Options specific to pouring #########################
-
-region	     	insreg cylinder z 10 10 8 10 18 side in units box
-region	    	cylreg cylinder z 10 10 10 0 20 side in units box
-
-variable	theta equal (step/400000)*2*PI
-
-region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
-region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
-
-region		mixer intersect 3 cylreg b1 b2 side in
-
-fix		grav all gravity ${gravity} vector 0 0 -1
-fix		grav all gravity 1 vector 0 0 -1
-fix		1 all nve/sphere
-
-fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
-fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
-
-fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
-fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
-Particle insertion: 444 every 84653 steps, 1000 by step 169307
-
-#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
-
-#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
-#dump_modify	2 pad 6
-
-thermo_style	custom step cpu atoms ke v_theta
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
-thermo_modify	flush yes lost warn
-
-run		200000
-
-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}
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
-   Step          CPU          Atoms        KinEng        v_theta    
-         0   0                      0  -0              0            
-      1000   0.069039547          444  -0              0.015707963  
-      2000   0.12867095           444  -0              0.031415927  
-      3000   0.18791426           444  -0              0.04712389   
-      4000   0.24614388           444  -0              0.062831853  
-      5000   0.30404486           444  -0              0.078539816  
-      6000   0.36105446           444  -0              0.09424778   
-      7000   0.41713358           444  -0              0.10995574   
-      8000   0.47282802           444  -0              0.12566371   
-      9000   0.52742586           444  -0              0.14137167   
-     10000   0.58233488           444  -0              0.15707963   
-     11000   0.62155506           444  -0              0.1727876    
-     12000   0.6605457            444  -0              0.18849556   
-     13000   0.69971591           444  -0              0.20420352   
-     14000   0.73821845           444  -0              0.21991149   
-     15000   0.77860211           444  -0              0.23561945   
-     16000   0.8188072            444  -0              0.25132741   
-     17000   0.85992964           444  -0              0.26703538   
-     18000   0.9008443            444  -0              0.28274334   
-     19000   0.94216466           444  -0              0.2984513    
-     20000   0.98508697           444  -0              0.31415927   
-     21000   1.0241468            444  -0              0.32986723   
-     22000   1.0606191            444  -0              0.34557519   
-     23000   1.0972735            444  -0              0.36128316   
-     24000   1.134726             444  -0              0.37699112   
-     25000   1.1723693            444  -0              0.39269908   
-     26000   1.211349             444  -0              0.40840704   
-     27000   1.250291             444  -0              0.42411501   
-     28000   1.2906408            444  -0              0.43982297   
-     29000   1.3307315            444  -0              0.45553093   
-     30000   1.3704867            444  -0              0.4712389    
-     31000   1.4064392            444  -0              0.48694686   
-     32000   1.4426955            444  -0              0.50265482   
-     33000   1.4789666            444  -0              0.51836279   
-     34000   1.5163037            444  -0              0.53407075   
-     35000   1.5534135            444  -0              0.54977871   
-     36000   1.5907054            444  -0              0.56548668   
-     37000   1.6296055            444  -0              0.58119464   
-     38000   1.6690167            444  -0              0.5969026    
-     39000   1.7082024            444  -0              0.61261057   
-     40000   1.7476796            444  -0              0.62831853   
-     41000   1.7847465            444  -0              0.64402649   
-     42000   1.8216975            444  -0              0.65973446   
-     43000   1.8594424            444  -0              0.67544242   
-     44000   1.8975401            444  -0              0.69115038   
-     45000   1.9361216            444  -0              0.70685835   
-     46000   1.9764821            444  -0              0.72256631   
-     47000   2.0221252            444  -0              0.73827427   
-     48000   2.0635337            444  -0              0.75398224   
-     49000   2.104472             444  -0              0.7696902    
-     50000   2.1447842            444  -0              0.78539816   
-     51000   2.1808558            444  -0              0.80110613   
-     52000   2.2180542            444  -0              0.81681409   
-     53000   2.2547243            444  -0              0.83252205   
-     54000   2.2934546            444  -0              0.84823002   
-     55000   2.3321909            444  -0              0.86393798   
-     56000   2.3732179            444  -0              0.87964594   
-     57000   2.4141133            444  -0              0.89535391   
-     58000   2.455667             444  -0              0.91106187   
-     59000   2.4983196            444  -0              0.92676983   
-     60000   2.5415086            444  -0              0.9424778    
-     61000   2.581342             444  -0              0.95818576   
-     62000   2.6215029            444  -0              0.97389372   
-     63000   2.6633884            444  -0              0.98960169   
-     64000   2.7048848            444  -0              1.0053096    
-     65000   2.7497607            444  -0              1.0210176    
-     66000   2.7952373            444  -0              1.0367256    
-     67000   2.8399748            444  -0              1.0524335    
-     68000   2.8851806            444  -0              1.0681415    
-     69000   2.9303317            444  -0              1.0838495    
-     70000   2.9815632            444  -0              1.0995574    
-     71000   3.0257986            444  -0              1.1152654    
-     72000   3.068788             444  -0              1.1309734    
-     73000   3.1130125            444  -0              1.1466813    
-     74000   3.1558178            444  -0              1.1623893    
-     75000   3.1993327            444  -0              1.1780972    
-     76000   3.2444469            444  -0              1.1938052    
-     77000   3.2901781            444  -0              1.2095132    
-     78000   3.3356302            444  -0              1.2252211    
-     79000   3.3814834            444  -0              1.2409291    
-     80000   3.4290631            444  -0              1.2566371    
-     81000   3.4715671            444  -0              1.272345     
-     82000   3.5136342            444  -0              1.288053     
-     83000   3.5566281            444  -0              1.303761     
-     84000   3.6001405            444  -0              1.3194689    
-     85000   3.6709788            888  -0              1.3351769    
-     86000   3.7652387            888  -0              1.3508848    
-     87000   3.8618109            888  -0              1.3665928    
-     88000   3.9546406            888  -0              1.3823008    
-     89000   4.0475587            888  -0              1.3980087    
-     90000   4.1424919            888  -0              1.4137167    
-     91000   4.2114594            888  -0              1.4294247    
-     92000   4.2842588            888  -0              1.4451326    
-     93000   4.3524161            888  -0              1.4608406    
-     94000   4.4204131            888  -0              1.4765485    
-     95000   4.4886628            888  -0              1.4922565    
-     96000   4.5588224            888  -0              1.5079645    
-     97000   4.6304943            888  -0              1.5236724    
-     98000   4.7018695            888  -0              1.5393804    
-     99000   4.774147             888  -0              1.5550884    
-    100000   4.847776             888  -0              1.5707963    
-    101000   4.9173562            888  -0              1.5865043    
-    102000   4.9886499            888  -0              1.6022123    
-    103000   5.0618801            888  -0              1.6179202    
-    104000   5.1331411            888  -0              1.6336282    
-    105000   5.205209             888  -0              1.6493361    
-    106000   5.2795148            888  -0              1.6650441    
-    107000   5.3523346            888  -0              1.6807521    
-    108000   5.4263886            888  -0              1.69646      
-    109000   5.5029416            888  -0              1.712168     
-    110000   5.5807033            888  -0              1.727876     
-    111000   5.6574852            888  -0              1.7435839    
-    112000   5.7320356            888  -0              1.7592919    
-    113000   5.8097178            888  -0              1.7749998    
-    114000   5.8858974            888  -0              1.7907078    
-    115000   5.9636528            888  -0              1.8064158    
-    116000   6.0421783            888  -0              1.8221237    
-    117000   6.12052              888  -0              1.8378317    
-    118000   6.2016349            888  -0              1.8535397    
-    119000   6.2834058            888  -0              1.8692476    
-    120000   6.3644485            888  -0              1.8849556    
-    121000   6.4398727            888  -0              1.9006636    
-    122000   6.5152081            888  -0              1.9163715    
-    123000   6.5916482            888  -0              1.9320795    
-    124000   6.6694407            888  -0              1.9477874    
-    125000   6.7474201            888  -0              1.9634954    
-    126000   6.8270768            888  -0              1.9792034    
-    127000   6.9060885            888  -0              1.9949113    
-    128000   6.9847809            888  -0              2.0106193    
-    129000   7.0660497            888  -0              2.0263273    
-    130000   7.1468939            888  -0              2.0420352    
-    131000   7.2275386            888  -0              2.0577432    
-    132000   7.3103515            888  -0              2.0734512    
-    133000   7.3904073            888  -0              2.0891591    
-    134000   7.4711333            888  -0              2.1048671    
-    135000   7.5529594            888  -0              2.120575     
-    136000   7.6399017            888  -0              2.136283     
-    137000   7.7263891            888  -0              2.151991     
-    138000   7.815523             888  -0              2.1676989    
-    139000   7.9041642            888  -0              2.1834069    
-    140000   7.9950145            888  -0              2.1991149    
-    141000   8.0776291            888  -0              2.2148228    
-    142000   8.1584715            888  -0              2.2305308    
-    143000   8.2409653            888  -0              2.2462387    
-    144000   8.326064             888  -0              2.2619467    
-    145000   8.4107211            888  -0              2.2776547    
-    146000   8.4946153            888  -0              2.2933626    
-    147000   8.5784663            888  -0              2.3090706    
-    148000   8.6648861            888  -0              2.3247786    
-    149000   8.7503472            888  -0              2.3404865    
-    150000   8.8378801            888  -0              2.3561945    
-    151000   8.9221381            888  -0              2.3719025    
-    152000   9.0101516            888  -0              2.3876104    
-    153000   9.0982387            888  -0              2.4033184    
-    154000   9.1851912            888  -0              2.4190263    
-    155000   9.2744741            888  -0              2.4347343    
-    156000   9.3697509            888  -0              2.4504423    
-    157000   9.4640354            888  -0              2.4661502    
-    158000   9.5594845            888  -0              2.4818582    
-    159000   9.6572972            888  -0              2.4975662    
-    160000   9.7543656            888  -0              2.5132741    
-    161000   9.8485073            888  -0              2.5289821    
-    162000   9.9446493            888  -0              2.54469      
-    163000   10.040013            888  -0              2.560398     
-    164000   10.137116            888  -0              2.576106     
-    165000   10.23506             888  -0              2.5918139    
-    166000   10.335537            888  -0              2.6075219    
-    167000   10.436607            888  -0              2.6232299    
-    168000   10.537429            888  -0              2.6389378    
-    169000   10.642458            888  -0              2.6546458    
-    170000   10.74705            1000  -0              2.6703538    
-    171000   10.857156           1000  -0              2.6860617    
-    172000   10.965939           1000  -0              2.7017697    
-    173000   11.076233           1000  -0              2.7174776    
-    174000   11.184172           1000  -0              2.7331856    
-    175000   11.293846           1000  -0              2.7488936    
-    176000   11.402493           1000  -0              2.7646015    
-    177000   11.513895           1000  -0              2.7803095    
-    178000   11.625438           1000  -0              2.7960175    
-    179000   11.738308           1000  -0              2.8117254    
-    180000   11.854793           1000  -0              2.8274334    
-    181000   11.968344           1000  -0              2.8431414    
-    182000   12.082268           1000  -0              2.8588493    
-    183000   12.196356           1000  -0              2.8745573    
-    184000   12.313359           1000  -0              2.8902652    
-    185000   12.429559           1000  -0              2.9059732    
-    186000   12.545853           1000  -0              2.9216812    
-    187000   12.661447           1000  -0              2.9373891    
-    188000   12.777355           1000  -0              2.9530971    
-    189000   12.894856           1000  -0              2.9688051    
-    190000   13.0103             1000  -0              2.984513     
-    191000   13.126221           1000  -0              3.000221     
-    192000   13.241507           1000  -0              3.0159289    
-    193000   13.356198           1000  -0              3.0316369    
-    194000   13.468168           1000  -0              3.0473449    
-    195000   13.582232           1000  -0              3.0630528    
-    196000   13.700446           1000  -0              3.0787608    
-    197000   13.816948           1000  -0              3.0944688    
-    198000   13.934106           1000  -0              3.1101767    
-    199000   14.053497           1000  -0              3.1258847    
-    200000   14.171799           1000  -0              3.1415927    
-Loop time of 14.1719 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 57614.644 tau/day, 14112.479 timesteps/s, 14.112 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    | 0.46468    | 0.82686    | 1.2428     |  39.9 |  5.83
-Neigh   | 0.010644   | 0.013047   | 0.015567   |   2.0 |  0.09
-Comm    | 2.2447     | 2.716      | 3.2525     |  28.2 | 19.16
-Output  | 0.0040193  | 0.0057101  | 0.0084742  |   2.2 |  0.04
-Modify  | 7.9913     | 8.6193     | 9.394      |  20.9 | 60.82
-Other   |            | 1.991      |            |       | 14.05
-
-Nlocal:            250 ave         266 max         237 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Nghost:            294 ave         335 max         253 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:         960.25 ave        1454 max         492 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 3841
-Ave neighs/atom = 3.841
-Neighbor list builds = 201
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
-Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.89 | 11.9 Mbytes
-   Step          CPU          Atoms        KinEng        v_theta    
-    200000   0                   1000   1.0060272      3.1415927    
-    201000   0.11023112          1000   1.0117513      3.1573006    
-    202000   0.22297119          1000   1.0121624      3.1730086    
-    203000   0.33090251          1000   1.0099707      3.1887165    
-    204000   0.43921623          1000   1.0099624      3.2044245    
-    205000   0.54813391          1000   1.009398       3.2201325    
-    206000   0.6597641           1000   0.99686298     3.2358404    
-    207000   0.76806828          1000   0.96520673     3.2515484    
-    208000   0.88217705          1000   0.96521294     3.2672564    
-    209000   0.99810181          1000   0.96501099     3.2829643    
-    210000   1.1113988           1000   0.96426624     3.2986723    
-    211000   1.2252752           1000   0.9564358      3.3143802    
-    212000   1.3381064           1000   0.95482019     3.3300882    
-    213000   1.4513852           1000   0.9446233      3.3457962    
-    214000   1.5630713           1000   0.92461651     3.3615041    
-    215000   1.6785702           1000   0.92106646     3.3772121    
-    216000   1.7937182           1000   0.92058667     3.3929201    
-    217000   1.9092992           1000   0.91797493     3.408628     
-    218000   2.0251567           1000   0.91351081     3.424336     
-    219000   2.1419482           1000   0.91991749     3.440044     
-    220000   2.258391            1000   0.92943198     3.4557519    
-    221000   2.3747328           1000   0.93176684     3.4714599    
-    222000   2.4930355           1000   0.92625008     3.4871678    
-    223000   2.6111794           1000   0.9216243      3.5028758    
-    224000   2.729971            1000   0.92332955     3.5185838    
-    225000   2.8489286           1000   0.91963985     3.5342917    
-    226000   2.97003             1000   0.91913679     3.5499997    
-    227000   3.0874646           1000   0.92381436     3.5657077    
-    228000   3.2089543           1000   0.93085242     3.5814156    
-    229000   3.3281962           1000   0.92872221     3.5971236    
-    230000   3.4476271           1000   0.92536664     3.6128316    
-    231000   3.5681706           1000   0.92953138     3.6285395    
-    232000   3.6911427           1000   0.93937257     3.6442475    
-    233000   3.8115833           1000   0.95916002     3.6599554    
-    234000   3.9301977           1000   0.96652709     3.6756634    
-    235000   4.0481963           1000   0.96753364     3.6913714    
-    236000   4.1684171           1000   0.96096249     3.7070793    
-    237000   4.2874672           1000   0.97028893     3.7227873    
-    238000   4.4072896           1000   0.95323014     3.7384953    
-    239000   4.5292898           1000   0.94143454     3.7542032    
-    240000   4.6529563           1000   0.9334569      3.7699112    
-    241000   4.7701737           1000   0.93340822     3.7856191    
-    242000   4.8891772           1000   0.93517762     3.8013271    
-    243000   5.0078759           1000   0.92632745     3.8170351    
-    244000   5.1260291           1000   0.91858996     3.832743     
-    245000   5.2472736           1000   0.90006015     3.848451     
-    246000   5.363907            1000   0.8850116      3.864159     
-    247000   5.4838317           1000   0.87807775     3.8798669    
-    248000   5.6039445           1000   0.85981326     3.8955749    
-    249000   5.7262584           1000   0.85764597     3.9112829    
-    250000   5.8488174           1000   0.86748856     3.9269908    
-    251000   5.9665578           1000   0.85889952     3.9426988    
-    252000   6.084021            1000   0.84476495     3.9584067    
-    253000   6.203987            1000   0.84094974     3.9741147    
-    254000   6.3221073           1000   0.82638568     3.9898227    
-    255000   6.441682            1000   0.81449512     4.0055306    
-    256000   6.5625653           1000   0.80130582     4.0212386    
-    257000   6.6860772           1000   0.79100139     4.0369466    
-    258000   6.8117355           1000   0.78531082     4.0526545    
-    259000   6.9379959           1000   0.7678277      4.0683625    
-    260000   7.0606907           1000   0.74798797     4.0840704    
-    261000   7.1846943           1000   0.73902576     4.0997784    
-    262000   7.3084818           1000   0.73326104     4.1154864    
-    263000   7.4304296           1000   0.7370234      4.1311943    
-    264000   7.5536012           1000   0.73817854     4.1469023    
-    265000   7.6792395           1000   0.74675482     4.1626103    
-    266000   7.8061753           1000   0.7480056      4.1783182    
-    267000   7.9331093           1000   0.748671       4.1940262    
-    268000   8.0593048           1000   0.74430146     4.2097342    
-    269000   8.1888555           1000   0.73246199     4.2254421    
-    270000   8.3184687           1000   0.71666285     4.2411501    
-    271000   8.4489277           1000   0.69699332     4.256858     
-    272000   8.5822473           1000   0.69724726     4.272566     
-    273000   8.7148666           1000   0.69752702     4.288274     
-    274000   8.8426159           1000   0.69393439     4.3039819    
-    275000   8.9746848           1000   0.67961922     4.3196899    
-    276000   9.1020134           1000   0.67808365     4.3353979    
-    277000   9.232486            1000   0.66241302     4.3511058    
-    278000   9.3607588           1000   0.65559661     4.3668138    
-    279000   9.4879578           1000   0.64949975     4.3825218    
-    280000   9.6142148           1000   0.65351945     4.3982297    
-    281000   9.7437802           1000   0.66566267     4.4139377    
-    282000   9.87097             1000   0.68284419     4.4296456    
-    283000   9.9975944           1000   0.68906456     4.4453536    
-    284000   10.124724           1000   0.69474503     4.4610616    
-    285000   10.25369            1000   0.71686298     4.4767695    
-    286000   10.38212            1000   0.70966561     4.4924775    
-    287000   10.513274           1000   0.70173402     4.5081855    
-    288000   10.641359           1000   0.69841037     4.5238934    
-    289000   10.765608           1000   0.68947449     4.5396014    
-    290000   10.893738           1000   0.68391661     4.5553093    
-    291000   11.018982           1000   0.69112115     4.5710173    
-    292000   11.146639           1000   0.70208247     4.5867253    
-    293000   11.269392           1000   0.70044553     4.6024332    
-    294000   11.39243            1000   0.69973655     4.6181412    
-    295000   11.517741           1000   0.70719661     4.6338492    
-    296000   11.643013           1000   0.69961909     4.6495571    
-    297000   11.771064           1000   0.7038606      4.6652651    
-    298000   11.899855           1000   0.70651383     4.6809731    
-    299000   12.024499           1000   0.72028817     4.696681     
-    300000   12.151124           1000   0.72141372     4.712389     
-    301000   12.278902           1000   0.73011344     4.7280969    
-    302000   12.402615           1000   0.74750506     4.7438049    
-    303000   12.524021           1000   0.74362139     4.7595129    
-    304000   12.645914           1000   0.73643471     4.7752208    
-    305000   12.766721           1000   0.73250587     4.7909288    
-    306000   12.945373           1000   0.72450933     4.8066368    
-    307000   13.084062           1000   0.71650682     4.8223447    
-    308000   13.210593           1000   0.71012044     4.8380527    
-    309000   13.339536           1000   0.7045498      4.8537606    
-    310000   13.477512           1000   0.69904261     4.8694686    
-    311000   13.617832           1000   0.69370407     4.8851766    
-    312000   13.802532           1000   0.70012261     4.9008845    
-    313000   13.9682             1000   0.69796658     4.9165925    
-    314000   14.139079           1000   0.70673901     4.9323005    
-    315000   14.290205           1000   0.70285296     4.9480084    
-    316000   14.414474           1000   0.69917788     4.9637164    
-    317000   14.541743           1000   0.69153454     4.9794244    
-    318000   14.672817           1000   0.69630312     4.9951323    
-    319000   14.800594           1000   0.70732059     5.0108403    
-    320000   14.982014           1000   0.71069744     5.0265482    
-    321000   15.126459           1000   0.70982909     5.0422562    
-    322000   15.264165           1000   0.70514067     5.0579642    
-    323000   15.391036           1000   0.70591206     5.0736721    
-    324000   15.518096           1000   0.70992653     5.0893801    
-    325000   15.644416           1000   0.70605327     5.1050881    
-    326000   15.772686           1000   0.70492617     5.120796     
-    327000   15.899812           1000   0.69711977     5.136504     
-    328000   16.050906           1000   0.68791974     5.152212     
-    329000   16.197987           1000   0.68350425     5.1679199    
-    330000   16.346901           1000   0.67886559     5.1836279    
-    331000   16.511885           1000   0.6838106      5.1993358    
-    332000   16.666556           1000   0.68570448     5.2150438    
-    333000   16.820557           1000   0.68347768     5.2307518    
-    334000   16.972048           1000   0.67352858     5.2464597    
-    335000   17.171176           1000   0.67154375     5.2621677    
-    336000   17.380218           1000   0.67050288     5.2778757    
-    337000   17.561848           1000   0.66093797     5.2935836    
-    338000   17.746525           1000   0.65261747     5.3092916    
-    339000   17.926411           1000   0.65084314     5.3249995    
-    340000   18.105197           1000   0.65003008     5.3407075    
-    341000   18.235972           1000   0.65397536     5.3564155    
-    342000   18.389741           1000   0.67129271     5.3721234    
-    343000   18.604032           1000   0.68934086     5.3878314    
-    344000   18.788879           1000   0.71225704     5.4035394    
-    345000   18.935273           1000   0.72645711     5.4192473    
-    346000   19.136926           1000   0.73153889     5.4349553    
-    347000   19.310095           1000   0.74047453     5.4506633    
-    348000   19.476545           1000   0.74508084     5.4663712    
-    349000   19.599138           1000   0.74030176     5.4820792    
-    350000   19.753114           1000   0.72037009     5.4977871    
-    351000   19.893497           1000   0.71009934     5.5134951    
-    352000   20.020982           1000   0.69475509     5.5292031    
-    353000   20.149857           1000   0.68883962     5.544911     
-    354000   20.278476           1000   0.68764856     5.560619     
-    355000   20.407747           1000   0.6853423      5.576327     
-    356000   20.53591            1000   0.69528948     5.5920349    
-    357000   20.668654           1000   0.70787069     5.6077429    
-    358000   20.802835           1000   0.70110924     5.6234508    
-    359000   20.950394           1000   0.69356484     5.6391588    
-    360000   21.076061           1000   0.69727901     5.6548668    
-    361000   21.224785           1000   0.69878093     5.6705747    
-    362000   21.416947           1000   0.70063124     5.6862827    
-    363000   21.632619           1000   0.68842038     5.7019907    
-    364000   21.836231           1000   0.68478573     5.7176986    
-    365000   21.963636           1000   0.68232032     5.7334066    
-    366000   22.092926           1000   0.66971225     5.7491146    
-    367000   22.219251           1000   0.67006227     5.7648225    
-    368000   22.344723           1000   0.6694355      5.7805305    
-    369000   22.470654           1000   0.66622377     5.7962384    
-    370000   22.59941            1000   0.66501888     5.8119464    
-    371000   22.732869           1000   0.66108622     5.8276544    
-    372000   22.859824           1000   0.65989005     5.8433623    
-    373000   22.989282           1000   0.65277032     5.8590703    
-    374000   23.116089           1000   0.64599939     5.8747783    
-    375000   23.243733           1000   0.64279675     5.8904862    
-    376000   23.371971           1000   0.64321129     5.9061942    
-    377000   23.505382           1000   0.65596736     5.9219022    
-    378000   23.638755           1000   0.68055295     5.9376101    
-    379000   23.770714           1000   0.71147476     5.9533181    
-    380000   23.906376           1000   0.7478441      5.969026     
-    381000   24.040685           1000   0.76216879     5.984734     
-    382000   24.173446           1000   0.78574658     6.000442     
-    383000   24.30114            1000   0.80947952     6.0161499    
-    384000   24.426872           1000   0.81514681     6.0318579    
-    385000   24.555905           1000   0.81469775     6.0475659    
-    386000   24.684891           1000   0.80579609     6.0632738    
-    387000   24.811946           1000   0.79952446     6.0789818    
-    388000   24.940028           1000   0.78668384     6.0946897    
-    389000   25.061479           1000   0.78375511     6.1103977    
-    390000   25.18315            1000   0.78124583     6.1261057    
-    391000   25.303012           1000   0.77072038     6.1418136    
-    392000   25.423275           1000   0.75748297     6.1575216    
-    393000   25.542996           1000   0.74703682     6.1732296    
-    394000   25.661826           1000   0.74135384     6.1889375    
-    395000   25.782254           1000   0.73344196     6.2046455    
-    396000   25.903156           1000   0.72305463     6.2203535    
-    397000   26.026207           1000   0.71221263     6.2360614    
-    398000   26.145498           1000   0.70602241     6.2517694    
-    399000   26.266146           1000   0.69822375     6.2674773    
-    400000   26.387762           1000   0.69567985     6.2831853    
-Loop time of 26.3878 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 30942.580 tau/day, 7579.263 timesteps/s, 7.579 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    | 1.6871     | 2.8172     | 3.925      |  64.8 | 10.68
-Neigh   | 0.017325   | 0.021917   | 0.026669   |   3.1 |  0.08
-Comm    | 4.7404     | 6.0917     | 7.4409     |  54.5 | 23.09
-Output  | 0.0043138  | 0.0065642  | 0.0087622  |   1.9 |  0.02
-Modify  | 13.258     | 14.716     | 16.132     |  35.6 | 55.77
-Other   |            | 2.735      |            |       | 10.36
-
-Nlocal:            250 ave         257 max         241 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:          387.5 ave         477 max         299 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:         1233.5 ave        1523 max         917 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 4934
-Ave neighs/atom = 4.934
-Neighbor list builds = 168
-Dangerous builds = 0
-Total wall time: 0:00:40

examples/granregion/log.27Jun24.granregion.box.g++.1

@@ -0,0 +1,482 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+# pouring spheres into container box
+
+units		lj
+atom_style      sphere
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -10 10 -10 10 -10 10 units box
+create_box      2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* * gran/hooke
+
+region          container block -6 6 -6 6 -6 6 units box
+fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic/dof yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic/dof yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic/dof yes
+
+#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify	2 pad 5
+
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 48 every 566 steps, 100 by step 1133
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+       100          30   0.803783       0.803783       0.39507978     0.0029137134 
+       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
+       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
+       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
+       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
+       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
+       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
+       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
+      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
+      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
+      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
+      1400          99   0.35615284     0.35615284     0.19785725     0.0046170772 
+      1500          99   0.31486693     0.31486693     0.17429055     0.0064903432 
+      1600          99   0.26369001     0.26369001     0.15095266     0.0045226847 
+      1700         100   0.1925923      0.1925923      0.11308104     0.007362313  
+      1800         100   0.13724978     0.13724978     0.083276845    0.0058136373 
+      1900         100   0.077212636    0.077212636    0.053159386    0.0016509598 
+      2000         100   0.065294031    0.065294031    0.04372752     0.0020346467 
+      2100         100   0.057431398    0.057431398    0.037977068    0.0012681098 
+      2200         100   0.059093045    0.059093045    0.037435193    0.00096610799
+      2300         100   0.03422338     0.03422338     0.025491304    0.00069886052
+      2400         100   0.020558284    0.020558284    0.016163009    0.0017260663 
+      2500         100   0.015339709    0.015339709    0.012329236    0.00041308031
+      2600         100   0.012891354    0.012891354    0.009766054    0.00030356722
+      2700         100   0.0092634449   0.0092634449   0.0073580108   0.00077723051
+      2800         100   0.0073925841   0.0073925841   0.0059932218   0.00016466767
+      2900         100   0.0081228267   0.0081228267   0.006281761    0.00013828388
+      3000         100   0.0041833223   0.0041833223   0.0035147096   0.00013160599
+      3100         100   0.0035930775   0.0035930775   0.0030039922   0.00060639771
+      3200         100   0.0030824465   0.0030824465   0.0026541293   0.00047391014
+      3300         100   0.0035087522   0.0035087522   0.0027664508   0.00014080317
+      3400         100   0.0018537868   0.0018537868   0.0017099705   6.3326674e-05
+      3500         100   0.0015371228   0.0015371228   0.0014155433   0.00021612522
+      3600         100   0.001708556    0.001708556    0.0014369892   8.1034202e-05
+      3700         100   0.00095948652  0.00095948652  0.0009788528   3.4694023e-05
+      3800         100   0.00091875668  0.00091875668  0.00086805146  3.9373686e-05
+      3900         100   0.001557068    0.001557068    0.001159526    2.5178607e-05
+      4000         100   0.00062012451  0.00062012451  0.00066806922  5.6680551e-06
+      4100         100   0.00060940771  0.00060940771  0.00065614741  1.0137901e-05
+      4200         100   0.00059538437  0.00059538437  0.00064501521  7.3679744e-06
+      4300         100   0.00052946048  0.00052946048  0.00059353641  5.9225081e-06
+      4400         100   0.00051202281  0.00051202281  0.00057524772  3.6198435e-05
+      4500         100   0.00049986632  0.00049986632  0.00055754521  2.2275519e-05
+      4600         100   0.00048187334  0.00048187334  0.00053988815  2.2015243e-05
+      4700         100   0.00045261491  0.00045261491  0.00050298355  8.9681339e-05
+      4800         100   0.00034965427  0.00034965427  0.0004278781   1.0983535e-05
+      4900         100   0.00033555621  0.00033555621  0.00041435167  2.9266598e-05
+      5000         100   0.00031387148  0.00031387148  0.00039605781  2.5628425e-05
+Loop time of 0.0497806 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 43390431.056 tau/day, 100440.813 timesteps/s, 10.044 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0052991  | 0.0052991  | 0.0052991  |   0.0 | 10.64
+Neigh   | 0.008529   | 0.008529   | 0.008529   |   0.0 | 17.13
+Comm    | 0.00050137 | 0.00050137 | 0.00050137 |   0.0 |  1.01
+Output  | 0.00028923 | 0.00028923 | 0.00028923 |   0.0 |  0.58
+Modify  | 0.033612   | 0.033612   | 0.033612   |   0.0 | 67.52
+Other   |            | 0.00155    |            |       |  3.11
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            164 ave         164 max         164 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 164
+Ave neighs/atom = 1.64
+Neighbor list builds = 281
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-5000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Region properties for region container changed between runs, resetting its motion (../fix_wall_gran_region.cpp:96)
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00031387148  0.00031387148  0.00039605781  2.6174978e-05
+      5100         100   0.54537023     0.54537023     0.30042175     0.0087427352 
+      5200         100   0.57210852     0.57210852     0.3192468      0.0098134067 
+      5300         100   0.7168108      0.7168108      0.38577893     0.011004584  
+      5400         100   0.78895524     0.78895524     0.41889428     0.013555713  
+      5500         100   0.87797874     0.87797874     0.45689223     0.01565356   
+      5600         100   0.95424379     0.95424379     0.48830429     0.014707858  
+      5700         100   1.0046012      1.0046012      0.51054927     0.01469179   
+      5800         100   1.0371453      1.0371453      0.5262568      0.015576788  
+      5900         100   1.0545743      1.0545743      0.5361173      0.01589889   
+      6000         100   1.0932949      1.0932949      0.55402214     0.017484573  
+      6100         100   1.1148364      1.1148364      0.56241126     0.01721788   
+      6200         100   1.1315267      1.1315267      0.57050887     0.017961246  
+      6300         100   1.1506124      1.1506124      0.58009471     0.017159062  
+      6400         100   1.1663328      1.1663328      0.5876586      0.017935311  
+      6500         100   1.1821086      1.1821086      0.59595161     0.018005315  
+      6600         100   1.2039397      1.2039397      0.60567524     0.021604662  
+      6700         100   1.2269912      1.2269912      0.61770225     0.018907995  
+      6800         100   1.2447035      1.2447035      0.6257652      0.020537656  
+      6900         100   1.2625323      1.2625323      0.63486698     0.020106131  
+      7000         100   1.2617127      1.2617127      0.63318163     0.019670429  
+      7100         100   1.260715       1.260715       0.63311254     0.01981063   
+      7200         100   1.2790404      1.2790404      0.64079        0.02021891   
+      7300         100   1.2760228      1.2760228      0.6395331      0.021749943  
+      7400         100   1.2799657      1.2799657      0.64139079     0.020472918  
+      7500         100   1.2846472      1.2846472      0.64343078     0.02061003   
+      7600         100   1.2883963      1.2883963      0.64491863     0.020748893  
+      7700         100   1.2926891      1.2926891      0.6468454      0.02059959   
+      7800         100   1.3033563      1.3033563      0.65126208     0.021822102  
+      7900         100   1.3025795      1.3025795      0.65069464     0.021213858  
+      8000         100   1.3052548      1.3052548      0.65209881     0.021398728  
+      8100         100   1.3069801      1.3069801      0.6530457      0.021245966  
+      8200         100   1.3092011      1.3092011      0.65438349     0.02122166   
+      8300         100   1.3101277      1.3101277      0.65518546     0.021329292  
+      8400         100   1.3117013      1.3117013      0.65550345     0.021460379  
+      8500         100   1.3144455      1.3144455      0.65685825     0.021604641  
+      8600         100   1.3164134      1.3164134      0.65789495     0.021563159  
+      8700         100   1.3186879      1.3186879      0.6591421      0.021754259  
+      8800         100   1.3216911      1.3216911      0.66041154     0.022161545  
+      8900         100   1.3207611      1.3207611      0.65988391     0.021812278  
+      9000         100   1.3213163      1.3213163      0.66021107     0.021890934  
+      9100         100   1.3224957      1.3224957      0.66088572     0.021825725  
+      9200         100   1.3240758      1.3240758      0.66183609     0.021785081  
+      9300         100   1.3254189      1.3254189      0.66280087     0.021665121  
+      9400         100   1.3325923      1.3325923      0.66627599     0.021935299  
+      9500         100   1.3403779      1.3403779      0.66969078     0.022258389  
+      9600         100   1.3360821      1.3360821      0.66729084     0.022125375  
+      9700         100   1.3364048      1.3364048      0.66733374     0.022084635  
+      9800         100   1.3348391      1.3348391      0.66653654     0.021957941  
+      9900         100   1.3340902      1.3340902      0.66619851     0.022132442  
+     10000         100   1.3341233      1.3341233      0.66625291     0.02242346   
+Loop time of 0.170031 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 12703591.746 tau/day, 29406.462 timesteps/s, 2.941 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.02428    | 0.02428    | 0.02428    |   0.0 | 14.28
+Neigh   | 0.02016    | 0.02016    | 0.02016    |   0.0 | 11.86
+Comm    | 0.00063308 | 0.00063308 | 0.00063308 |   0.0 |  0.37
+Output  | 0.00026926 | 0.00026926 | 0.00026926 |   0.0 |  0.16
+Modify  | 0.12295    | 0.12295    | 0.12295    |   0.0 | 72.31
+Other   |            | 0.001744   |            |       |  1.03
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            186 ave         186 max         186 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 186
+Ave neighs/atom = 1.86
+Neighbor list builds = 626
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   1.3341233      1.3341233      0.66625291     0.022389629  
+     10100         100   0.29934208     0.29934208     0.17559716     0.0080511663 
+     10200         100   0.15937333     0.15937333     0.10361049     0.0052770441 
+     10300         100   0.083457844    0.083457844    0.067443759    0.0019700613 
+     10400         100   0.065692832    0.065692832    0.055653291    0.0018339668 
+     10500         100   0.052804438    0.052804438    0.045281034    0.0016027455 
+     10600         100   0.04328663     0.04328663     0.037333736    0.0010520803 
+     10700         100   0.034758594    0.034758594    0.030913039    0.00098209982
+     10800         100   0.031059386    0.031059386    0.027743119    0.00043771073
+     10900         100   0.025257043    0.025257043    0.023417455    0.00057319686
+     11000         100   0.020661736    0.020661736    0.019736355    0.00027957807
+     11100         100   0.017347891    0.017347891    0.017523904    0.00033806442
+     11200         100   0.013838843    0.013838843    0.013891648    0.0004814668 
+     11300         100   0.010848849    0.010848849    0.011429994    0.00017218727
+     11400         100   0.0087243303   0.0087243303   0.0089442702   0.00075858277
+     11500         100   0.0073404505   0.0073404505   0.0074359014   0.00016419055
+     11600         100   0.005593778    0.005593778    0.0059169171   0.00067508582
+     11700         100   0.0051164194   0.0051164194   0.0053270943   8.4490639e-05
+     11800         100   0.00441161     0.00441161     0.0046984183   8.1750645e-05
+     11900         100   0.0040823871   0.0040823871   0.0044273607   0.00057274663
+     12000         100   0.0036457853   0.0036457853   0.0041171254   6.4466313e-05
+     12100         100   0.0034927566   0.0034927566   0.0039732335   0.00010435211
+     12200         100   0.0034030997   0.0034030997   0.0038913895   7.5846038e-05
+     12300         100   0.0032970662   0.0032970662   0.0036879396   8.4270392e-05
+     12400         100   0.0031107627   0.0031107627   0.0034222463   0.00010403492
+     12500         100   0.0029402407   0.0029402407   0.0033029532   3.6385479e-05
+     12600         100   0.0027926657   0.0027926657   0.0031897566   4.143403e-05 
+     12700         100   0.0026584426   0.0026584426   0.0030863436   0.00017608636
+     12800         100   0.0020593472   0.0020593472   0.0024174548   2.5484422e-05
+     12900         100   0.0019445876   0.0019445876   0.0023331214   1.3291393e-05
+     13000         100   0.0019356798   0.0019356798   0.0023208275   3.7775631e-05
+     13100         100   0.001917674    0.001917674    0.0023067328   2.3731216e-05
+     13200         100   0.0018402122   0.0018402122   0.0022290175   2.3227838e-05
+     13300         100   0.0017947406   0.0017947406   0.0021839926   5.68555e-05  
+     13400         100   0.0016930751   0.0016930751   0.0020981569   3.762312e-05 
+     13500         100   0.0016591044   0.0016591044   0.0020636607   2.0531417e-05
+     13600         100   0.0015170608   0.0015170608   0.0019236349   2.87871e-05  
+     13700         100   0.0014040099   0.0014040099   0.0017412115   3.7091497e-05
+     13800         100   0.0013892837   0.0013892837   0.0017134626   1.7192386e-05
+     13900         100   0.0013189709   0.0013189709   0.0016364794   0.00022920131
+     14000         100   0.0012610766   0.0012610766   0.0015926858   1.5605822e-05
+     14100         100   0.0010746324   0.0010746324   0.0014018754   1.8598362e-05
+     14200         100   0.0010259837   0.0010259837   0.0013546872   1.7918726e-05
+     14300         100   0.0008919653   0.0008919653   0.0011534101   0.00015490093
+     14400         100   0.00087001531  0.00087001531  0.0011016258   1.0766439e-05
+     14500         100   0.00083846397  0.00083846397  0.0010767041   1.0375992e-05
+     14600         100   0.0008155908   0.0008155908   0.00105642     1.2582086e-05
+     14700         100   0.00080868405  0.00080868405  0.00104978     7.027334e-05 
+     14800         100   0.00073613153  0.00073613153  0.00098179118  3.236684e-05 
+     14900         100   0.00071371931  0.00071371931  0.00095309072  8.6245124e-06
+     15000         100   0.00070031746  0.00070031746  0.0009423403   2.4693888e-05
+Loop time of 0.0531531 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 40637346.357 tau/day, 94067.931 timesteps/s, 9.407 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0049693  | 0.0049693  | 0.0049693  |   0.0 |  9.35
+Neigh   | 0.0033529  | 0.0033529  | 0.0033529  |   0.0 |  6.31
+Comm    | 0.00045859 | 0.00045859 | 0.00045859 |   0.0 |  0.86
+Output  | 0.00031163 | 0.00031163 | 0.00031163 |   0.0 |  0.59
+Modify  | 0.042417   | 0.042417   | 0.042417   |   0.0 | 79.80
+Other   |            | 0.001644   |            |       |  3.09
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            157 ave         157 max         157 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 157
+Ave neighs/atom = 1.57
+Neighbor list builds = 101
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-15000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00070031746  0.00070031746  0.0009423403   2.4820402e-05
+     15100         100   1.0378931      1.0378931      0.67940294     0.014665698  
+     15200         100   1.0517533      1.0517533      0.69115597     0.01309217   
+     15300         100   1.1062671      1.1062671      0.73515555     0.015692859  
+     15400         100   1.385963       1.385963       0.89710836     0.022187064  
+     15500         100   1.5008849      1.5008849      0.94689573     0.030001316  
+     15600         100   1.6919387      1.6919387      1.0471028      0.026806301  
+     15700         100   1.8311512      1.8311512      1.1071134      0.024492529  
+     15800         100   1.8517819      1.8517819      1.1216762      0.028629961  
+     15900         100   1.8895616      1.8895616      1.1177621      0.028934483  
+     16000         100   2.0691195      2.0691195      1.1848851      0.032794489  
+     16100         100   2.2520282      2.2520282      1.26292        0.030167679  
+     16200         100   2.2879859      2.2879859      1.2866695      0.02974115   
+     16300         100   2.3679798      2.3679798      1.3150501      0.032771704  
+     16400         100   2.3846251      2.3846251      1.3122933      0.029948284  
+     16500         100   2.528765       2.528765       1.3886857      0.032511301  
+     16600         100   2.5465734      2.5465734      1.4009546      0.033614459  
+     16700         100   2.6883939      2.6883939      1.457327       0.039494183  
+     16800         100   2.8655546      2.8655546      1.5468292      0.036099395  
+     16900         100   2.8919695      2.8919695      1.5768619      0.037384016  
+     17000         100   3.0433407      3.0433407      1.6445056      0.037344364  
+     17100         100   3.2283804      3.2283804      1.7335616      0.041395151  
+     17200         100   3.3098823      3.3098823      1.7794605      0.04616548   
+     17300         100   3.3890828      3.3890828      1.8289994      0.050512368  
+     17400         100   3.278912       3.278912       1.7770308      0.04270684   
+     17500         100   3.3373113      3.3373113      1.7927421      0.056764855  
+     17600         100   3.3264731      3.3264731      1.8066541      0.045863538  
+     17700         100   3.0707481      3.0707481      1.6881602      0.047285321  
+     17800         100   3.0911023      3.0911023      1.7142589      0.040005715  
+     17900         100   3.1368         3.1368         1.7314207      0.043475979  
+     18000         100   3.1705064      3.1705064      1.7503598      0.042272578  
+     18100         100   3.2348301      3.2348301      1.7599183      0.042974559  
+     18200         100   3.4676237      3.4676237      1.8675014      0.051937094  
+     18300         100   3.460493       3.460493       1.8710624      0.04615202   
+     18400         100   3.4132328      3.4132328      1.8379148      0.048316249  
+     18500         100   3.6046         3.6046         1.936101       0.046093227  
+     18600         100   3.6898847      3.6898847      1.985425       0.048623681  
+     18700         100   3.8073645      3.8073645      2.0517694      0.051139644  
+     18800         100   3.9453683      3.9453683      2.121645       0.053091211  
+     18900         100   3.891796       3.891796       2.1038949      0.047975378  
+     19000         100   3.9805517      3.9805517      2.143216       0.052740909  
+     19100         100   3.8032187      3.8032187      2.0535533      0.060896481  
+     19200         100   3.8956813      3.8956813      2.1023053      0.055995941  
+     19300         100   3.8441465      3.8441465      2.0783298      0.055586425  
+     19400         100   3.6983054      3.6983054      1.9993476      0.051487825  
+     19500         100   3.9082901      3.9082901      2.110386       0.055361137  
+     19600         100   3.8183806      3.8183806      2.0521248      0.054637936  
+     19700         100   3.9479599      3.9479599      2.123487       0.05654763   
+     19800         100   3.7900356      3.7900356      2.0309629      0.055030689  
+     19900         100   3.8526352      3.8526352      2.079537       0.052237722  
+     20000         100   3.7004965      3.7004965      2.0054313      0.052260073  
+Loop time of 0.141466 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 15268708.811 tau/day, 35344.233 timesteps/s, 3.534 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0092801  | 0.0092801  | 0.0092801  |   0.0 |  6.56
+Neigh   | 0.030749   | 0.030749   | 0.030749   |   0.0 | 21.74
+Comm    | 0.00076276 | 0.00076276 | 0.00076276 |   0.0 |  0.54
+Output  | 0.00026657 | 0.00026657 | 0.00026657 |   0.0 |  0.19
+Modify  | 0.098434   | 0.098434   | 0.098434   |   0.0 | 69.58
+Other   |            | 0.001973   |            |       |  1.39
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            144 ave         144 max         144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 144
+Ave neighs/atom = 1.44
+Neighbor list builds = 906
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   3.7004965      3.7004965      2.0054313      0.051978523  
+     20100         100   1.0456682      1.0456682      0.65203589     0.01426764   
+     20200         100   0.92132571     0.92132571     0.56692143     0.016160496  
+     20300         100   0.9080139      0.9080139      0.54653258     0.011333456  
+     20400         100   0.95504442     0.95504442     0.56626124     0.011989567  
+     20500         100   0.85373295     0.85373295     0.5162143      0.011906206  
+     20600         100   1.0224737      1.0224737      0.59801919     0.012676175  
+     20700         100   0.98041767     0.98041767     0.57722359     0.015534239  
+     20800         100   0.94580127     0.94580127     0.54452681     0.014648617  
+     20900         100   0.92685337     0.92685337     0.52998999     0.012221026  
+     21000         100   0.67355263     0.67355263     0.38349088     0.0096954349 
+     21100         100   0.30344447     0.30344447     0.20123228     0.0065577613 
+     21200         100   0.16818819     0.16818819     0.12097279     0.0042401405 
+     21300         100   0.10742131     0.10742131     0.082910182    0.0032814832 
+     21400         100   0.096764554    0.096764554    0.071534839    0.0029435039 
+     21500         100   0.046970465    0.046970465    0.04129138     0.0017468115 
+     21600         100   0.032766377    0.032766377    0.026265793    0.0016491276 
+     21700         100   0.022152668    0.022152668    0.019394268    0.00050552315
+     21800         100   0.020778       0.020778       0.017776111    0.00098557239
+     21900         100   0.020778283    0.020778283    0.017641295    0.00074778783
+     22000         100   0.01698488     0.01698488     0.01429695     0.0005628648 
+     22100         100   0.01418614     0.01418614     0.012102299    0.00051794337
+     22200         100   0.013346276    0.013346276    0.011394805    0.00032236098
+     22300         100   0.0079928433   0.0079928433   0.0077723623   0.00022112873
+     22400         100   0.0076254375   0.0076254375   0.0073027877   0.00031949798
+     22500         100   0.0069692597   0.0069692597   0.0069664447   0.00021312177
+     22600         100   0.006390305    0.006390305    0.0064208682   0.00041289648
+     22700         100   0.0056975941   0.0056975941   0.0057521988   0.00030399038
+     22800         100   0.0044357329   0.0044357329   0.0045549598   0.00017846882
+     22900         100   0.0036644546   0.0036644546   0.0038064043   0.00023078463
+     23000         100   0.002829538    0.002829538    0.0032135364   0.00022739562
+     23100         100   0.0027443908   0.0027443908   0.0030949164   0.00020554818
+     23200         100   0.0026840272   0.0026840272   0.00304758     0.00016936931
+     23300         100   0.0024070816   0.0024070816   0.0027285777   0.00016201789
+     23400         100   0.0021175586   0.0021175586   0.0023871632   0.00029731473
+     23500         100   0.0020591834   0.0020591834   0.0022740401   0.00015989214
+     23600         100   0.0020569788   0.0020569788   0.0022646534   0.00015753267
+     23700         100   0.0019823585   0.0019823585   0.0021969033   0.00015346211
+     23800         100   0.0021461846   0.0021461846   0.0022696006   0.00025075823
+     23900         100   0.001964677    0.001964677    0.0021583248   0.00014863082
+     24000         100   0.0019474488   0.0019474488   0.0021316684   0.00013004574
+     24100         100   0.0024970295   0.0024970295   0.0023832844   9.8929573e-05
+     24200         100   0.0017561148   0.0017561148   0.0019839926   7.1132622e-05
+     24300         100   0.0016986298   0.0016986298   0.001930582    7.1465912e-05
+     24400         100   0.001571577    0.001571577    0.0018168131   0.00015652173
+     24500         100   0.0015605078   0.0015605078   0.001789223    6.9843415e-05
+     24600         100   0.0018490208   0.0018490208   0.0019049916   5.2092258e-05
+     24700         100   0.0014134222   0.0014134222   0.0016814396   4.4173713e-05
+     24800         100   0.0013062268   0.0013062268   0.001520288    3.6497646e-05
+     24900         100   0.0012718438   0.0012718438   0.0014563564   3.8597512e-05
+     25000         100   0.0012686432   0.0012686432   0.0014211643   4.791856e-05 
+Loop time of 0.0562653 on 1 procs for 5000 steps with 100 atoms
+
+Performance: 38389540.983 tau/day, 88864.678 timesteps/s, 8.886 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0068337  | 0.0068337  | 0.0068337  |   0.0 | 12.15
+Neigh   | 0.0087607  | 0.0087607  | 0.0087607  |   0.0 | 15.57
+Comm    | 0.00052045 | 0.00052045 | 0.00052045 |   0.0 |  0.92
+Output  | 0.00029698 | 0.00029698 | 0.00029698 |   0.0 |  0.53
+Modify  | 0.038112   | 0.038112   | 0.038112   |   0.0 | 67.74
+Other   |            | 0.001742   |            |       |  3.10
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            150 ave         150 max         150 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 150
+Ave neighs/atom = 1.5
+Neighbor list builds = 267
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/granregion/log.27Jun24.granregion.box.g++.4

@@ -0,0 +1,482 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+# pouring spheres into container box
+
+units		lj
+atom_style      sphere
+boundary        f f f
+dimension	3
+comm_modify     vel yes
+
+region          box block -10 10 -10 10 -10 10 units box
+create_box      2 box
+Created orthogonal box = (-10 -10 -10) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
+pair_coeff	* * gran/hooke
+
+region          container block -6 6 -6 6 -6 6 units box
+fix		container all wall/gran/region hooke/history 		4000.0 NULL 100.0 NULL 0.5 1 region container
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             2 all nve/sphere
+fix		3 all gravity 1.0 vector 0 0 -1
+
+region          slab block -2 2 -2 2 -2 2 units box
+fix             ins all pour 100 2 4767548 vol 0.4 10 	        diam one 1.0 region slab ignore
+
+timestep	0.005
+
+compute         1 all temp
+compute_modify  1 dynamic/dof yes
+
+compute         2 all temp/sphere
+compute_modify  2 dynamic/dof yes
+
+thermo		100
+thermo_style	custom step atoms temp c_1 c_2 press
+thermo_modify   lost ignore
+compute_modify  thermo_temp dynamic/dof yes
+
+#dump		2 all image 100 image.*.jpg type type #		zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
+#dump_modify	2 pad 5
+
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 48 every 566 steps, 100 by step 1133
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 1.3
+  binsize = 0.65, bins = 31 31 31
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke, perpetual
+      attributes: half, newton on, size
+      pair build: half/size/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+         0           0   0              0              0              0            
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+       100          30   0.803783       0.803783       0.39507978     0.0029137134 
+       200          30   1.1967995      1.1967995      0.5882574      0.0043383984 
+       300          30   1.2814686      1.2814686      0.62987441     0.0046453238 
+       400          30   0.82331082     0.82331082     0.41173176     0.0029845017 
+       500          30   0.7708462      0.7708462      0.38777784     0.0043831147 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+       600          64   0.51564897     0.51564897     0.26631577     0.0040059368 
+       700          64   0.57239348     0.57239348     0.29566901     0.0045075987 
+       800          64   0.61837087     0.61837087     0.32195387     0.0048123564 
+       900          64   0.53061888     0.53061888     0.28564763     0.0055906552 
+      1000          64   0.496299       0.496299       0.26801572     0.0061169128 
+      1100          64   0.46068308     0.46068308     0.24699057     0.0055717699 
+WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
+      1200          99   0.39206225     0.39206225     0.21356546     0.0066294211 
+      1300          99   0.38624966     0.38624966     0.21345854     0.0049051051 
+      1400          99   0.35615284     0.35615284     0.19785725     0.0046170774 
+      1500          99   0.31486691     0.31486691     0.17429054     0.0064903404 
+      1600          99   0.26369        0.26369        0.15095263     0.0045226821 
+      1700         100   0.19259352     0.19259352     0.11308184     0.0073603886 
+      1800         100   0.1372448      0.1372448      0.083273652    0.0058163062 
+      1900         100   0.077253038    0.077253038    0.053166156    0.0017440856 
+      2000         100   0.065472093    0.065472093    0.04375349     0.0018416047 
+      2100         100   0.057213469    0.057213469    0.037773954    0.001226231  
+      2200         100   0.058857437    0.058857437    0.0372655      0.00090812381
+      2300         100   0.035066108    0.035066108    0.025934054    0.00072114554
+      2400         100   0.021272125    0.021272125    0.016635107    0.0018506654 
+      2500         100   0.015530432    0.015530432    0.012533546    0.0013883971 
+      2600         100   0.012603946    0.012603946    0.0096981459   0.00038648118
+      2700         100   0.0097347475   0.0097347475   0.0076016624   0.00057313888
+      2800         100   0.0067081771   0.0067081771   0.0056944431   0.00085080075
+      2900         100   0.0089177981   0.0089177981   0.0065036822   0.00028986539
+      3000         100   0.0057840287   0.0057840287   0.0044989265   0.00016111737
+      3100         100   0.0038909621   0.0038909621   0.0031511938   0.0001708892 
+      3200         100   0.0029043214   0.0029043214   0.0025807767   9.2473673e-05
+      3300         100   0.0022769336   0.0022769336   0.0021487157   0.00022312666
+      3400         100   0.0015571397   0.0015571397   0.0016669068   0.0003381372 
+      3500         100   0.0015978184   0.0015978184   0.001707772    4.9930818e-05
+      3600         100   0.0023358916   0.0023358916   0.0020709426   9.7687609e-05
+      3700         100   0.0011186736   0.0011186736   0.0012146914   9.3338234e-05
+      3800         100   0.0011657036   0.0011657036   0.0012313764   3.1931251e-05
+      3900         100   0.0014998387   0.0014998387   0.0014015491   2.4226798e-05
+      4000         100   0.0010858335   0.0010858335   0.0010623286   1.6359241e-05
+      4100         100   0.0010464314   0.0010464314   0.0010123557   1.2949588e-05
+      4200         100   0.0010022428   0.0010022428   0.00097338971  1.2402332e-05
+      4300         100   0.00080622372  0.00080622372  0.00084329652  0.00033857037
+      4400         100   0.00073613921  0.00073613921  0.00078373608  1.0103949e-05
+      4500         100   0.00071402196  0.00071402196  0.00076658004  8.8360218e-06
+      4600         100   0.00064851765  0.00064851765  0.00071533461  1.0736438e-05
+      4700         100   0.00061146699  0.00061146699  0.00068274687  4.1341755e-06
+      4800         100   0.00059511472  0.00059511472  0.0006625527   7.3645447e-06
+      4900         100   0.00057700347  0.00057700347  0.0006468562   1.5411897e-05
+      5000         100   0.00056205001  0.00056205001  0.00063592505  7.8813845e-06
+Loop time of 0.0666388 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 32413524.665 tau/day, 75031.307 timesteps/s, 7.503 Matom-step/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.001133   | 0.0024206  | 0.0039594  |   2.6 |  3.63
+Neigh   | 0.0040192  | 0.0046633  | 0.0052296  |   0.8 |  7.00
+Comm    | 0.015155   | 0.021785   | 0.029291   |   4.1 | 32.69
+Output  | 0.0012323  | 0.0014638  | 0.0016021  |   0.4 |  2.20
+Modify  | 0.0026785  | 0.011483   | 0.021199   |   8.2 | 17.23
+Other   |            | 0.02482    |            |       | 37.25
+
+Nlocal:             25 ave          53 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:              4 ave           8 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           40.5 ave          92 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 162
+Ave neighs/atom = 1.62
+Neighbor list builds = 288
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-5000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 0 0 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Region properties for region container changed between runs, resetting its motion (../fix_wall_gran_region.cpp:96)
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+      5000         100   0.00056205001  0.00056205001  0.00063592505  7.871665e-06 
+      5100         100   0.59585977     0.59585977     0.32464933     0.0141718    
+      5200         100   0.67306764     0.67306764     0.35872096     0.013373672  
+      5300         100   0.76065187     0.76065187     0.39925025     0.011460301  
+      5400         100   0.87984446     0.87984446     0.45261417     0.013937042  
+      5500         100   0.95548319     0.95548319     0.48706892     0.013601658  
+      5600         100   0.9993278      0.9993278      0.50830306     0.015663766  
+      5700         100   1.0449415      1.0449415      0.52967249     0.016797841  
+      5800         100   1.0767598      1.0767598      0.54508699     0.016128855  
+      5900         100   1.118688       1.118688       0.56530849     0.016830117  
+      6000         100   1.1535698      1.1535698      0.58290663     0.01715335   
+      6100         100   1.1753828      1.1753828      0.59419088     0.019273207  
+      6200         100   1.1994171      1.1994171      0.60433264     0.018391566  
+      6300         100   1.2244707      1.2244707      0.61626199     0.018842556  
+      6400         100   1.2507994      1.2507994      0.62829386     0.019538413  
+      6500         100   1.2684644      1.2684644      0.63747702     0.020794729  
+      6600         100   1.2704726      1.2704726      0.63929889     0.020253985  
+      6700         100   1.2737302      1.2737302      0.63970688     0.020858602  
+      6800         100   1.287922       1.287922       0.64460894     0.021589773  
+      6900         100   1.3028782      1.3028782      0.65197802     0.02135295   
+      7000         100   1.306633       1.306633       0.65371741     0.021291182  
+      7100         100   1.3161393      1.3161393      0.65785404     0.022554896  
+      7200         100   1.3228158      1.3228158      0.6609031      0.021811977  
+      7300         100   1.3245632      1.3245632      0.66161966     0.02206776   
+      7400         100   1.3266822      1.3266822      0.662738       0.022070761  
+      7500         100   1.3265138      1.3265138      0.6624472      0.021944768  
+      7600         100   1.3286802      1.3286802      0.66338775     0.0219393    
+      7700         100   1.332829       1.332829       0.66547051     0.022142398  
+      7800         100   1.3323535      1.3323535      0.66534513     0.022787777  
+      7900         100   1.3372424      1.3372424      0.66777556     0.02192759   
+      8000         100   1.3396201      1.3396201      0.66910123     0.022439596  
+      8100         100   1.3422271      1.3422271      0.67060566     0.023784952  
+      8200         100   1.3468062      1.3468062      0.6728991      0.02243345   
+      8300         100   1.3439408      1.3439408      0.6717529      0.022312339  
+      8400         100   1.3484134      1.3484134      0.67346027     0.022770922  
+      8500         100   1.3490032      1.3490032      0.67378177     0.022427863  
+      8600         100   1.349789       1.349789       0.67398897     0.022494049  
+      8700         100   1.3513512      1.3513512      0.67475613     0.022413559  
+      8800         100   1.3535168      1.3535168      0.67589784     0.022356566  
+      8900         100   1.3505765      1.3505765      0.67442168     0.022240615  
+      9000         100   1.3499918      1.3499918      0.67419831     0.02226049   
+      9100         100   1.3518103      1.3518103      0.67489482     0.022399038  
+      9200         100   1.3526275      1.3526275      0.67529852     0.022395079  
+      9300         100   1.353741       1.353741       0.67585205     0.022471008  
+      9400         100   1.3538758      1.3538758      0.67589523     0.022461734  
+      9500         100   1.3537199      1.3537199      0.67586527     0.022370169  
+      9600         100   1.3539788      1.3539788      0.67602899     0.022400771  
+      9700         100   1.3544874      1.3544874      0.67619552     0.022648464  
+      9800         100   1.3555422      1.3555422      0.67666186     0.022367319  
+      9900         100   1.3560106      1.3560106      0.6768751      0.02236585   
+     10000         100   1.3563578      1.3563578      0.6770434      0.022359307  
+Loop time of 0.117825 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 18332213.198 tau/day, 42435.679 timesteps/s, 4.244 Matom-step/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00088578 | 0.0090104  | 0.017735   |   8.5 |  7.65
+Neigh   | 0.0078603  | 0.0087927  | 0.0097327  |   1.0 |  7.46
+Comm    | 0.006411   | 0.013582   | 0.022547   |   6.1 | 11.53
+Output  | 0.0011273  | 0.0015902  | 0.0019777  |   1.0 |  1.35
+Modify  | 0.0095221  | 0.034125   | 0.058989   |  13.2 | 28.96
+Other   |            | 0.05073    |            |       | 43.05
+
+Nlocal:             25 ave          52 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:              3 ave           6 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:          48.25 ave         109 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 193
+Ave neighs/atom = 1.93
+Neighbor list builds = 626
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     10000         100   1.3563578      1.3563578      0.6770434      0.022433108  
+     10100         100   0.32881547     0.32881547     0.18968913     0.0063460187 
+     10200         100   0.19880113     0.19880113     0.12812646     0.0074601538 
+     10300         100   0.12614062     0.12614062     0.090121373    0.0028337336 
+     10400         100   0.088358363    0.088358363    0.067236815    0.0020269846 
+     10500         100   0.071199344    0.071199344    0.055567135    0.0016191769 
+     10600         100   0.053909616    0.053909616    0.042301996    0.00098643468
+     10700         100   0.039560745    0.039560745    0.032482256    0.00089240864
+     10800         100   0.032130432    0.032130432    0.02705329     0.00058669881
+     10900         100   0.02462494     0.02462494     0.021121496    0.0017376127 
+     11000         100   0.020941068    0.020941068    0.017866781    0.00031112553
+     11100         100   0.016775675    0.016775675    0.014620214    0.00026856842
+     11200         100   0.015005732    0.015005732    0.012803923    0.00067036626
+     11300         100   0.012099209    0.012099209    0.010308221    0.00032666902
+     11400         100   0.010559421    0.010559421    0.0090243729   0.00013645685
+     11500         100   0.0093738615   0.0093738615   0.0080176514   0.00098541099
+     11600         100   0.0081900702   0.0081900702   0.0070256953   0.00025935992
+     11700         100   0.0068100165   0.0068100165   0.0058703223   0.00014866816
+     11800         100   0.0060475708   0.0060475708   0.0052518105   0.00017895168
+     11900         100   0.0055607485   0.0055607485   0.0047184164   0.00011358846
+     12000         100   0.0053149064   0.0053149064   0.0045168418   0.00015222428
+     12100         100   0.0050909525   0.0050909525   0.0043196952   6.3000537e-05
+     12200         100   0.0041810842   0.0041810842   0.0036835522   4.6423956e-05
+     12300         100   0.0034305227   0.0034305227   0.0031222649   0.00020251115
+     12400         100   0.0031763077   0.0031763077   0.0028956456   0.00030307787
+     12500         100   0.0027440829   0.0027440829   0.0025087304   0.00010418607
+     12600         100   0.0024581964   0.0024581964   0.0022200229   3.042018e-05 
+     12700         100   0.002259527    0.002259527    0.0020708869   4.192368e-05 
+     12800         100   0.0019143448   0.0019143448   0.0018088032   4.6200439e-05
+     12900         100   0.0017935964   0.0017935964   0.0017028317   2.2195756e-05
+     13000         100   0.0017286429   0.0017286429   0.0016396753   2.3108871e-05
+     13100         100   0.0017055291   0.0017055291   0.0016122058   2.2444611e-05
+     13200         100   0.0016539275   0.0016539275   0.0015570166   2.0467353e-05
+     13300         100   0.0015777788   0.0015777788   0.0014852505   1.9525012e-05
+     13400         100   0.0015372199   0.0015372199   0.0014497102   2.3203566e-05
+     13500         100   0.0015066638   0.0015066638   0.0014097203   1.8644964e-05
+     13600         100   0.0012290618   0.0012290618   0.0012056216   1.3235643e-05
+     13700         100   0.0011781948   0.0011781948   0.0011685226   3.4312262e-05
+     13800         100   0.0011530136   0.0011530136   0.0011433171   2.8832126e-05
+     13900         100   0.0011085224   0.0011085224   0.0011052764   1.444139e-05 
+     14000         100   0.0010656788   0.0010656788   0.0010702461   1.3187775e-05
+     14100         100   0.001029277    0.001029277    0.0010469537   1.2837267e-05
+     14200         100   0.0009750904   0.0009750904   0.0009915384   1.209089e-05 
+     14300         100   0.00094893337  0.00094893337  0.00096909301  1.1743051e-05
+     14400         100   0.00087708427  0.00087708427  0.00087575318  1.9027338e-05
+     14500         100   0.00086229913  0.00086229913  0.0008643568   1.0670952e-05
+     14600         100   0.00084206808  0.00084206808  0.0008268172   3.2391722e-05
+     14700         100   0.00077682873  0.00077682873  0.00077186085  9.6132555e-06
+     14800         100   0.00074736908  0.00074736908  0.00074958372  9.2486924e-06
+     14900         100   0.00074456847  0.00074456847  0.00074779946  9.2140349e-06
+     15000         100   0.00073830282  0.00073830282  0.0007426924   9.1364974e-06
+Loop time of 0.0608167 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 35516589.034 tau/day, 82214.326 timesteps/s, 8.221 Matom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00059197 | 0.0022122  | 0.0043047  |   3.5 |  3.64
+Neigh   | 0.00087477 | 0.0012077  | 0.001588   |   1.0 |  1.99
+Comm    | 0.0017826  | 0.010005   | 0.018966   |   8.1 | 16.45
+Output  | 0.0010587  | 0.0013365  | 0.0015183  |   0.5 |  2.20
+Modify  | 0.00046958 | 0.012924   | 0.027298   |  11.0 | 21.25
+Other   |            | 0.03313    |            |       | 54.48
+
+Nlocal:             25 ave          53 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:           3.75 ave           8 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:          39.25 ave          82 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 157
+Ave neighs/atom = 1.57
+Neighbor list builds = 100
+Dangerous builds = 0
+
+region          container delete
+variable        theta equal (step-15000)*(4.0*PI/5000)
+region          container block -6 6 -6 6 -6 6 units box                 rotate v_theta 0 0 0 1 1 1
+run	        5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     15000         100   0.00073830282  0.00073830282  0.0007426924   9.1364974e-06
+     15100         100   1.1048281      1.1048281      0.7023727      0.018379275  
+     15200         100   1.2022249      1.2022249      0.77748962     0.015662439  
+     15300         100   1.2561351      1.2561351      0.82563065     0.01835048   
+     15400         100   1.4372446      1.4372446      0.92907923     0.02087065   
+     15500         100   1.6414713      1.6414713      1.0284489      0.025654324  
+     15600         100   1.7844655      1.7844655      1.0861866      0.025170346  
+     15700         100   2.034248       2.034248       1.2017171      0.040341642  
+     15800         100   2.1253699      2.1253699      1.2228657      0.029297194  
+     15900         100   2.1940232      2.1940232      1.2470589      0.033866758  
+     16000         100   2.2624419      2.2624419      1.2828225      0.030063645  
+     16100         100   2.3208536      2.3208536      1.3118956      0.0323489    
+     16200         100   2.3564971      2.3564971      1.3261173      0.032882494  
+     16300         100   2.3956066      2.3956066      1.3260307      0.03292972   
+     16400         100   2.5025831      2.5025831      1.3817693      0.031132988  
+     16500         100   2.5947914      2.5947914      1.4152657      0.036126782  
+     16600         100   2.7688769      2.7688769      1.4975686      0.037497127  
+     16700         100   2.812503       2.812503       1.5216659      0.039316167  
+     16800         100   2.8977424      2.8977424      1.5599254      0.039996029  
+     16900         100   3.045802       3.045802       1.6332888      0.041406156  
+     17000         100   3.2195366      3.2195366      1.7247171      0.040023634  
+     17100         100   3.2597294      3.2597294      1.7527958      0.04828292   
+     17200         100   3.293587       3.293587       1.7693254      0.044001441  
+     17300         100   3.1861836      3.1861836      1.7142076      0.049158822  
+     17400         100   3.4593561      3.4593561      1.8426619      0.053469673  
+     17500         100   3.3813767      3.3813767      1.8079958      0.058776299  
+     17600         100   3.5834203      3.5834203      1.9094759      0.053256842  
+     17700         100   3.2243306      3.2243306      1.7425111      0.064354789  
+     17800         100   3.358228       3.358228       1.8202932      0.046798524  
+     17900         100   3.2257908      3.2257908      1.7678964      0.043655204  
+     18000         100   3.237732       3.237732       1.7598181      0.050850672  
+     18100         100   3.2042441      3.2042441      1.751979       0.045582006  
+     18200         100   3.1562775      3.1562775      1.7336068      0.042210739  
+     18300         100   3.2630507      3.2630507      1.7925333      0.046412778  
+     18400         100   3.4150588      3.4150588      1.8668408      0.044386435  
+     18500         100   3.4913198      3.4913198      1.9125495      0.043329829  
+     18600         100   3.5290036      3.5290036      1.9184098      0.048302721  
+     18700         100   3.4852698      3.4852698      1.8865833      0.059566124  
+     18800         100   3.7157551      3.7157551      2.0082235      0.051356305  
+     18900         100   3.9504619      3.9504619      2.1377018      0.051553987  
+     19000         100   3.9711274      3.9711274      2.1549121      0.051555312  
+     19100         100   3.90954        3.90954        2.1135174      0.0548311    
+     19200         100   4.0672819      4.0672819      2.1837089      0.064431553  
+     19300         100   3.998355       3.998355       2.1572884      0.056830399  
+     19400         100   3.9172127      3.9172127      2.1130164      0.051264041  
+     19500         100   3.9120291      3.9120291      2.1088399      0.052545115  
+     19600         100   3.8613614      3.8613614      2.0752883      0.055466569  
+     19700         100   3.8428824      3.8428824      2.0787804      0.05129261   
+     19800         100   3.5686751      3.5686751      1.9356553      0.059177256  
+     19900         100   3.5573788      3.5573788      1.9430183      0.054618794  
+     20000         100   3.5453022      3.5453022      1.9413343      0.047640543  
+Loop time of 0.120564 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 17915781.606 tau/day, 41471.717 timesteps/s, 4.147 Matom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0022864  | 0.0035398  | 0.0056964  |   2.2 |  2.94
+Neigh   | 0.0095136  | 0.011233   | 0.012853   |   1.1 |  9.32
+Comm    | 0.043338   | 0.044586   | 0.046388   |   0.6 | 36.98
+Output  | 0.0011632  | 0.0012814  | 0.0013677  |   0.2 |  1.06
+Modify  | 0.01756    | 0.026391   | 0.03297    |   3.5 | 21.89
+Other   |            | 0.03353    |            |       | 27.81
+
+Nlocal:             25 ave          36 max          13 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost:              5 ave           9 max           2 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:           37.5 ave          53 max          15 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 150
+Ave neighs/atom = 1.5
+Neighbor list builds = 913
+Dangerous builds = 0
+
+region          container delete
+region          container block -6 6 -6 6 -6 6 units box
+run             5000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
+   Step        Atoms         Temp           c_1            c_2           Press     
+     20000         100   3.5453022      3.5453022      1.9413343      0.047178052  
+     20100         100   1.0878587      1.0878587      0.68666704     0.016139979  
+     20200         100   1.0230655      1.0230655      0.63593494     0.014642345  
+     20300         100   0.94958824     0.94958824     0.59306601     0.011745659  
+     20400         100   0.93038108     0.93038108     0.57232527     0.01154829   
+     20500         100   0.92183816     0.92183816     0.55466942     0.01212559   
+     20600         100   1.0175846      1.0175846      0.59940035     0.013815361  
+     20700         100   1.0564615      1.0564615      0.60726745     0.013073711  
+     20800         100   0.99967869     0.99967869     0.57665019     0.012450813  
+     20900         100   0.97051084     0.97051084     0.5574217      0.015686955  
+     21000         100   0.639185       0.639185       0.37441942     0.017594616  
+     21100         100   0.24979014     0.24979014     0.17121567     0.0084027295 
+     21200         100   0.15147941     0.15147941     0.11124349     0.0030435746 
+     21300         100   0.13117502     0.13117502     0.091432638    0.0029110318 
+     21400         100   0.11158272     0.11158272     0.076264692    0.0021951204 
+     21500         100   0.056660993    0.056660993    0.043503807    0.0010993096 
+     21600         100   0.028640836    0.028640836    0.026000267    0.0010440792 
+     21700         100   0.025816483    0.025816483    0.021922896    0.00081674646
+     21800         100   0.023929555    0.023929555    0.019936972    0.0010383614 
+     21900         100   0.022271339    0.022271339    0.017947505    0.0014630387 
+     22000         100   0.019277834    0.019277834    0.015483116    0.00058751407
+     22100         100   0.019997809    0.019997809    0.015919504    0.00064176101
+     22200         100   0.015870543    0.015870543    0.01244838     0.0004205505 
+     22300         100   0.011797587    0.011797587    0.0096491363   0.00034907063
+     22400         100   0.010745212    0.010745212    0.008874218    0.00035427537
+     22500         100   0.0082372399   0.0082372399   0.0071217811   0.00028179943
+     22600         100   0.007942576    0.007942576    0.0067248822   0.001507115  
+     22700         100   0.0061733667   0.0061733667   0.0053092324   0.00056018554
+     22800         100   0.0058287651   0.0058287651   0.004972189    0.00023807695
+     22900         100   0.0051352339   0.0051352339   0.004324157    0.00020849263
+     23000         100   0.0040107769   0.0040107769   0.0035769703   0.00022626101
+     23100         100   0.0040288854   0.0040288854   0.0034355474   0.00019107621
+     23200         100   0.003277858    0.003277858    0.0030013165   0.00016119888
+     23300         100   0.0033633749   0.0033633749   0.0030188927   0.00014459404
+     23400         100   0.003468042    0.003468042    0.0030079205   0.00013778427
+     23500         100   0.0027616702   0.0027616702   0.0024994596   0.00011834915
+     23600         100   0.0022531303   0.0022531303   0.0021182802   0.0002279623 
+     23700         100   0.002067768    0.002067768    0.0019631752   0.00014341503
+     23800         100   0.0020069255   0.0020069255   0.0019209587   0.00010673435
+     23900         100   0.0019630617   0.0019630617   0.0018748221   0.00011856923
+     24000         100   0.0018800646   0.0018800646   0.0018190347   0.00010707562
+     24100         100   0.0018028137   0.0018028137   0.0017067233   0.00010884117
+     24200         100   0.0017278932   0.0017278932   0.0016251004   0.00013664683
+     24300         100   0.0016373288   0.0016373288   0.0015529481   0.00010025414
+     24400         100   0.0019876848   0.0019876848   0.0016912033   0.00011235942
+     24500         100   0.0013677345   0.0013677345   0.0012839488   7.8669645e-05
+     24600         100   0.0012852614   0.0012852614   0.0012065052   0.00010172361
+     24700         100   0.0011145002   0.0011145002   0.0010748344   7.5021689e-05
+     24800         100   0.0012860792   0.0012860792   0.0011429675   5.7939624e-05
+     24900         100   0.00097198499  0.00097198499  0.00096175911  5.443837e-05 
+     25000         100   0.00096224466  0.00096224466  0.00095159089  5.4245409e-05
+Loop time of 0.0658283 on 4 procs for 5000 steps with 100 atoms
+
+Performance: 32812622.584 tau/day, 75955.145 timesteps/s, 7.596 Matom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00079402 | 0.002735   | 0.0055522  |   3.9 |  4.15
+Neigh   | 0.0027088  | 0.003273   | 0.0038077  |   0.9 |  4.97
+Comm    | 0.010018   | 0.017119   | 0.024875   |   4.8 | 26.01
+Output  | 0.0010937  | 0.0013253  | 0.0015108  |   0.5 |  2.01
+Modify  | 0.0012967  | 0.011558   | 0.023237   |   9.5 | 17.56
+Other   |            | 0.02982    |            |       | 45.30
+
+Nlocal:             25 ave          56 max           0 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:            5.5 ave          12 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:             40 ave         101 max           0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 160
+Ave neighs/atom = 1.6
+Neighbor list builds = 275
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/granregion/log.27Jun24.granregion.funnel.g++.1

@@ -0,0 +1,643 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable	name string funnel_pour
+
+thermo_modify	flush yes
+units 		si
+variable	PI equal 3.141592653589
+variable	seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	xlo equal 10
+variable	xhi equal 40
+variable	ylo equal 10
+variable	yhi equal 40
+variable	zlo equal -20
+variable	zhi equal 50
+
+variable	xc equal 25
+variable	yc equal 25
+
+variable	zconehi equal 50
+variable	zconelo equal 10
+variable	zcyllo equal 0
+variable	radconelo equal 2
+variable	radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable 	skin equal ${rhi}
+variable 	skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	density equal 1.0
+variable	EYoung equal 10^5
+variable 	Poisson equal 2.0/7.0
+variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+0.285714285714286))
+
+variable	gravity equal 1.0
+
+variable	reff equal 0.5*(${rhi}+${rlo})
+variable	reff equal 0.5*(0.5+${rlo})
+variable	reff equal 0.5*(0.5+0.25)
+variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable        kt equal 4.0*${GShear}/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable	a equal (-2.0*log(${coeffRes})/${PI})^2
+variable	a equal (-2.0*log(0.1)/${PI})^2
+variable	a equal (-2.0*log(0.1)/3.141592653589)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 903.503751814138*0.5
+
+variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable	dt equal ${tcol}*0.05
+variable	dt equal 0.00210943016014969*0.05
+timestep	${dt}
+timestep	0.000105471508007485
+
+###############################################
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		off
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 -20 ${zhi}
+region		boxreg block 10 40 10 40 -20 50
+create_box	1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.5 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 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 = 0
+  ghost atom cutoff = 0
+  binsize = 30, bins = 1 1 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/multi/atomonly/newtoff
+      stencil: full/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
+
+region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
+region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
+
+region		hopreg union 2 conereg cylreg
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+
+fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
+
+#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
+thermo_modify	flush yes lost warn
+
+# Initial run to fill up the cone
+
+run		20000
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
+   Step          CPU          Atoms        KinEng    
+         0   0                      0  -0            
+      1000   0.42422547          2000  -0            
+      2000   0.61303447          2000  -0            
+      3000   0.80093891          2000  -0            
+      4000   0.9870726           2000  -0            
+      5000   1.174735            2000  -0            
+      6000   1.3615338           2000  -0            
+      7000   1.5481574           2000  -0            
+      8000   1.7332676           2000  -0            
+      9000   1.9202086           2000  -0            
+     10000   2.1067651           2000  -0            
+     11000   2.2904529           2000  -0            
+     12000   2.4750549           2000  -0            
+     13000   2.6588335           2000  -0            
+     14000   2.8432942           2000  -0            
+     15000   3.0276634           2000  -0            
+     16000   3.2143893           2000  -0            
+     17000   3.3989855           2000  -0            
+     18000   3.5835207           2000  -0            
+     19000   3.7684773           2000  -0            
+     20000   3.9550272           2000  -0            
+Loop time of 3.95505 on 1 procs for 20000 steps with 2000 atoms
+
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.40709    | 0.40709    | 0.40709    |   0.0 | 10.29
+Neigh   | 0.065613   | 0.065613   | 0.065613   |   0.0 |  1.66
+Comm    | 0.0076015  | 0.0076015  | 0.0076015  |   0.0 |  0.19
+Output  | 0.00041671 | 0.00041671 | 0.00041671 |   0.0 |  0.01
+Modify  | 3.3895     | 3.3895     | 3.3895     |   0.0 | 85.70
+Other   |            | 0.08486    |            |       |  2.15
+
+Nlocal:           2000 ave        2000 max        2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1607 ave        1607 max        1607 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1607
+Ave neighs/atom = 0.8035
+Neighbor list builds = 71
+Dangerous builds = 0
+unfix 		ins
+run		150000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
+   Step          CPU          Atoms        KinEng    
+     20000   0                   2000   6652.2957    
+     21000   0.18540841          2000   6807.2201    
+     22000   0.37080157          2000   6973.9359    
+     23000   0.55573123          2000   7142.3648    
+     24000   0.74112501          2000   7276.9717    
+     25000   0.92686283          2000   7369.4191    
+     26000   1.1145958           2000   7497.6526    
+     27000   1.3033904           2000   7638.946     
+     28000   1.4921406           2000   7780.0339    
+     29000   1.6824098           2000   7881.8177    
+     30000   1.8751801           2000   7967.2641    
+     31000   2.0698118           2000   7994.9273    
+     32000   2.2682778           2000   7937.0671    
+     33000   2.4695819           2000   7774.0508    
+     34000   2.675988            2000   7591.1491    
+     35000   2.886376            2000   7357.5176    
+     36000   3.102007            2000   7147.2024    
+     37000   3.321435            2000   6979.1604    
+     38000   3.5426417           2000   6813.2152    
+     39000   3.7660203           2000   6660.2701    
+     40000   3.998044            2000   6502.8957    
+     41000   4.234151            2000   6324.3951    
+     42000   4.4731702           2000   6132.7516    
+     43000   4.7137403           2000   5913.1841    
+     44000   4.9572451           2000   5732.2095    
+     45000   5.2042391           2000   5508.8322    
+     46000   5.462849            2000   5306.8932    
+     47000   5.724072            2000   5152.0521    
+     48000   5.987507            2000   5028.2274    
+     49000   6.2495317           2000   4896.102     
+     50000   6.5151951           2000   4723.5189    
+     51000   6.7809368           2000   4583.7526    
+     52000   7.0554059           2000   4447.0187    
+     53000   7.5371151           2000   4303.2307    
+     54000   7.8249388           2000   4168.5251    
+     55000   8.1204418           2000   4036.9704    
+     56000   8.4176628           2000   3901.1183    
+     57000   8.7222873           2000   3716.7071    
+     58000   9.0346411           2000   3473.5422    
+     59000   9.3526758           2000   3245.1223    
+     60000   9.6699173           2000   3039.7845    
+     61000   9.9903491           2000   2780.0187    
+     62000   10.318591           2000   2577.3345    
+     63000   10.65279            2000   2346.2488    
+     64000   10.993148           2000   2116.7298    
+     65000   11.335466           2000   1903.7828    
+     66000   11.686936           2000   1631.1676    
+     67000   12.046515           2000   1431.0198    
+     68000   12.413611           2000   1212.875     
+     69000   12.783883           2000   995.45046    
+     70000   13.156707           2000   811.54766    
+     71000   13.532628           2000   624.08622    
+     72000   13.91241            2000   471.00862    
+     73000   14.296186           2000   358.33486    
+     74000   14.680961           2000   284.39416    
+     75000   15.06644            2000   234.26671    
+     76000   15.447805           2000   185.61836    
+     77000   15.825601           2000   152.95918    
+     78000   16.205661           2000   122.49023    
+     79000   16.582292           2000   102.29396    
+     80000   16.96433            2000   86.284684    
+     81000   17.347289           2000   73.984781    
+     82000   17.739993           2000   63.042918    
+     83000   18.142078           2000   53.338428    
+     84000   18.547853           2000   45.89585     
+     85000   18.95343            2000   40.412826    
+     86000   19.35904            2000   34.183381    
+     87000   19.765916           2000   29.671524    
+     88000   20.18651            2000   26.90414     
+     89000   20.598969           2000   24.362631    
+     90000   21.016445           2000   21.887341    
+     91000   21.437072           2000   19.985662    
+     92000   21.86331            2000   18.728162    
+     93000   22.291217           2000   16.99941     
+     94000   22.724102           2000   15.71941     
+     95000   23.155367           2000   14.744057    
+     96000   23.590722           2000   14.214918    
+     97000   24.028273           2000   13.450182    
+     98000   24.47017            2000   12.79222     
+     99000   24.913929           2000   12.10595     
+    100000   25.361256           2000   11.281863    
+    101000   25.807117           2000   10.025419    
+    102000   26.257292           2000   9.9574468    
+    103000   26.70767            2000   9.4078117    
+    104000   27.161728           2000   8.9079161    
+    105000   27.617856           2000   8.6269302    
+    106000   28.069631           2000   8.5512649    
+    107000   28.526606           2000   8.4703948    
+    108000   28.982832           2000   8.2747542    
+    109000   29.441422           2000   8.2895118    
+    110000   29.906198           2000   8.1785613    
+    111000   30.36715            2000   7.8443234    
+    112000   30.829642           2000   7.7436124    
+    113000   31.319634           2000   7.8118604    
+    114000   31.791602           2000   7.3806177    
+    115000   32.260138           2000   7.0857235    
+    116000   32.725698           2000   7.1346752    
+    117000   33.192963           2000   7.0653751    
+    118000   33.661517           2000   6.6314104    
+    119000   34.127108           2000   6.2169614    
+    120000   34.597123           2000   5.8988829    
+    121000   35.064919           2000   5.4197277    
+    122000   35.535855           2000   4.6381303    
+    123000   36.005284           2000   4.4949206    
+    124000   36.47519            2000   4.4261118    
+    125000   36.945117           2000   4.4223703    
+    126000   37.417732           2000   4.4858898    
+    127000   37.888171           2000   4.3312536    
+    128000   38.360713           2000   3.7124973    
+    129000   38.835798           2000   3.5467396    
+    130000   39.311234           2000   3.5104139    
+    131000   39.783409           2000   3.5725612    
+    132000   40.255871           2000   3.669455     
+    133000   40.728998           2000   3.6168912    
+    134000   41.203148           2000   3.3598517    
+    135000   41.677786           2000   3.3743407    
+    136000   42.15241            2000   3.1109764    
+    137000   42.627707           2000   3.0720146    
+    138000   43.100904           2000   3.1303776    
+    139000   43.574775           2000   3.2052806    
+    140000   44.050804           2000   2.8958882    
+    141000   44.525409           2000   2.9931572    
+    142000   44.999822           2000   3.0967832    
+    143000   45.476054           2000   3.0576365    
+    144000   45.951361           2000   3.2016943    
+    145000   46.429655           2000   3.3817709    
+    146000   46.905577           2000   3.4527239    
+    147000   47.38743            2000   3.5928733    
+    148000   47.86409            2000   3.7784682    
+    149000   48.342003           2000   3.6587944    
+    150000   48.823792           2000   3.7945669    
+    151000   49.30105            2000   3.5551557    
+    152000   49.780315           2000   3.6248848    
+    153000   50.257553           2000   3.7361463    
+    154000   50.737624           2000   3.8534319    
+    155000   51.218208           2000   4.0101408    
+    156000   51.695675           2000   3.7670652    
+    157000   52.176961           2000   3.1487676    
+    158000   52.657466           2000   2.980076     
+    159000   53.134109           2000   3.0350592    
+    160000   53.615609           2000   3.125389     
+    161000   54.093868           2000   2.7516115    
+    162000   54.576681           2000   2.413911     
+    163000   55.055496           2000   2.297713     
+    164000   55.538174           2000   2.3190806    
+    165000   56.020458           2000   2.2868879    
+    166000   56.501206           2000   2.1658547    
+    167000   56.983465           2000   1.7511071    
+    168000   57.466833           2000   1.4112478    
+    169000   57.949757           2000   1.3623558    
+    170000   58.43349            2000   1.3701579    
+Loop time of 58.4335 on 1 procs for 150000 steps with 2000 atoms
+
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 29.221     | 29.221     | 29.221     |   0.0 | 50.01
+Neigh   | 0.57927    | 0.57927    | 0.57927    |   0.0 |  0.99
+Comm    | 0.060749   | 0.060749   | 0.060749   |   0.0 |  0.10
+Output  | 0.20563    | 0.20563    | 0.20563    |   0.0 |  0.35
+Modify  | 27.674     | 27.674     | 27.674     |   0.0 | 47.36
+Other   |            | 0.6922     |            |       |  1.18
+
+Nlocal:           2000 ave        2000 max        2000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          15308 ave       15308 max       15308 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15308
+Ave neighs/atom = 7.654
+Neighbor list builds = 367
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region	  	cylreg delete
+region		hopreg delete
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
+
+region		hopreg union 2 cylreg conereg
+
+unfix		hopper3
+fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run		100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
+   Step          CPU          Atoms        KinEng    
+    170000   0                   2000   1.3701579    
+    171000   0.48431316          2000   2.3724823    
+    172000   0.96523693          2000   3.5881441    
+    173000   1.4349569           2000   5.3771633    
+    174000   1.902564            2000   7.5896471    
+    175000   2.3637344           2000   10.77251     
+    176000   2.817277            2000   14.806868    
+    177000   3.2682365           2000   19.607624    
+    178000   3.7215391           2000   25.426227    
+    179000   4.1716711           2000   32.23584     
+    180000   4.621872            2000   39.930468    
+    181000   5.0676618           2000   47.686304    
+    182000   5.5105545           2000   56.506806    
+    183000   5.9489081           2000   66.514326    
+    184000   6.3843739           2000   77.554644    
+    185000   6.8189889           2000   89.224002    
+    186000   7.2526358           2000   102.07846    
+    187000   7.6807565           2000   116.08141    
+    188000   8.1050895           2000   130.97964    
+    189000   8.52413             2000   146.77806    
+    190000   8.9479211           2000   162.79858    
+    191000   9.3652194           2000   179.02052    
+    192000   9.780893            2000   196.26683    
+    193000   10.192876           2000   214.38928    
+    194000   10.606655           2000   232.32068    
+    195000   11.018129           2000   251.74644    
+    196000   11.424821           2000   272.25231    
+    197000   11.833891           2000   294.64075    
+    198000   12.237613           2000   318.32895    
+    199000   12.640094           2000   342.44005    
+    200000   13.045535           2000   368.35469    
+    201000   13.445497           2000   395.2465     
+    202000   13.85102            2000   422.63599    
+    203000   14.254213           2000   450.45248    
+    204000   14.654729           2000   479.60812    
+    205000   15.057527           2000   510.44155    
+    206000   15.456223           2000   543.25751    
+    207000   15.849932           2000   577.35928    
+    208000   16.240706           2000   612.29718    
+    209000   16.629756           2000   647.8951     
+    210000   17.019318           2000   683.79409    
+    211000   17.40949            2000   720.36556    
+    212000   17.802521           2000   759.27331    
+    213000   18.192311           2000   798.27302    
+    214000   18.582347           2000   837.93849    
+    215000   18.970586           2000   877.92945    
+    216000   19.362316           2000   919.62532    
+    217000   19.755364           2000   962.83509    
+    218000   20.146845           2000   1008.5243    
+    219000   20.530427           2000   1054.5769    
+    220000   20.914645           2000   1103.1843    
+    221000   21.296153           2000   1153.0349    
+    222000   21.681747           2000   1204.5599    
+    223000   22.06794            2000   1257.1367    
+    224000   22.45394            2000   1308.6735    
+WARNING: Lost atoms: original 2000 current 1999 (../thermo.cpp:499)
+    225000   22.843026           1999   1360.1205    
+    226000   23.221639           1998   1404.8405    
+    227000   23.603256           1996   1448.4869    
+    228000   23.985547           1992   1491.8112    
+    229000   24.359685           1985   1518.7013    
+    230000   24.733284           1971   1507.6699    
+    231000   25.100372           1965   1533.5096    
+    232000   25.470109           1948   1489.4128    
+    233000   25.840892           1933   1477.4536    
+    234000   26.207893           1915   1425.8398    
+    235000   26.570401           1904   1410.1451    
+    236000   26.931189           1892   1401.7595    
+    237000   27.28796            1880   1368.893     
+    238000   27.642985           1868   1341.8885    
+    239000   27.998754           1850   1286.7968    
+    240000   28.353974           1833   1219.5123    
+    241000   28.709461           1820   1173.3608    
+    242000   29.065121           1806   1106.0727    
+    243000   29.418519           1788   1035.912     
+    244000   29.770812           1779   1021.6147    
+    245000   30.11704            1767   969.40032    
+    246000   30.457702           1757   939.12022    
+    247000   30.800392           1739   840.9396     
+    248000   31.141047           1730   822.06575    
+    249000   31.483192           1719   762.11057    
+    250000   31.831879           1707   708.50308    
+    251000   32.176299           1700   692.12647    
+    252000   32.520059           1697   694.5812     
+    253000   32.884872           1686   652.36951    
+    254000   33.229261           1682   662.95256    
+    255000   33.557987           1677   637.34619    
+    256000   33.891681           1672   630.71277    
+    257000   34.230081           1669   641.87365    
+    258000   34.571663           1665   635.862      
+    259000   34.913723           1664   658.5339     
+    260000   35.253805           1662   669.95468    
+    261000   35.587547           1660   676.93495    
+    262000   35.920661           1657   681.72646    
+    263000   36.25079            1655   687.4078     
+    264000   36.5838             1651   681.61352    
+    265000   36.914146           1647   673.20622    
+    266000   37.245414           1644   677.30073    
+    267000   37.571588           1641   671.05897    
+    268000   37.896337           1639   689.55776    
+    269000   38.22279            1637   711.98809    
+    270000   38.550831           1633   705.29974    
+Loop time of 38.5508 on 1 procs for 100000 steps with 1633 atoms
+
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 20.145     | 20.145     | 20.145     |   0.0 | 52.25
+Neigh   | 0.42523    | 0.42523    | 0.42523    |   0.0 |  1.10
+Comm    | 0.042119   | 0.042119   | 0.042119   |   0.0 |  0.11
+Output  | 0.0022978  | 0.0022978  | 0.0022978  |   0.0 |  0.01
+Modify  | 17.495     | 17.495     | 17.495     |   0.0 | 45.38
+Other   |            | 0.4416     |            |       |  1.15
+
+Nlocal:           1633 ave        1633 max        1633 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          11358 ave       11358 max       11358 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 11358
+Ave neighs/atom = 6.955297
+Neighbor list builds = 244
+Dangerous builds = 0
+Total wall time: 0:01:40

examples/granregion/log.27Jun24.granregion.funnel.g++.4

@@ -0,0 +1,643 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+# pour particles into cone-shaped funnel, settle them, let them run out bottom
+
+variable	name string funnel_pour
+
+thermo_modify	flush yes
+units 		si
+variable	PI equal 3.141592653589
+variable	seed equal 14314
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	xlo equal 10
+variable	xhi equal 40
+variable	ylo equal 10
+variable	yhi equal 40
+variable	zlo equal -20
+variable	zhi equal 50
+
+variable	xc equal 25
+variable	yc equal 25
+
+variable	zconehi equal 50
+variable	zconelo equal 10
+variable	zcyllo equal 0
+variable	radconelo equal 2
+variable	radconehi equal 20
+
+################################################
+# Particle sizes
+################################################
+
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable 	skin equal ${rhi}
+variable 	skin equal 0.5
+
+###############################################
+# Granular contact parameters
+###############################################
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	density equal 1.0
+variable	EYoung equal 10^5
+variable 	Poisson equal 2.0/7.0
+variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+${Poisson}))
+variable	GShear equal 100000/(2*(1+0.285714285714286))
+
+variable	gravity equal 1.0
+
+variable	reff equal 0.5*(${rhi}+${rlo})
+variable	reff equal 0.5*(0.5+${rlo})
+variable	reff equal 0.5*(0.5+0.25)
+variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
+variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
+variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
+variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
+variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
+variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
+
+## Typical way to set kn, kt, etc.:
+variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
+variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
+variable        kt equal 4.0*${GShear}/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
+variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)
+
+variable	a equal (-2.0*log(${coeffRes})/${PI})^2
+variable	a equal (-2.0*log(0.1)/${PI})^2
+variable	a equal (-2.0*log(0.1)/3.141592653589)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 903.503751814138*0.5
+
+variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
+variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
+
+variable	dt equal ${tcol}*0.05
+variable	dt equal 0.00210943016014969*0.05
+timestep	${dt}
+timestep	0.000105471508007485
+
+###############################################
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		off
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 ${zlo} ${zhi}
+region		boxreg block 10 40 10 40 -20 ${zhi}
+region		boxreg block 10 40 10 40 -20 50
+create_box	1 boxreg
+Created orthogonal box = (10 10 -20) to (40 40 50)
+  1 by 1 by 4 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
+pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.5 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 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 = 0
+  ghost atom cutoff = 0
+  binsize = 30, bins = 1 1 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/multi/atomonly/newtoff
+      stencil: full/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+# insertion region for fix/pour
+
+region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
+region	     	insreg cylinder z 25 25 10 30 50 side in units box
+
+# define cone and cylinder regions - see lammps doc on region command
+# note new open options
+
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 
+
+region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
+region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
+region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 
+
+region		hopreg union 2 conereg cylreg
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+
+fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
+fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1
+
+#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
+thermo_modify	flush yes lost warn
+
+# Initial run to fill up the cone
+
+run		20000
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 3000 every 59965 steps, 2000 by step 1
+Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
+   Step          CPU          Atoms        KinEng    
+         0   0                      0  -0            
+      1000   0.44807882          2000  -0            
+      2000   0.63550417          2000  -0            
+      3000   0.82082211          2000  -0            
+      4000   1.0004254           2000  -0            
+      5000   1.1738611           2000  -0            
+      6000   1.3426033           2000  -0            
+      7000   1.5076494           2000  -0            
+      8000   1.6673766           2000  -0            
+      9000   1.8244007           2000  -0            
+     10000   1.9794011           2000  -0            
+     11000   2.049584            2000  -0            
+     12000   2.1210622           2000  -0            
+     13000   2.1917604           2000  -0            
+     14000   2.2631006           2000  -0            
+     15000   2.3361511           2000  -0            
+     16000   2.4131306           2000  -0            
+     17000   2.4938482           2000  -0            
+     18000   2.5771299           2000  -0            
+     19000   2.6633207           2000  -0            
+     20000   2.7541527           2000  -0            
+Loop time of 2.75417 on 4 procs for 20000 steps with 2000 atoms
+
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.028725   | 0.079701   | 0.18206    |  21.3 |  2.89
+Neigh   | 0.0072627  | 0.013673   | 0.023071   |   5.0 |  0.50
+Comm    | 0.084562   | 0.18785    | 0.28115    |  18.6 |  6.82
+Output  | 0.00088257 | 0.0016453  | 0.0021961  |   1.2 |  0.06
+Modify  | 0.66551    | 1.1062     | 1.9324     |  46.7 | 40.16
+Other   |            | 1.365      |            |       | 49.57
+
+Nlocal:            500 ave         510 max         493 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:            154 ave         227 max          79 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:          415.5 ave         610 max         258 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 1662
+Ave neighs/atom = 0.831
+Neighbor list builds = 71
+Dangerous builds = 0
+unfix 		ins
+run		150000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
+   Step          CPU          Atoms        KinEng    
+     20000   0                   2000   6652.2957    
+     21000   0.064679537         2000   6807.2201    
+     22000   0.13180546          2000   6973.9359    
+     23000   0.20116485          2000   7142.3648    
+     24000   0.27404997          2000   7276.9717    
+     25000   0.35093997          2000   7369.4191    
+     26000   0.43258785          2000   7497.6526    
+     27000   0.51758599          2000   7638.946     
+     28000   0.60693744          2000   7780.0339    
+     29000   0.7014587           2000   7881.8177    
+     30000   0.80119592          2000   7967.2641    
+     31000   0.87335402          2000   7994.9273    
+     32000   0.95320537          2000   7937.0672    
+     33000   1.0398918           2000   7774.0508    
+     34000   1.1351184           2000   7591.1511    
+     35000   1.2382665           2000   7357.5032    
+     36000   1.3492928           2000   7147.3776    
+     37000   1.467685            2000   6980.0719    
+     38000   1.5926331           2000   6813.0872    
+     39000   1.7265338           2000   6657.0693    
+     40000   1.8700751           2000   6505.1155    
+     41000   1.9833133           2000   6330.2864    
+     42000   2.1004898           2000   6147.8022    
+     43000   2.2208699           2000   5932.9244    
+     44000   2.3442041           2000   5755.296     
+     45000   2.4697527           2000   5511.622     
+     46000   2.6055398           2000   5332.3171    
+     47000   2.7455054           2000   5162.4926    
+     48000   2.8851384           2000   5044.5764    
+     49000   3.0239861           2000   4901.1141    
+     50000   3.1614979           2000   4731.1949    
+     51000   3.2810383           2000   4575.418     
+     52000   3.4070575           2000   4428.9425    
+     53000   3.5378444           2000   4291.7282    
+     54000   3.6714875           2000   4154.1885    
+     55000   3.8108149           2000   3994.9402    
+     56000   3.9546982           2000   3855.5977    
+     57000   4.0997167           2000   3672.9504    
+     58000   4.2491708           2000   3435.3395    
+     59000   4.408196            2000   3200.7379    
+     60000   4.5700117           2000   2986.5411    
+     61000   4.723306            2000   2747.3628    
+     62000   4.878128            2000   2542.0805    
+     63000   5.0341944           2000   2336.7687    
+     64000   5.1923913           2000   2151.6388    
+     65000   5.3556896           2000   1933.6773    
+     66000   5.5238885           2000   1699.0747    
+     67000   5.6948336           2000   1467.7209    
+     68000   5.8690421           2000   1227.3577    
+     69000   6.0509636           2000   1016.2766    
+     70000   6.2387022           2000   812.90843    
+     71000   6.4073364           2000   632.88108    
+     72000   6.577617            2000   470.67731    
+     73000   6.7470437           2000   360.47748    
+     74000   6.9135965           2000   286.10584    
+     75000   7.0795553           2000   229.70386    
+     76000   7.2433614           2000   179.62654    
+     77000   7.4108991           2000   142.40417    
+     78000   7.5787629           2000   113.55745    
+     79000   7.7455158           2000   93.787669    
+     80000   7.9119881           2000   80.646319    
+     81000   8.0788298           2000   70.944319    
+     82000   8.2481597           2000   59.2275      
+     83000   8.4164166           2000   49.633808    
+     84000   8.5904585           2000   42.882698    
+     85000   8.768017            2000   36.841824    
+     86000   8.9516342           2000   31.776681    
+     87000   9.1361653           2000   28.25076     
+     88000   9.3230302           2000   25.228966    
+     89000   9.5111334           2000   22.593627    
+     90000   9.7013966           2000   21.15796     
+     91000   9.8899455           2000   19.941629    
+     92000   10.082329           2000   18.375654    
+     93000   10.276769           2000   17.056701    
+     94000   10.474742           2000   16.192511    
+     95000   10.674727           2000   15.572922    
+     96000   10.874807           2000   14.827788    
+     97000   11.075291           2000   13.919613    
+     98000   11.275072           2000   13.19525     
+     99000   11.475537           2000   11.993376    
+    100000   11.677999           2000   11.258787    
+    101000   11.88024            2000   10.641688    
+    102000   12.084353           2000   10.430435    
+    103000   12.288658           2000   9.518069     
+    104000   12.4935             2000   9.1332086    
+    105000   12.70028            2000   9.2151611    
+    106000   12.908347           2000   9.0035132    
+    107000   13.116082           2000   8.7835861    
+    108000   13.324126           2000   8.5124479    
+    109000   13.53208            2000   8.2975453    
+    110000   13.740687           2000   8.3483043    
+    111000   13.948107           2000   8.4658572    
+    112000   14.156079           2000   8.4771784    
+    113000   14.364341           2000   7.8937975    
+    114000   14.574123           2000   7.2472953    
+    115000   14.783651           2000   6.5812074    
+    116000   14.99421            2000   5.5651566    
+    117000   15.204441           2000   5.3015807    
+    118000   15.415336           2000   5.0133941    
+    119000   15.625609           2000   4.8746036    
+    120000   15.836675           2000   4.9133073    
+    121000   16.047261           2000   4.3337392    
+    122000   16.257951           2000   4.3374836    
+    123000   16.468869           2000   4.3721818    
+    124000   16.680533           2000   4.3894508    
+    125000   16.890783           2000   4.1811774    
+    126000   17.103698           2000   4.3011002    
+    127000   17.315003           2000   4.442228     
+    128000   17.526696           2000   4.6170394    
+    129000   17.738415           2000   4.8184318    
+    130000   17.952565           2000   4.8442096    
+    131000   18.165389           2000   4.9668117    
+    132000   18.378094           2000   4.8364562    
+    133000   18.592482           2000   4.6658645    
+    134000   18.804443           2000   4.5758487    
+    135000   19.016578           2000   4.7251949    
+    136000   19.230118           2000   4.5846492    
+    137000   19.443202           2000   4.7565986    
+    138000   19.656431           2000   4.8186623    
+    139000   19.867627           2000   4.6571647    
+    140000   20.080227           2000   4.0730143    
+    141000   20.292696           2000   4.0605542    
+    142000   20.503397           2000   4.1457179    
+    143000   20.714516           2000   4.3418042    
+    144000   20.925902           2000   4.0323813    
+    145000   21.139161           2000   3.8064958    
+    146000   21.352466           2000   3.1802044    
+    147000   21.564201           2000   2.7947641    
+    148000   21.772853           2000   2.7384164    
+    149000   21.983847           2000   2.7428829    
+    150000   22.196524           2000   2.7802186    
+    151000   22.408229           2000   2.6703451    
+    152000   22.619074           2000   2.3357647    
+    153000   22.829739           2000   1.9855305    
+    154000   23.039835           2000   1.9442713    
+    155000   23.252204           2000   1.7348027    
+    156000   23.464375           2000   1.5699942    
+    157000   23.677869           2000   1.5224944    
+    158000   23.888064           2000   1.4850914    
+    159000   24.099703           2000   1.4461048    
+    160000   24.312523           2000   1.3759525    
+    161000   24.522295           2000   0.83754463   
+    162000   24.733904           2000   0.7952922    
+    163000   24.944962           2000   0.69670143   
+    164000   25.155399           2000   0.66253723   
+    165000   25.36618            2000   0.64602969   
+    166000   25.576713           2000   0.60229858   
+    167000   25.788559           2000   0.5757589    
+    168000   25.998455           2000   0.5996023    
+    169000   26.209944           2000   0.62130448   
+    170000   26.420855           2000   0.63888277   
+Loop time of 26.4209 on 4 procs for 150000 steps with 2000 atoms
+
+97.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.6691     | 8.9481     | 11.368     |  85.5 | 33.87
+Neigh   | 0.087705   | 0.14369    | 0.18343    |   9.2 |  0.54
+Comm    | 1.9172     | 3.5612     | 4.2565     |  50.7 | 13.48
+Output  | 0.0045151  | 0.0090615  | 0.016477   |   4.7 |  0.03
+Modify  | 5.4247     | 7.6604     | 9.1464     |  49.8 | 28.99
+Other   |            | 6.099      |            |       | 23.08
+
+Nlocal:            500 ave         538 max         419 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Nghost:          445.5 ave         688 max         200 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:        4500.25 ave        5610 max        3443 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 18001
+Ave neighs/atom = 9.0005
+Neighbor list builds = 362
+Dangerous builds = 0
+
+# remove "plug" - need to redefine cylinder region & union
+
+region	  	cylreg delete
+region		hopreg delete
+region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
+region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
+region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 
+
+region		hopreg union 2 cylreg conereg
+
+unfix		hopper3
+fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
+fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
+
+run		100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
+   Step          CPU          Atoms        KinEng    
+    170000   0                   2000   0.63888277   
+    171000   0.21222344          2000   1.4139245    
+    172000   0.42521156          2000   2.2400138    
+    173000   0.63924412          2000   3.8034979    
+    174000   0.85157975          2000   6.116727     
+    175000   1.065247            2000   8.9536458    
+    176000   1.2785495           2000   12.74348     
+    177000   1.4916668           2000   17.410816    
+    178000   1.7042214           2000   22.879174    
+    179000   1.9186225           2000   28.966022    
+    180000   2.1345716           2000   35.449239    
+    181000   2.3486488           2000   42.694882    
+    182000   2.5624316           2000   50.913279    
+    183000   2.7760261           2000   60.098465    
+    184000   2.9883219           2000   70.133474    
+    185000   3.2007559           2000   80.950013    
+    186000   3.4107595           2000   92.495525    
+    187000   3.6204368           2000   104.83034    
+    188000   3.8298085           2000   118.04659    
+    189000   4.0383423           2000   132.7403     
+    190000   4.2477798           2000   148.31955    
+    191000   4.4421194           2000   164.26321    
+    192000   4.6373112           2000   180.6933     
+    193000   4.829991            2000   197.72012    
+    194000   5.02323             2000   215.43637    
+    195000   5.2162947           2000   234.29738    
+    196000   5.4075928           2000   254.03407    
+    197000   5.5974162           2000   274.58626    
+    198000   5.7869821           2000   296.88915    
+    199000   5.976701            2000   320.45001    
+    200000   6.1650648           2000   344.75891    
+    201000   6.3509022           2000   370.14016    
+    202000   6.5363704           2000   395.72827    
+    203000   6.7222457           2000   420.42026    
+    204000   6.9107246           2000   446.08079    
+    205000   7.0996055           2000   473.62963    
+    206000   7.2878276           2000   501.05693    
+    207000   7.4753237           2000   530.40427    
+    208000   7.6643827           2000   560.62015    
+    209000   7.8553563           2000   593.00113    
+    210000   8.0454619           2000   626.36661    
+    211000   8.2342734           2000   661.34861    
+    212000   8.4248464           2000   697.41001    
+    213000   8.6166264           2000   735.12299    
+    214000   8.8061303           2000   773.89126    
+    215000   8.9932827           2000   813.83268    
+    216000   9.1797117           2000   854.63669    
+    217000   9.3642361           2000   896.59089    
+    218000   9.5486397           2000   938.70251    
+    219000   9.7300675           2000   982.10773    
+    220000   9.9142511           2000   1025.2953    
+    221000   10.098593           2000   1069.8382    
+    222000   10.284654           2000   1115.4449    
+    223000   10.47145            2000   1161.6742    
+    224000   10.656994           2000   1211.289     
+    225000   10.839264           2000   1262.8074    
+    226000   11.019273           2000   1316.6353    
+    227000   11.198463           2000   1370.7434    
+WARNING: Lost atoms: original 2000 current 1991 (../thermo.cpp:499)
+    228000   11.377846           1991   1382.0924    
+    229000   11.557302           1986   1407.1543    
+    230000   11.737106           1975   1415.708     
+    231000   11.915389           1968   1430.6498    
+    232000   12.095672           1957   1421.0352    
+    233000   12.275267           1939   1376.0322    
+    234000   12.452526           1925   1350.1292    
+    235000   12.629207           1912   1337.0529    
+    236000   12.80204            1893   1273.2219    
+    237000   12.975817           1879   1207.0473    
+    238000   13.152228           1861   1132.0109    
+    239000   13.331267           1846   1083.1042    
+    240000   13.510046           1826   1004.3265    
+    241000   13.67647            1819   989.36186    
+    242000   13.842216           1812   983.26132    
+    243000   14.006163           1805   985.79932    
+    244000   14.168208           1794   936.34844    
+    245000   14.331979           1784   889.17423    
+    246000   14.495868           1770   846.65018    
+    247000   14.662081           1753   751.16306    
+    248000   14.830163           1740   709.23095    
+    249000   14.999432           1732   687.61586    
+    250000   15.166285           1721   638.82967    
+    251000   15.331363           1714   618.71543    
+    252000   15.493524           1709   611.25444    
+    253000   15.651829           1705   606.6846     
+    254000   15.809586           1702   601.7236     
+    255000   15.966097           1697   575.97244    
+    256000   16.12731            1695   577.1712     
+    257000   16.292272           1691   576.93668    
+    258000   16.460463           1688   586.63687    
+    259000   16.628863           1686   581.52487    
+    260000   16.797813           1682   566.49544    
+    261000   16.95041            1681   586.18628    
+    262000   17.101549           1678   582.11927    
+    263000   17.251379           1675   589.96041    
+    264000   17.403824           1672   577.55581    
+    265000   17.556094           1669   570.45998    
+    266000   17.710318           1666   574.0576     
+    267000   17.865801           1662   578.07385    
+    268000   18.019798           1660   587.65705    
+    269000   18.177178           1657   584.43358    
+    270000   18.332227           1654   591.22601    
+Loop time of 18.3323 on 4 procs for 100000 steps with 1654 atoms
+
+96.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.7775     | 6.3596     | 9.2369     |  92.3 | 34.69
+Neigh   | 0.088842   | 0.10453    | 0.12331    |   4.2 |  0.57
+Comm    | 1.1938     | 2.7006     | 3.3247     |  53.6 | 14.73
+Output  | 0.0013814  | 0.0063655  | 0.013334   |   5.5 |  0.03
+Modify  | 4.3454     | 4.8952     | 5.3813     |  20.7 | 26.70
+Other   |            | 4.266      |            |       | 23.27
+
+Nlocal:          413.5 ave         429 max         408 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:         408.25 ave         653 max         182 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:        3486.25 ave        4367 max        2213 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 13945
+Ave neighs/atom = 8.4310762
+Neighbor list builds = 227
+Dangerous builds = 0
+Total wall time: 0:00:47

examples/granregion/log.27Jun24.granregion.mixer.g++.1

@@ -0,0 +1,642 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+variable	name string mixer
+
+thermo_modify	flush yes
+variable	seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable	rlo equal 0.3
+variable	rhi equal 0.6
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.3
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.6
+variable 	skin equal ${rhi}
+variable 	skin equal 0.6
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	kn equal 10^5
+variable	kt equal 0.2*${kn}
+variable	kt equal 0.2*100000
+
+variable	gravity equal 1.0
+variable	density equal 1.0
+
+variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable	a equal (-2.0*log(${coeffRes})/PI)^2
+variable	a equal (-2.0*log(0.1)/PI)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 806.699778405191*0.5
+
+variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable	dt equal ${tcol}*0.02
+variable	dt equal 0.00236257621510454*0.02
+timestep	${dt}
+timestep	4.72515243020908e-05
+
+###############################################
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		on
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block 0 20 0 20 0 20
+create_box	1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.6 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 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 = 0
+  ghost atom cutoff = 0
+  binsize = 20, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/multi/atomonly/newton
+      stencil: half/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region	     	insreg cylinder z 10 10 8 10 18 side in units box
+region	    	cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable	theta equal (step/400000)*2*PI
+
+region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
+region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
+
+region		mixer intersect 3 cylreg b1 b2 side in
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
+
+#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
+thermo_modify	flush yes lost warn
+
+run		200000
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+         0   0                      0  -0              0            
+      1000   0.081165379          444  -0              0.015707963  
+      2000   0.15754332           444  -0              0.031415927  
+      3000   0.23012784           444  -0              0.04712389   
+      4000   0.30324079           444  -0              0.062831853  
+      5000   0.37566627           444  -0              0.078539816  
+      6000   0.4478183            444  -0              0.09424778   
+      7000   0.52130598           444  -0              0.10995574   
+      8000   0.59583276           444  -0              0.12566371   
+      9000   0.67333641           444  -0              0.14137167   
+     10000   0.75133989           444  -0              0.15707963   
+     11000   0.88621821           444  -0              0.1727876    
+     12000   0.96223543           444  -0              0.18849556   
+     13000   1.0406719            444  -0              0.20420352   
+     14000   1.1209824            444  -0              0.21991149   
+     15000   1.2017612            444  -0              0.23561945   
+     16000   1.2818653            444  -0              0.25132741   
+     17000   1.36192              444  -0              0.26703538   
+     18000   1.4377702            444  -0              0.28274334   
+     19000   1.5144381            444  -0              0.2984513    
+     20000   1.5913902            444  -0              0.31415927   
+     21000   1.6673472            444  -0              0.32986723   
+     22000   1.7434481            444  -0              0.34557519   
+     23000   1.8190585            444  -0              0.36128316   
+     24000   1.8962389            444  -0              0.37699112   
+     25000   1.9736636            444  -0              0.39269908   
+     26000   2.0534547            444  -0              0.40840704   
+     27000   2.1298466            444  -0              0.42411501   
+     28000   2.206882             444  -0              0.43982297   
+     29000   2.2836177            444  -0              0.45553093   
+     30000   2.4525793            444  -0              0.4712389    
+     31000   2.528444             444  -0              0.48694686   
+     32000   2.6062516            444  -0              0.50265482   
+     33000   2.6838811            444  -0              0.51836279   
+     34000   2.7618967            444  -0              0.53407075   
+     35000   3.1234167            444  -0              0.54977871   
+     36000   3.1992217            444  -0              0.56548668   
+     37000   3.2744137            444  -0              0.58119464   
+     38000   3.3504088            444  -0              0.5969026    
+     39000   3.4259728            444  -0              0.61261057   
+     40000   3.5020768            444  -0              0.62831853   
+     41000   3.5794542            444  -0              0.64402649   
+     42000   3.657433             444  -0              0.65973446   
+     43000   3.7353763            444  -0              0.67544242   
+     44000   3.8131676            444  -0              0.69115038   
+     45000   3.8924163            444  -0              0.70685835   
+     46000   3.973914             444  -0              0.72256631   
+     47000   4.0525907            444  -0              0.73827427   
+     48000   4.131257             444  -0              0.75398224   
+     49000   4.2096226            444  -0              0.7696902    
+     50000   4.2879179            444  -0              0.78539816   
+     51000   4.3673368            444  -0              0.80110613   
+     52000   4.4496186            444  -0              0.81681409   
+     53000   4.5285675            444  -0              0.83252205   
+     54000   4.6132205            444  -0              0.84823002   
+     55000   4.6992461            444  -0              0.86393798   
+     56000   4.7864008            444  -0              0.87964594   
+     57000   4.8715403            444  -0              0.89535391   
+     58000   4.9547161            444  -0              0.91106187   
+     59000   5.0403186            444  -0              0.92676983   
+     60000   5.123722             444  -0              0.9424778    
+     61000   5.2068168            444  -0              0.95818576   
+     62000   5.2899206            444  -0              0.97389372   
+     63000   5.3725203            444  -0              0.98960169   
+     64000   5.4561614            444  -0              1.0053096    
+     65000   5.5399537            444  -0              1.0210176    
+     66000   5.6233183            444  -0              1.0367256    
+     67000   5.7075311            444  -0              1.0524335    
+     68000   5.7921332            444  -0              1.0681415    
+     69000   5.8772289            444  -0              1.0838495    
+     70000   5.9626083            444  -0              1.0995574    
+     71000   6.0468013            444  -0              1.1152654    
+     72000   6.1325358            444  -0              1.1309734    
+     73000   6.217391             444  -0              1.1466813    
+     74000   6.3029286            444  -0              1.1623893    
+     75000   6.3892387            444  -0              1.1780972    
+     76000   6.4757637            444  -0              1.1938052    
+     77000   6.5633899            444  -0              1.2095132    
+     78000   6.6494516            444  -0              1.2252211    
+     79000   6.7363426            444  -0              1.2409291    
+     80000   6.8243808            444  -0              1.2566371    
+     81000   6.9120999            444  -0              1.272345     
+     82000   7.0004402            444  -0              1.288053     
+     83000   7.0882632            444  -0              1.303761     
+     84000   7.176153             444  -0              1.3194689    
+     85000   7.2980017            888  -0              1.3351769    
+     86000   7.4665034            888  -0              1.3508848    
+     87000   7.634481             888  -0              1.3665928    
+     88000   7.8021372            888  -0              1.3823008    
+     89000   7.9705032            888  -0              1.3980087    
+     90000   8.1395213            888  -0              1.4137167    
+     91000   8.3093436            888  -0              1.4294247    
+     92000   8.4791404            888  -0              1.4451326    
+     93000   8.6448257            888  -0              1.4608406    
+     94000   8.8096695            888  -0              1.4765485    
+     95000   8.9806056            888  -0              1.4922565    
+     96000   9.1479017            888  -0              1.5079645    
+     97000   9.3159102            888  -0              1.5236724    
+     98000   9.4817887            888  -0              1.5393804    
+     99000   9.6484134            888  -0              1.5550884    
+    100000   9.8145145            888  -0              1.5707963    
+    101000   9.9833565            888  -0              1.5865043    
+    102000   10.153126            888  -0              1.6022123    
+    103000   10.32344             888  -0              1.6179202    
+    104000   10.493544            888  -0              1.6336282    
+    105000   10.663787            888  -0              1.6493361    
+    106000   10.834335            888  -0              1.6650441    
+    107000   11.004695            888  -0              1.6807521    
+    108000   11.175239            888  -0              1.69646      
+    109000   11.350053            888  -0              1.712168     
+    110000   11.525953            888  -0              1.727876     
+    111000   11.702706            888  -0              1.7435839    
+    112000   11.880308            888  -0              1.7592919    
+    113000   12.058561            888  -0              1.7749998    
+    114000   12.236372            888  -0              1.7907078    
+    115000   12.414617            888  -0              1.8064158    
+    116000   12.592501            888  -0              1.8221237    
+    117000   12.770926            888  -0              1.8378317    
+    118000   12.949072            888  -0              1.8535397    
+    119000   13.128801            888  -0              1.8692476    
+    120000   13.311101            888  -0              1.8849556    
+    121000   13.489781            888  -0              1.9006636    
+    122000   13.669833            888  -0              1.9163715    
+    123000   13.85109             888  -0              1.9320795    
+    124000   14.032358            888  -0              1.9477874    
+    125000   14.213661            888  -0              1.9634954    
+    126000   14.393846            888  -0              1.9792034    
+    127000   14.574645            888  -0              1.9949113    
+    128000   14.755261            888  -0              2.0106193    
+    129000   14.939145            888  -0              2.0263273    
+    130000   15.123073            888  -0              2.0420352    
+    131000   15.303459            888  -0              2.0577432    
+    132000   15.484755            888  -0              2.0734512    
+    133000   15.665288            888  -0              2.0891591    
+    134000   15.845779            888  -0              2.1048671    
+    135000   16.026283            888  -0              2.120575     
+    136000   16.20857             888  -0              2.136283     
+    137000   16.39054             888  -0              2.151991     
+    138000   16.574105            888  -0              2.1676989    
+    139000   16.758949            888  -0              2.1834069    
+    140000   16.943594            888  -0              2.1991149    
+    141000   17.127119            888  -0              2.2148228    
+    142000   17.311688            888  -0              2.2305308    
+    143000   17.498924            888  -0              2.2462387    
+    144000   17.68621             888  -0              2.2619467    
+    145000   17.873463            888  -0              2.2776547    
+    146000   18.061679            888  -0              2.2933626    
+    147000   18.248264            888  -0              2.3090706    
+    148000   18.434172            888  -0              2.3247786    
+    149000   18.620894            888  -0              2.3404865    
+    150000   18.807222            888  -0              2.3561945    
+    151000   18.993959            888  -0              2.3719025    
+    152000   19.183597            888  -0              2.3876104    
+    153000   19.372979            888  -0              2.4033184    
+    154000   19.560741            888  -0              2.4190263    
+    155000   19.760386            888  -0              2.4347343    
+    156000   19.968774            888  -0              2.4504423    
+    157000   20.179252            888  -0              2.4661502    
+    158000   20.388599            888  -0              2.4818582    
+    159000   20.598976            888  -0              2.4975662    
+    160000   20.80891             888  -0              2.5132741    
+    161000   21.026202            888  -0              2.5289821    
+    162000   21.239367            888  -0              2.54469      
+    163000   21.452486            888  -0              2.560398     
+    164000   21.665343            888  -0              2.576106     
+    165000   21.879421            888  -0              2.5918139    
+    166000   22.093404            888  -0              2.6075219    
+    167000   22.307097            888  -0              2.6232299    
+    168000   22.521133            888  -0              2.6389378    
+    169000   22.735535            888  -0              2.6546458    
+    170000   22.968021           1000  -0              2.6703538    
+    171000   23.205371           1000  -0              2.6860617    
+    172000   23.44698            1000  -0              2.7017697    
+    173000   23.689107           1000  -0              2.7174776    
+    174000   23.930244           1000  -0              2.7331856    
+    175000   24.168568           1000  -0              2.7488936    
+    176000   24.405774           1000  -0              2.7646015    
+    177000   24.645769           1000  -0              2.7803095    
+    178000   24.886311           1000  -0              2.7960175    
+    179000   25.129675           1000  -0              2.8117254    
+    180000   25.375354           1000  -0              2.8274334    
+    181000   25.620074           1000  -0              2.8431414    
+    182000   25.867063           1000  -0              2.8588493    
+    183000   26.111737           1000  -0              2.8745573    
+    184000   26.356693           1000  -0              2.8902652    
+    185000   26.601965           1000  -0              2.9059732    
+    186000   26.847594           1000  -0              2.9216812    
+    187000   27.09479            1000  -0              2.9373891    
+    188000   27.343645           1000  -0              2.9530971    
+    189000   27.593252           1000  -0              2.9688051    
+    190000   27.84598            1000  -0              2.984513     
+    191000   28.097785           1000  -0              3.000221     
+    192000   28.347653           1000  -0              3.0159289    
+    193000   28.588968           1000  -0              3.0316369    
+    194000   28.82728            1000  -0              3.0473449    
+    195000   29.066565           1000  -0              3.0630528    
+    196000   29.309153           1000  -0              3.0787608    
+    197000   29.894236           1000  -0              3.0944688    
+    198000   30.138713           1000  -0              3.1101767    
+    199000   30.381879           1000  -0              3.1258847    
+    200000   30.627512           1000  -0              3.1415927    
+Loop time of 30.6275 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 26659.225 tau/day, 6530.072 timesteps/s, 6.530 Matom-step/s
+97.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4017     | 2.4017     | 2.4017     |   0.0 |  7.84
+Neigh   | 0.038916   | 0.038916   | 0.038916   |   0.0 |  0.13
+Comm    | 0.35872    | 0.35872    | 0.35872    |   0.0 |  1.17
+Output  | 0.78641    | 0.78641    | 0.78641    |   0.0 |  2.57
+Modify  | 26.719     | 26.719     | 26.719     |   0.0 | 87.24
+Other   |            | 0.3225     |            |       |  1.05
+
+Nlocal:           1000 ave        1000 max        1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            186 ave         186 max         186 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           3782 ave        3782 max        3782 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3782
+Ave neighs/atom = 3.782
+Neighbor list builds = 200
+Dangerous builds = 0
+unfix 		ins
+run		200000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+    200000   0                   1000   1.0680935      3.1415927    
+    201000   0.23768219          1000   1.0599937      3.1573006    
+    202000   0.47603693          1000   1.0366355      3.1730086    
+    203000   0.71459797          1000   1.0189286      3.1887165    
+    204000   0.95145301          1000   1.001478       3.2044245    
+    205000   1.1869146           1000   0.99637635     3.2201325    
+    206000   1.4249684           1000   0.99361197     3.2358404    
+    207000   1.6635344           1000   0.99529657     3.2515484    
+    208000   1.8992251           1000   0.98997171     3.2672564    
+    209000   2.1484862           1000   0.97666133     3.2829643    
+    210000   2.4012768           1000   0.97683679     3.2986723    
+    211000   2.6554877           1000   0.98150752     3.3143802    
+    212000   2.9093673           1000   0.97585316     3.3300882    
+    213000   3.161481            1000   0.97389688     3.3457962    
+    214000   3.4184197           1000   0.96426468     3.3615041    
+    215000   3.6711643           1000   0.96552353     3.3772121    
+    216000   3.9243061           1000   0.97713174     3.3929201    
+    217000   4.1757021           1000   0.97062546     3.408628     
+    218000   4.4291788           1000   0.97111212     3.424336     
+    219000   4.6819445           1000   0.97645659     3.440044     
+    220000   4.9376967           1000   0.98148797     3.4557519    
+    221000   5.1883947           1000   0.97386268     3.4714599    
+    222000   5.4387287           1000   0.97322415     3.4871678    
+    223000   5.6878448           1000   0.95781163     3.5028758    
+    224000   5.9358535           1000   0.93919542     3.5185838    
+    225000   6.1822635           1000   0.9313702      3.5342917    
+    226000   6.4302601           1000   0.92788207     3.5499997    
+    227000   6.6795172           1000   0.91026919     3.5657077    
+    228000   6.9286832           1000   0.89557479     3.5814156    
+    229000   7.1797845           1000   0.89173643     3.5971236    
+    230000   7.432965            1000   0.89292723     3.6128316    
+    231000   7.6848123           1000   0.89944536     3.6285395    
+    232000   7.9361745           1000   0.89319113     3.6442475    
+    233000   8.1896078           1000   0.89273543     3.6599554    
+    234000   8.4447838           1000   0.87360829     3.6756634    
+    235000   8.7028153           1000   0.86841591     3.6913714    
+    236000   8.9582068           1000   0.86559907     3.7070793    
+    237000   9.2150326           1000   0.86231762     3.7227873    
+    238000   9.4701361           1000   0.85170772     3.7384953    
+    239000   9.7272256           1000   0.85616849     3.7542032    
+    240000   9.985268            1000   0.86809668     3.7699112    
+    241000   10.243685           1000   0.88066532     3.7856191    
+    242000   10.50579            1000   0.89440189     3.8013271    
+    243000   10.768046           1000   0.8939512      3.8170351    
+    244000   11.030389           1000   0.8963829      3.832743     
+    245000   11.29267            1000   0.88074176     3.848451     
+    246000   11.553505           1000   0.8733699      3.864159     
+    247000   11.81124            1000   0.86130993     3.8798669    
+    248000   12.068927           1000   0.86035503     3.8955749    
+    249000   12.326723           1000   0.84878437     3.9112829    
+    250000   12.584681           1000   0.83989297     3.9269908    
+    251000   12.841147           1000   0.82781463     3.9426988    
+    252000   13.101351           1000   0.8142641      3.9584067    
+    253000   13.361975           1000   0.80683745     3.9741147    
+    254000   13.621901           1000   0.809379       3.9898227    
+    255000   13.879382           1000   0.81147846     4.0055306    
+    256000   14.136754           1000   0.79574281     4.0212386    
+    257000   14.393097           1000   0.78339098     4.0369466    
+    258000   14.65084            1000   0.7799887      4.0526545    
+    259000   14.909563           1000   0.7848995      4.0683625    
+    260000   15.171732           1000   0.78284201     4.0840704    
+    261000   15.434923           1000   0.7776263      4.0997784    
+    262000   15.699673           1000   0.77405185     4.1154864    
+    263000   15.964731           1000   0.78130382     4.1311943    
+    264000   16.231068           1000   0.81006815     4.1469023    
+    265000   16.494447           1000   0.79467298     4.1626103    
+    266000   16.757296           1000   0.78592963     4.1783182    
+    267000   17.020773           1000   0.76857233     4.1940262    
+    268000   17.281914           1000   0.76483523     4.2097342    
+    269000   17.543254           1000   0.76549297     4.2254421    
+    270000   17.807266           1000   0.75564385     4.2411501    
+    271000   18.083451           1000   0.75445102     4.256858     
+    272000   18.34927            1000   0.7514406      4.272566     
+    273000   18.6133             1000   0.75170218     4.288274     
+    274000   18.874318           1000   0.76454717     4.3039819    
+    275000   19.137188           1000   0.75991671     4.3196899    
+    276000   19.398218           1000   0.75817752     4.3353979    
+    277000   19.65797            1000   0.7621338      4.3511058    
+    278000   19.917364           1000   0.77239256     4.3668138    
+    279000   20.178778           1000   0.7667469      4.3825218    
+    280000   20.441559           1000   0.75761494     4.3982297    
+    281000   20.704047           1000   0.74370218     4.4139377    
+    282000   20.967325           1000   0.734955       4.4296456    
+    283000   21.226371           1000   0.72783614     4.4453536    
+    284000   21.485188           1000   0.72349874     4.4610616    
+    285000   21.742828           1000   0.71585562     4.4767695    
+    286000   22.002099           1000   0.70846101     4.4924775    
+    287000   22.262387           1000   0.69307445     4.5081855    
+    288000   22.523992           1000   0.68469722     4.5238934    
+    289000   22.786885           1000   0.67892956     4.5396014    
+    290000   23.050769           1000   0.67872999     4.5553093    
+    291000   23.313704           1000   0.6820098      4.5710173    
+    292000   23.576713           1000   0.67663229     4.5867253    
+    293000   23.828165           1000   0.67477934     4.6024332    
+    294000   24.081047           1000   0.67452515     4.6181412    
+    295000   24.335392           1000   0.67341495     4.6338492    
+    296000   24.590438           1000   0.67888865     4.6495571    
+    297000   24.84277            1000   0.68373518     4.6652651    
+    298000   25.097993           1000   0.68612329     4.6809731    
+    299000   25.355621           1000   0.68169877     4.696681     
+    300000   25.612938           1000   0.68602699     4.712389     
+    301000   25.866694           1000   0.68485644     4.7280969    
+    302000   26.120968           1000   0.68101185     4.7438049    
+    303000   26.374411           1000   0.67663031     4.7595129    
+    304000   26.628686           1000   0.67771638     4.7752208    
+    305000   26.881546           1000   0.67525788     4.7909288    
+    306000   27.163762           1000   0.6709689      4.8066368    
+    307000   27.421347           1000   0.68328286     4.8223447    
+    308000   27.674664           1000   0.70273998     4.8380527    
+    309000   27.937573           1000   0.70461978     4.8537606    
+    310000   28.206728           1000   0.70307737     4.8694686    
+    311000   28.473159           1000   0.70087936     4.8851766    
+    312000   28.739452           1000   0.70449303     4.9008845    
+    313000   29.001716           1000   0.71030367     4.9165925    
+    314000   29.267562           1000   0.71113177     4.9323005    
+    315000   29.533541           1000   0.71089537     4.9480084    
+    316000   29.798996           1000   0.70713116     4.9637164    
+    317000   30.068605           1000   0.71002087     4.9794244    
+    318000   30.339303           1000   0.71804737     4.9951323    
+    319000   30.609227           1000   0.71925831     5.0108403    
+    320000   30.879193           1000   0.72835371     5.0265482    
+    321000   31.147328           1000   0.7236586      5.0422562    
+    322000   31.413246           1000   0.71432128     5.0579642    
+    323000   31.675418           1000   0.70905325     5.0736721    
+    324000   31.938939           1000   0.71323674     5.0893801    
+    325000   32.20437            1000   0.72466784     5.1050881    
+    326000   32.471213           1000   0.72956158     5.120796     
+    327000   32.739168           1000   0.74478918     5.136504     
+    328000   33.005983           1000   0.74404284     5.152212     
+    329000   33.273193           1000   0.74051597     5.1679199    
+    330000   33.541489           1000   0.73438585     5.1836279    
+    331000   33.805988           1000   0.73023911     5.1993358    
+    332000   34.071435           1000   0.7373459      5.2150438    
+    333000   34.337809           1000   0.73137848     5.2307518    
+    334000   34.602061           1000   0.72917991     5.2464597    
+    335000   34.87065            1000   0.72945658     5.2621677    
+    336000   35.140112           1000   0.72046325     5.2778757    
+    337000   35.411283           1000   0.72224629     5.2935836    
+    338000   35.681774           1000   0.72177721     5.3092916    
+    339000   35.952034           1000   0.72852277     5.3249995    
+    340000   36.220116           1000   0.73244024     5.3407075    
+    341000   36.484799           1000   0.74123436     5.3564155    
+    342000   36.752429           1000   0.74117339     5.3721234    
+    343000   37.019401           1000   0.74360263     5.3878314    
+    344000   37.284441           1000   0.74998018     5.4035394    
+    345000   37.548209           1000   0.75026985     5.4192473    
+    346000   37.812297           1000   0.74415875     5.4349553    
+    347000   38.078351           1000   0.73219169     5.4506633    
+    348000   38.343692           1000   0.72316753     5.4663712    
+    349000   38.60829            1000   0.71747804     5.4820792    
+    350000   38.873334           1000   0.72055215     5.4977871    
+    351000   39.135591           1000   0.71525775     5.5134951    
+    352000   39.397948           1000   0.7157435      5.5292031    
+    353000   39.65874            1000   0.71883293     5.544911     
+    354000   39.921649           1000   0.72106381     5.560619     
+    355000   40.184118           1000   0.7126019      5.576327     
+    356000   40.44828            1000   0.70018005     5.5920349    
+    357000   40.711808           1000   0.6948238      5.6077429    
+    358000   40.974553           1000   0.70261087     5.6234508    
+    359000   41.240667           1000   0.70651692     5.6391588    
+    360000   41.508869           1000   0.71812614     5.6548668    
+    361000   41.775889           1000   0.72247116     5.6705747    
+    362000   42.044747           1000   0.73675936     5.6862827    
+    363000   42.311154           1000   0.75136966     5.7019907    
+    364000   42.577458           1000   0.75745313     5.7176986    
+    365000   42.846131           1000   0.7541109      5.7334066    
+    366000   43.113639           1000   0.75340643     5.7491146    
+    367000   43.3804             1000   0.74817232     5.7648225    
+    368000   43.644839           1000   0.73555712     5.7805305    
+    369000   43.907875           1000   0.72911144     5.7962384    
+    370000   44.173474           1000   0.72223387     5.8119464    
+    371000   44.435762           1000   0.72012879     5.8276544    
+    372000   44.698339           1000   0.72050435     5.8433623    
+    373000   44.96325            1000   0.72789287     5.8590703    
+    374000   45.228536           1000   0.74234609     5.8747783    
+    375000   45.49447            1000   0.74808952     5.8904862    
+    376000   45.76007            1000   0.74096035     5.9061942    
+    377000   46.027203           1000   0.74052775     5.9219022    
+    378000   46.294627           1000   0.74206885     5.9376101    
+    379000   46.567974           1000   0.74385723     5.9533181    
+    380000   46.837323           1000   0.74901717     5.969026     
+    381000   47.104723           1000   0.760668       5.984734     
+    382000   47.37249            1000   0.76622105     6.000442     
+    383000   47.642871           1000   0.77784236     6.0161499    
+    384000   47.913238           1000   0.78443266     6.0318579    
+    385000   48.179637           1000   0.77604024     6.0475659    
+    386000   48.444304           1000   0.76126822     6.0632738    
+    387000   48.708424           1000   0.74932674     6.0789818    
+    388000   48.972518           1000   0.7394025      6.0946897    
+    389000   49.236663           1000   0.73446106     6.1103977    
+    390000   49.502321           1000   0.73226431     6.1261057    
+    391000   49.772781           1000   0.72676072     6.1418136    
+    392000   50.047483           1000   0.7283395      6.1575216    
+    393000   50.308297           1000   0.7289238      6.1732296    
+    394000   50.564792           1000   0.72479408     6.1889375    
+    395000   50.819957           1000   0.71014812     6.2046455    
+    396000   51.078032           1000   0.70351995     6.2203535    
+    397000   51.336319           1000   0.70221306     6.2360614    
+    398000   51.593057           1000   0.70748482     6.2517694    
+    399000   51.853527           1000   0.7046252      6.2674773    
+    400000   52.1092             1000   0.70581734     6.2831853    
+Loop time of 52.1092 on 1 procs for 200000 steps with 1000 atoms
+
+Performance: 15669.134 tau/day, 3838.093 timesteps/s, 3.838 Matom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7952     | 7.7952     | 7.7952     |   0.0 | 14.96
+Neigh   | 0.062504   | 0.062504   | 0.062504   |   0.0 |  0.12
+Comm    | 1.0937     | 1.0937     | 1.0937     |   0.0 |  2.10
+Output  | 0.0038447  | 0.0038447  | 0.0038447  |   0.0 |  0.01
+Modify  | 42.69      | 42.69      | 42.69      |   0.0 | 81.92
+Other   |            | 0.4642     |            |       |  0.89
+
+Nlocal:           1000 ave        1000 max        1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            285 ave         285 max         285 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           5094 ave        5094 max        5094 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5094
+Ave neighs/atom = 5.094
+Neighbor list builds = 158
+Dangerous builds = 0
+Total wall time: 0:01:22

examples/granregion/log.27Jun24.granregion.mixer.g++.4

@@ -0,0 +1,642 @@
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
+variable	name string mixer
+
+thermo_modify	flush yes
+variable	seed equal 14314
+
+###############################################
+# Particle parameters
+################################################
+
+variable	rlo equal 0.3
+variable	rhi equal 0.6
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.3
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.6
+variable 	skin equal ${rhi}
+variable 	skin equal 0.6
+
+variable	coeffRes equal 0.1
+variable	coeffFric equal 0.5
+
+variable	kn equal 10^5
+variable	kt equal 0.2*${kn}
+variable	kt equal 0.2*100000
+
+variable	gravity equal 1.0
+variable	density equal 1.0
+
+variable	min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
+variable	min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
+variable	a equal (-2.0*log(${coeffRes})/PI)^2
+variable	a equal (-2.0*log(0.1)/PI)^2
+variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
+variable        gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
+variable        gamma_t equal ${gamma_n}*0.5
+variable        gamma_t equal 806.699778405191*0.5
+
+variable	tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
+variable	tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
+
+variable	dt equal ${tcol}*0.02
+variable	dt equal 0.00236257621510454*0.02
+timestep	${dt}
+timestep	4.72515243020908e-05
+
+###############################################
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+newton 		on
+atom_style	sphere
+
+boundary	p p f
+
+region		boxreg block 0 20 0 20 0 20
+create_box	1 boxreg
+Created orthogonal box = (0 0 0) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+
+pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
+pair_style	gran/hertz/history 		100000 20000 806.699778405191 403.349889202595 0.5 1
+pair_coeff	* *
+
+neighbor        ${skin} multi
+neighbor        0.6 multi
+thermo 		${logfreq}
+thermo 		1000
+
+comm_style	brick
+comm_modify 	mode multi group all vel yes
+balance		1.1 shift xyz 20 1.1
+Balancing ...
+Generated 0 of 0 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 = 0
+  ghost atom cutoff = 0
+  binsize = 20, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hertz/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/multi/atomonly/newton
+      stencil: half/multi/3d
+      bin: multi
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
+fix		bal all balance 10000 1.1 shift xyz 20 1.01
+
+####################### Options specific to pouring #########################
+
+region	     	insreg cylinder z 10 10 8 10 18 side in units box
+region	    	cylreg cylinder z 10 10 10 0 20 side in units box
+
+variable	theta equal (step/400000)*2*PI
+
+region          b1 block 2 18 9 11 0 4 side out                 rotate v_theta 10 10 0 0 0 1 units box
+region          b2 block 9 11 2 18 0 3.99999 side out                 rotate v_theta 10 10 0 0 0 1 units box
+
+region		mixer intersect 3 cylreg b1 b2 side in
+
+fix		grav all gravity ${gravity} vector 0 0 -1
+fix		grav all gravity 1 vector 0 0 -1
+fix		1 all nve/sphere
+
+fix		mixwall all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
+fix		mixwall all wall/gran/region hertz/history                 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
+
+fix		ins all pour 1000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 ${dhi} dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens ${density} ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 ${density}
+fix		ins all pour 1000 1 42424 region insreg 		diam range 0.6 1.2 dens 1 1
+
+#dump		1 all custom ${dumpfreq} ${name}_pour.dump #		id type mass diameter x y z
+
+#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 1.5 #                box no 0.0 axes no 0.0 0.0
+#dump_modify	2 pad 6
+
+thermo_style	custom step cpu atoms ke v_theta
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
+thermo_modify	flush yes lost warn
+
+run		200000
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 444 every 84653 steps, 1000 by step 169307
+Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+         0   0                      0  -0              0            
+      1000   0.088111932          444  -0              0.015707963  
+      2000   0.14514013           444  -0              0.031415927  
+      3000   0.19901283           444  -0              0.04712389   
+      4000   0.25271154           444  -0              0.062831853  
+      5000   0.30627277           444  -0              0.078539816  
+      6000   0.35966654           444  -0              0.09424778   
+      7000   0.41280835           444  -0              0.10995574   
+      8000   0.46584491           444  -0              0.12566371   
+      9000   0.51843618           444  -0              0.14137167   
+     10000   0.57151612           444  -0              0.15707963   
+     11000   0.61192936           444  -0              0.1727876    
+     12000   0.65265862           444  -0              0.18849556   
+     13000   0.69377116           444  -0              0.20420352   
+     14000   0.73526123           444  -0              0.21991149   
+     15000   0.77783987           444  -0              0.23561945   
+     16000   0.82128542           444  -0              0.25132741   
+     17000   0.86603751           444  -0              0.26703538   
+     18000   0.90981059           444  -0              0.28274334   
+     19000   0.95383173           444  -0              0.2984513    
+     20000   0.99782061           444  -0              0.31415927   
+     21000   1.0370303            444  -0              0.32986723   
+     22000   1.0764103            444  -0              0.34557519   
+     23000   1.1154891            444  -0              0.36128316   
+     24000   1.1549694            444  -0              0.37699112   
+     25000   1.1953727            444  -0              0.39269908   
+     26000   1.2364474            444  -0              0.40840704   
+     27000   1.2777508            444  -0              0.42411501   
+     28000   1.3195763            444  -0              0.43982297   
+     29000   1.3618971            444  -0              0.45553093   
+     30000   1.404607             444  -0              0.4712389    
+     31000   1.4428952            444  -0              0.48694686   
+     32000   1.4818254            444  -0              0.50265482   
+     33000   1.5205701            444  -0              0.51836279   
+     34000   1.559401             444  -0              0.53407075   
+     35000   1.5987318            444  -0              0.54977871   
+     36000   1.6379014            444  -0              0.56548668   
+     37000   1.6781504            444  -0              0.58119464   
+     38000   1.7190533            444  -0              0.5969026    
+     39000   1.7604269            444  -0              0.61261057   
+     40000   1.8019216            444  -0              0.62831853   
+     41000   1.8402535            444  -0              0.64402649   
+     42000   1.8791646            444  -0              0.65973446   
+     43000   1.9188237            444  -0              0.67544242   
+     44000   1.9584939            444  -0              0.69115038   
+     45000   1.9992043            444  -0              0.70685835   
+     46000   2.04024              444  -0              0.72256631   
+     47000   2.0814641            444  -0              0.73827427   
+     48000   2.123407             444  -0              0.75398224   
+     49000   2.165223             444  -0              0.7696902    
+     50000   2.2074047            444  -0              0.78539816   
+     51000   2.2456301            444  -0              0.80110613   
+     52000   2.2839661            444  -0              0.81681409   
+     53000   2.3227369            444  -0              0.83252205   
+     54000   2.3618801            444  -0              0.84823002   
+     55000   2.401451             444  -0              0.86393798   
+     56000   2.4414565            444  -0              0.87964594   
+     57000   2.4813918            444  -0              0.89535391   
+     58000   2.5221831            444  -0              0.91106187   
+     59000   2.5637488            444  -0              0.92676983   
+     60000   2.6055953            444  -0              0.9424778    
+     61000   2.6456326            444  -0              0.95818576   
+     62000   2.6857299            444  -0              0.97389372   
+     63000   2.7259082            444  -0              0.98960169   
+     64000   2.7665767            444  -0              1.0053096    
+     65000   2.8082755            444  -0              1.0210176    
+     66000   2.8503373            444  -0              1.0367256    
+     67000   2.8938769            444  -0              1.0524335    
+     68000   2.9373604            444  -0              1.0681415    
+     69000   2.9810674            444  -0              1.0838495    
+     70000   3.0246587            444  -0              1.0995574    
+     71000   3.0655215            444  -0              1.1152654    
+     72000   3.1075971            444  -0              1.1309734    
+     73000   3.1497688            444  -0              1.1466813    
+     74000   3.1915941            444  -0              1.1623893    
+     75000   3.2352454            444  -0              1.1780972    
+     76000   3.2799164            444  -0              1.1938052    
+     77000   3.3245184            444  -0              1.2095132    
+     78000   3.3693626            444  -0              1.2252211    
+     79000   3.4144403            444  -0              1.2409291    
+     80000   3.4609593            444  -0              1.2566371    
+     81000   3.5037956            444  -0              1.272345     
+     82000   3.5460391            444  -0              1.288053     
+     83000   3.5890988            444  -0              1.303761     
+     84000   3.6329781            444  -0              1.3194689    
+     85000   3.6969324            888  -0              1.3351769    
+     86000   3.7764618            888  -0              1.3508848    
+     87000   3.855693             888  -0              1.3665928    
+     88000   3.9341142            888  -0              1.3823008    
+     89000   4.0125134            888  -0              1.3980087    
+     90000   4.0915705            888  -0              1.4137167    
+     91000   4.1526623            888  -0              1.4294247    
+     92000   4.2142478            888  -0              1.4451326    
+     93000   4.2776631            888  -0              1.4608406    
+     94000   4.3413071            888  -0              1.4765485    
+     95000   4.4047448            888  -0              1.4922565    
+     96000   4.4682904            888  -0              1.5079645    
+     97000   4.5328349            888  -0              1.5236724    
+     98000   4.5968674            888  -0              1.5393804    
+     99000   4.6612212            888  -0              1.5550884    
+    100000   4.7263166            888  -0              1.5707963    
+    101000   4.7899218            888  -0              1.5865043    
+    102000   4.8548615            888  -0              1.6022123    
+    103000   4.9201477            888  -0              1.6179202    
+    104000   4.9848694            888  -0              1.6336282    
+    105000   5.0511867            888  -0              1.6493361    
+    106000   5.1167808            888  -0              1.6650441    
+    107000   5.1831053            888  -0              1.6807521    
+    108000   5.250398             888  -0              1.69646      
+    109000   5.3169814            888  -0              1.712168     
+    110000   5.3857277            888  -0              1.727876     
+    111000   5.4527691            888  -0              1.7435839    
+    112000   5.5214505            888  -0              1.7592919    
+    113000   5.5892604            888  -0              1.7749998    
+    114000   5.6579089            888  -0              1.7907078    
+    115000   5.7279007            888  -0              1.8064158    
+    116000   5.7971602            888  -0              1.8221237    
+    117000   5.867895             888  -0              1.8378317    
+    118000   5.9400645            888  -0              1.8535397    
+    119000   6.0117635            888  -0              1.8692476    
+    120000   6.0851132            888  -0              1.8849556    
+    121000   6.1539323            888  -0              1.9006636    
+    122000   6.2231605            888  -0              1.9163715    
+    123000   6.2930557            888  -0              1.9320795    
+    124000   6.3632912            888  -0              1.9477874    
+    125000   6.4336358            888  -0              1.9634954    
+    126000   6.5042786            888  -0              1.9792034    
+    127000   6.5747889            888  -0              1.9949113    
+    128000   6.6452984            888  -0              2.0106193    
+    129000   6.7169482            888  -0              2.0263273    
+    130000   6.7865487            888  -0              2.0420352    
+    131000   6.8576956            888  -0              2.0577432    
+    132000   6.9296299            888  -0              2.0734512    
+    133000   7.0024987            888  -0              2.0891591    
+    134000   7.0753126            888  -0              2.1048671    
+    135000   7.1492322            888  -0              2.120575     
+    136000   7.2243825            888  -0              2.136283     
+    137000   7.3005224            888  -0              2.151991     
+    138000   7.378849             888  -0              2.1676989    
+    139000   7.4574391            888  -0              2.1834069    
+    140000   7.5370788            888  -0              2.1991149    
+    141000   7.6104683            888  -0              2.2148228    
+    142000   7.6840599            888  -0              2.2305308    
+    143000   7.7594508            888  -0              2.2462387    
+    144000   7.8338839            888  -0              2.2619467    
+    145000   7.9104471            888  -0              2.2776547    
+    146000   7.9862744            888  -0              2.2933626    
+    147000   8.0621903            888  -0              2.3090706    
+    148000   8.1403104            888  -0              2.3247786    
+    149000   8.2192751            888  -0              2.3404865    
+    150000   8.2988877            888  -0              2.3561945    
+    151000   8.3771585            888  -0              2.3719025    
+    152000   8.4559615            888  -0              2.3876104    
+    153000   8.5340116            888  -0              2.4033184    
+    154000   8.612764             888  -0              2.4190263    
+    155000   8.6925848            888  -0              2.4347343    
+    156000   8.7739307            888  -0              2.4504423    
+    157000   8.8541471            888  -0              2.4661502    
+    158000   8.9371669            888  -0              2.4818582    
+    159000   9.0204947            888  -0              2.4975662    
+    160000   9.1037153            888  -0              2.5132741    
+    161000   9.1860231            888  -0              2.5289821    
+    162000   9.2695251            888  -0              2.54469      
+    163000   9.3537318            888  -0              2.560398     
+    164000   9.4396954            888  -0              2.576106     
+    165000   9.5265215            888  -0              2.5918139    
+    166000   9.6140047            888  -0              2.6075219    
+    167000   9.7019854            888  -0              2.6232299    
+    168000   9.7918781            888  -0              2.6389378    
+    169000   9.8831043            888  -0              2.6546458    
+    170000   9.9785874           1000  -0              2.6703538    
+    171000   10.073548           1000  -0              2.6860617    
+    172000   10.164183           1000  -0              2.7017697    
+    173000   10.256327           1000  -0              2.7174776    
+    174000   10.353455           1000  -0              2.7331856    
+    175000   10.451392           1000  -0              2.7488936    
+    176000   10.549792           1000  -0              2.7646015    
+    177000   10.648615           1000  -0              2.7803095    
+    178000   10.747357           1000  -0              2.7960175    
+    179000   10.84476            1000  -0              2.8117254    
+    180000   10.942242           1000  -0              2.8274334    
+    181000   11.040635           1000  -0              2.8431414    
+    182000   11.139273           1000  -0              2.8588493    
+    183000   11.239382           1000  -0              2.8745573    
+    184000   11.339673           1000  -0              2.8902652    
+    185000   11.441311           1000  -0              2.9059732    
+    186000   11.543812           1000  -0              2.9216812    
+    187000   11.64542            1000  -0              2.9373891    
+    188000   11.74731            1000  -0              2.9530971    
+    189000   11.850149           1000  -0              2.9688051    
+    190000   11.952154           1000  -0              2.984513     
+    191000   12.055857           1000  -0              3.000221     
+    192000   12.158418           1000  -0              3.0159289    
+    193000   12.261926           1000  -0              3.0316369    
+    194000   12.364315           1000  -0              3.0473449    
+    195000   12.466776           1000  -0              3.0630528    
+    196000   12.568419           1000  -0              3.0787608    
+    197000   12.670258           1000  -0              3.0944688    
+    198000   12.771091           1000  -0              3.1101767    
+    199000   12.873654           1000  -0              3.1258847    
+    200000   12.976411           1000  -0              3.1415927    
+Loop time of 12.9764 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 62922.248 tau/day, 15412.556 timesteps/s, 15.413 Matom-step/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.35493    | 0.65797    | 0.98979    |  36.8 |  5.07
+Neigh   | 0.0084865  | 0.011137   | 0.013852   |   2.4 |  0.09
+Comm    | 3.7509     | 4.2375     | 4.7882     |  23.1 | 32.66
+Output  | 0.0027947  | 0.0036594  | 0.0042822  |   0.9 |  0.03
+Modify  | 5.6694     | 6.3746     | 7.0279     |  24.5 | 49.12
+Other   |            | 1.692      |            |       | 13.04
+
+Nlocal:            250 ave         260 max         242 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Nghost:         279.25 ave         325 max         232 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:         939.75 ave        1397 max         509 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 3759
+Ave neighs/atom = 3.759
+Neighbor list builds = 201
+Dangerous builds = 0
+unfix 		ins
+run		200000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.88 | 11.89 Mbytes
+   Step          CPU          Atoms        KinEng        v_theta    
+    200000   0                   1000   1.0071568      3.1415927    
+    201000   0.093433184         1000   1.0036239      3.1573006    
+    202000   0.18902203          1000   0.99846844     3.1730086    
+    203000   0.28432792          1000   0.98236169     3.1887165    
+    204000   0.38011419          1000   0.98625572     3.2044245    
+    205000   0.47468558          1000   0.9893407      3.2201325    
+    206000   0.56918796          1000   1.0012123      3.2358404    
+    207000   0.66393867          1000   1.0231892      3.2515484    
+    208000   0.75739212          1000   1.0265912      3.2672564    
+    209000   0.85184147          1000   1.0190202      3.2829643    
+    210000   0.94643219          1000   1.0267754      3.2986723    
+    211000   1.0419472           1000   1.0186847      3.3143802    
+    212000   1.1365263           1000   1.0159848      3.3300882    
+    213000   1.232359            1000   0.99326329     3.3457962    
+    214000   1.3262519           1000   0.97263135     3.3615041    
+    215000   1.4200243           1000   0.97246409     3.3772121    
+    216000   1.5161944           1000   0.96000626     3.3929201    
+    217000   1.6118944           1000   0.95730432     3.408628     
+    218000   1.7110719           1000   0.95605591     3.424336     
+    219000   1.8103017           1000   0.94983        3.440044     
+    220000   1.9104019           1000   0.95291888     3.4557519    
+    221000   2.0104337           1000   0.93612997     3.4714599    
+    222000   2.1116636           1000   0.93414081     3.4871678    
+    223000   2.2119333           1000   0.93321246     3.5028758    
+    224000   2.3141              1000   0.93026943     3.5185838    
+    225000   2.4159209           1000   0.930478       3.5342917    
+    226000   2.5183511           1000   0.92909096     3.5499997    
+    227000   2.6187905           1000   0.92308495     3.5657077    
+    228000   2.7162318           1000   0.91075986     3.5814156    
+    229000   2.8156901           1000   0.9006662      3.5971236    
+    230000   2.9175496           1000   0.88869212     3.6128316    
+    231000   3.0178436           1000   0.8877611      3.6285395    
+    232000   3.1199496           1000   0.89409636     3.6442475    
+    233000   3.2221471           1000   0.90866091     3.6599554    
+    234000   3.3254883           1000   0.90454601     3.6756634    
+    235000   3.4290048           1000   0.89408327     3.6913714    
+    236000   3.5311688           1000   0.8881044      3.7070793    
+    237000   3.6334192           1000   0.89322168     3.7227873    
+    238000   3.7368611           1000   0.89018045     3.7384953    
+    239000   3.8423369           1000   0.88771268     3.7542032    
+    240000   3.9476493           1000   0.88957717     3.7699112    
+    241000   4.0539657           1000   0.89362036     3.7856191    
+    242000   4.16111             1000   0.90967472     3.8013271    
+    243000   4.2703542           1000   0.91366381     3.8170351    
+    244000   4.3773387           1000   0.9150959      3.832743     
+    245000   4.4845495           1000   0.92725789     3.848451     
+    246000   4.5930315           1000   0.93024722     3.864159     
+    247000   4.7046291           1000   0.93297974     3.8798669    
+    248000   4.8170945           1000   0.94755869     3.8955749    
+    249000   4.9268016           1000   0.94761679     3.9112829    
+    250000   5.0368647           1000   0.92701064     3.9269908    
+    251000   5.1471839           1000   0.91365252     3.9426988    
+    252000   5.2579805           1000   0.90918381     3.9584067    
+    253000   5.3685628           1000   0.90612685     3.9741147    
+    254000   5.4809889           1000   0.90352142     3.9898227    
+    255000   5.5948165           1000   0.90421567     4.0055306    
+    256000   5.7098724           1000   0.90024688     4.0212386    
+    257000   5.8267005           1000   0.88540341     4.0369466    
+    258000   5.9410582           1000   0.87890423     4.0526545    
+    259000   6.0566794           1000   0.86833748     4.0683625    
+    260000   6.1707105           1000   0.85465694     4.0840704    
+    261000   6.2863098           1000   0.83941242     4.0997784    
+    262000   6.4015542           1000   0.81790404     4.1154864    
+    263000   6.5166913           1000   0.82284562     4.1311943    
+    264000   6.6306328           1000   0.80961447     4.1469023    
+    265000   6.7436467           1000   0.80567073     4.1626103    
+    266000   6.855163            1000   0.79577448     4.1783182    
+    267000   6.9684761           1000   0.78489106     4.1940262    
+    268000   7.0840143           1000   0.77348757     4.2097342    
+    269000   7.1995596           1000   0.76606696     4.2254421    
+    270000   7.3149459           1000   0.7649744      4.2411501    
+    271000   7.4296104           1000   0.76050309     4.256858     
+    272000   7.545919            1000   0.75378759     4.272566     
+    273000   7.6616623           1000   0.75633811     4.288274     
+    274000   7.7787912           1000   0.75703106     4.3039819    
+    275000   7.8956703           1000   0.75227453     4.3196899    
+    276000   8.0137649           1000   0.76003902     4.3353979    
+    277000   8.1334933           1000   0.76274661     4.3511058    
+    278000   8.2489616           1000   0.75888482     4.3668138    
+    279000   8.3645369           1000   0.75071875     4.3825218    
+    280000   8.4781847           1000   0.75454927     4.3982297    
+    281000   8.5925071           1000   0.75617824     4.4139377    
+    282000   8.7079255           1000   0.75230835     4.4296456    
+    283000   8.8225434           1000   0.75417571     4.4453536    
+    284000   8.9358224           1000   0.74559345     4.4610616    
+    285000   9.0494588           1000   0.73274661     4.4767695    
+    286000   9.1624226           1000   0.72385193     4.4924775    
+    287000   9.2738683           1000   0.72398899     4.5081855    
+    288000   9.3858476           1000   0.72009027     4.5238934    
+    289000   9.496472            1000   0.72026686     4.5396014    
+    290000   9.6064673           1000   0.72330145     4.5553093    
+    291000   9.7157088           1000   0.71630656     4.5710173    
+    292000   9.8251432           1000   0.71089192     4.5867253    
+    293000   9.9340203           1000   0.70584923     4.6024332    
+    294000   10.041427           1000   0.71350398     4.6181412    
+    295000   10.150066           1000   0.72781836     4.6338492    
+    296000   10.258912           1000   0.72285512     4.6495571    
+    297000   10.368299           1000   0.71649517     4.6652651    
+    298000   10.480058           1000   0.71132209     4.6809731    
+    299000   10.592962           1000   0.73602072     4.696681     
+    300000   10.706549           1000   0.74400837     4.712389     
+    301000   10.818871           1000   0.76618562     4.7280969    
+    302000   10.930873           1000   0.77476041     4.7438049    
+    303000   11.040635           1000   0.77124283     4.7595129    
+    304000   11.150729           1000   0.7625748      4.7752208    
+    305000   11.260184           1000   0.74979361     4.7909288    
+    306000   11.36913            1000   0.74515733     4.8066368    
+    307000   11.477137           1000   0.74302741     4.8223447    
+    308000   11.584107           1000   0.73732959     4.8380527    
+    309000   11.692852           1000   0.73368237     4.8537606    
+    310000   11.800777           1000   0.72374292     4.8694686    
+    311000   11.906901           1000   0.72107784     4.8851766    
+    312000   12.015001           1000   0.72944426     4.9008845    
+    313000   12.122634           1000   0.73958637     4.9165925    
+    314000   12.231473           1000   0.75160847     4.9323005    
+    315000   12.343728           1000   0.74419683     4.9480084    
+    316000   12.455114           1000   0.74652593     4.9637164    
+    317000   12.564048           1000   0.74933482     4.9794244    
+    318000   12.672355           1000   0.74200509     4.9951323    
+    319000   12.778931           1000   0.7346024      5.0108403    
+    320000   12.886067           1000   0.72806145     5.0265482    
+    321000   12.993743           1000   0.72147888     5.0422562    
+    322000   13.101955           1000   0.71460041     5.0579642    
+    323000   13.212177           1000   0.70255075     5.0736721    
+    324000   13.322528           1000   0.70640327     5.0893801    
+    325000   13.435038           1000   0.70643428     5.1050881    
+    326000   13.545443           1000   0.69751794     5.120796     
+    327000   13.657538           1000   0.69035108     5.136504     
+    328000   13.770475           1000   0.68068243     5.152212     
+    329000   13.883136           1000   0.69123492     5.1679199    
+    330000   13.995043           1000   0.70326515     5.1836279    
+    331000   14.109604           1000   0.70551726     5.1993358    
+    332000   14.222995           1000   0.70514444     5.2150438    
+    333000   14.336604           1000   0.71102045     5.2307518    
+    334000   14.44933            1000   0.71336747     5.2464597    
+    335000   14.56056            1000   0.70816388     5.2621677    
+    336000   14.67143            1000   0.69502472     5.2778757    
+    337000   14.783295           1000   0.69314289     5.2935836    
+    338000   14.893816           1000   0.68565794     5.3092916    
+    339000   15.005631           1000   0.67268053     5.3249995    
+    340000   15.119406           1000   0.68313196     5.3407075    
+    341000   15.233786           1000   0.68782815     5.3564155    
+    342000   15.349691           1000   0.6989326      5.3721234    
+    343000   15.466599           1000   0.694926       5.3878314    
+    344000   15.583585           1000   0.7006474      5.4035394    
+    345000   15.702299           1000   0.70783177     5.4192473    
+    346000   15.819367           1000   0.71334276     5.4349553    
+    347000   15.935892           1000   0.72917419     5.4506633    
+    348000   16.051074           1000   0.74315705     5.4663712    
+    349000   16.165316           1000   0.76731311     5.4820792    
+    350000   16.281794           1000   0.79761434     5.4977871    
+    351000   16.397615           1000   0.80447724     5.5134951    
+    352000   16.514271           1000   0.80118728     5.5292031    
+    353000   16.632427           1000   0.77990459     5.544911     
+    354000   16.750052           1000   0.76453299     5.560619     
+    355000   16.868875           1000   0.76538392     5.576327     
+    356000   16.985762           1000   0.76310698     5.5920349    
+    357000   17.103471           1000   0.75897095     5.6077429    
+    358000   17.223037           1000   0.75071115     5.6234508    
+    359000   17.340073           1000   0.74034801     5.6391588    
+    360000   17.457867           1000   0.72671924     5.6548668    
+    361000   17.57503            1000   0.72111017     5.6705747    
+    362000   17.69138            1000   0.71875181     5.6862827    
+    363000   17.808661           1000   0.71469706     5.7019907    
+    364000   17.925895           1000   0.70470493     5.7176986    
+    365000   18.042976           1000   0.70863047     5.7334066    
+    366000   18.162079           1000   0.70850561     5.7491146    
+    367000   18.283911           1000   0.71413452     5.7648225    
+    368000   18.407692           1000   0.71314184     5.7805305    
+    369000   18.53068            1000   0.71309549     5.7962384    
+    370000   18.652767           1000   0.71132937     5.8119464    
+    371000   18.772131           1000   0.70788039     5.8276544    
+    372000   18.892439           1000   0.71780071     5.8433623    
+    373000   19.012886           1000   0.72352571     5.8590703    
+    374000   19.132857           1000   0.71723739     5.8747783    
+    375000   19.25312            1000   0.71556941     5.8904862    
+    376000   19.372783           1000   0.70935312     5.9061942    
+    377000   19.493215           1000   0.71551157     5.9219022    
+    378000   19.614604           1000   0.7235163      5.9376101    
+    379000   19.735704           1000   0.73896421     5.9533181    
+    380000   19.856219           1000   0.74906169     5.969026     
+    381000   19.974782           1000   0.75303336     5.984734     
+    382000   20.093831           1000   0.75359492     6.000442     
+    383000   20.213075           1000   0.75579354     6.0161499    
+    384000   20.334366           1000   0.75178368     6.0318579    
+    385000   20.455027           1000   0.74412159     6.0475659    
+    386000   20.574847           1000   0.7360955      6.0632738    
+    387000   20.691183           1000   0.73461103     6.0789818    
+    388000   20.80664            1000   0.72496617     6.0946897    
+    389000   20.92229            1000   0.7219047      6.1103977    
+    390000   21.037387           1000   0.71837013     6.1261057    
+    391000   21.152412           1000   0.71495923     6.1418136    
+    392000   21.267451           1000   0.71436707     6.1575216    
+    393000   21.382024           1000   0.71447834     6.1732296    
+    394000   21.496952           1000   0.71334298     6.1889375    
+    395000   21.611699           1000   0.71510229     6.2046455    
+    396000   21.726328           1000   0.7121714      6.2203535    
+    397000   21.840614           1000   0.70818894     6.2360614    
+    398000   21.955122           1000   0.70059455     6.2517694    
+    399000   22.068714           1000   0.69960089     6.2674773    
+    400000   22.182962           1000   0.70261998     6.2831853    
+Loop time of 22.183 on 4 procs for 200000 steps with 1000 atoms
+
+Performance: 36807.772 tau/day, 9015.918 timesteps/s, 9.016 Matom-step/s
+95.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.1609     | 2.0592     | 2.957      |  61.9 |  9.28
+Neigh   | 0.013526   | 0.018287   | 0.022861   |   3.3 |  0.08
+Comm    | 7.707      | 8.9501     | 10.214     |  41.1 | 40.35
+Output  | 0.0027437  | 0.0039021  | 0.0045769  |   1.1 |  0.02
+Modify  | 7.9431     | 9.4082     | 10.711     |  40.5 | 42.41
+Other   |            | 1.743      |            |       |  7.86
+
+Nlocal:            250 ave         258 max         241 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Nghost:            412 ave         492 max         332 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:         1258.5 ave        1588 max         953 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 5034
+Ave neighs/atom = 5.034
+Neighbor list builds = 159
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/granular/log.27Jun24.pour.drum.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (28 Mar 2023 - Development)
+LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
 # pour two types of particles (cohesive and non-cohesive) into cylinder
 # 'turn' cylinder by changing direction of gravity, then rotate it.
 # This simulates a rotating drum powder characterization experiment.
@@ -92,13 +92,11 @@ fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} de
 fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
 fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
 fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
 fix             ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
 fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
 fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
 fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
 fix             ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
-Particle insertion: 9396 every 490 steps, 2000 by step 1
 
 comm_modify     vel yes
 
@@ -126,6 +124,8 @@ dynamic group delgroup defined
 
 run             2000
 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Particle insertion: 9396 every 2449 steps, 2000 by step 1
+Particle insertion: 9396 every 2449 steps, 2000 by step 1
 Neighbor list info ...
   update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
@@ -135,7 +135,7 @@ Neighbor list info ...
   1 neighbor lists, perpetual/occasional/extra = 1 0 0
   (1) pair granular, perpetual
       attributes: half, newton on, size, history
-      pair build: half/size/bin/newton
+      pair build: half/size/bin/atomonly/newton
       stencil: half/bin/3d
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 15.95 | 15.95 | 15.95 Mbytes
@@ -161,20 +161,20 @@ Per MPI rank memory allocation (min/avg/max) = 15.95 | 15.95 | 15.95 Mbytes
       1800        4000  -0              0            
       1900        4000  -0              0            
       2000        4000  -0              0            
-Loop time of 2.86367 on 1 procs for 2000 steps with 4000 atoms
+Loop time of 2.46916 on 1 procs for 2000 steps with 4000 atoms
 
-Performance: 60342.153 tau/day, 698.405 timesteps/s, 2.794 Matom-step/s
+Performance: 69983.324 tau/day, 809.992 timesteps/s, 3.240 Matom-step/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.36474    | 0.36474    | 0.36474    |   0.0 | 12.74
+Pair    | 0.32379    | 0.32379    | 0.32379    |   0.0 | 13.11
-Neigh   | 1.0694     | 1.0694     | 1.0694     |   0.0 | 37.35
+Neigh   | 0.98775    | 0.98775    | 0.98775    |   0.0 | 40.00
-Comm    | 0.043549   | 0.043549   | 0.043549   |   0.0 |  1.52
+Comm    | 0.03762    | 0.03762    | 0.03762    |   0.0 |  1.52
-Output  | 0.00054587 | 0.00054587 | 0.00054587 |   0.0 |  0.02
+Output  | 0.0004273  | 0.0004273  | 0.0004273  |   0.0 |  0.02
-Modify  | 1.3281     | 1.3281     | 1.3281     |   0.0 | 46.38
+Modify  | 1.0824     | 1.0824     | 1.0824     |   0.0 | 43.84
-Other   |            | 0.05731    |            |       |  2.00
+Other   |            | 0.03719    |            |       |  1.51
 
 Nlocal:           4000 ave        4000 max        4000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -213,60 +213,60 @@ Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Per MPI rank memory allocation (min/avg/max) = 22.3 | 22.3 | 22.3 Mbytes
    Step        Atoms        KinEng        v_theta    
       2000        4000   59.748184      0            
-      2100        4000   47.337202      0.031415927  
+      2100        4000   47.350194      0.031415927  
-      2200        4000   33.303567      0.062831853  
+      2200        4000   33.365489      0.062831853  
-      2300        4000   24.246806      0.09424778   
+      2300        4000   24.167007      0.09424778   
-      2400        4000   17.165844      0.12566371   
+      2400        4000   17.169385      0.12566371   
-      2500        4000   18.415922      0.15707963   
+      2500        4000   18.361204      0.15707963   
-      2600        4000   17.3084        0.18849556   
+      2600        4000   17.259574      0.18849556   
-      2700        4000   15.985202      0.21991149   
+      2700        4000   16.022776      0.21991149   
-      2800        4000   14.084599      0.25132741   
+      2800        4000   14.177071      0.25132741   
-      2900        4000   11.526622      0.28274334   
+      2900        4000   11.594949      0.28274334   
-      3000        4000   8.9364793      0.31415927   
+      3000        4000   8.8305692      0.31415927   
-      3100        4000   6.844209       0.34557519   
+      3100        4000   6.777187       0.34557519   
-      3200        4000   5.8243926      0.37699112   
+      3200        4000   5.7660641      0.37699112   
-      3300        4000   5.5616671      0.40840704   
+      3300        4000   5.6477598      0.40840704   
-      3400        4000   5.7219459      0.43982297   
+      3400        4000   5.7778867      0.43982297   
-      3500        4000   6.2482952      0.4712389    
+      3500        4000   6.1873342      0.4712389    
-      3600        4000   6.396804       0.50265482   
+      3600        4000   6.2232869      0.50265482   
-      3700        4000   6.6017236      0.53407075   
+      3700        4000   6.3635239      0.53407075   
-      3800        4000   6.684913       0.56548668   
+      3800        4000   6.523255       0.56548668   
-      3900        4000   6.5988588      0.5969026    
+      3900        4000   6.5008528      0.5969026    
-      4000        4000   6.4839456      0.62831853   
+      4000        4000   6.2394922      0.62831853   
-      4100        4000   6.104233       0.65973446   
+      4100        4000   5.9742801      0.65973446   
-      4200        4000   5.6021757      0.69115038   
+      4200        4000   5.3949422      0.69115038   
-      4300        4000   4.9670639      0.72256631   
+      4300        4000   4.9123859      0.72256631   
-      4400        4000   4.3298233      0.75398224   
+      4400        4000   4.3863176      0.75398224   
-      4500        4000   3.8833884      0.78539816   
+      4500        4000   3.8729959      0.78539816   
-      4600        4000   3.4626401      0.81681409   
+      4600        4000   3.4734137      0.81681409   
-      4700        4000   3.0367615      0.84823002   
+      4700        4000   3.0478845      0.84823002   
-      4800        4000   2.762543       0.87964594   
+      4800        4000   2.8232582      0.87964594   
-      4900        4000   2.5627778      0.91106187   
+      4900        4000   2.6314234      0.91106187   
-      5000        4000   2.4007014      0.9424778    
+      5000        4000   2.429883       0.9424778    
-Loop time of 9.68472 on 1 procs for 3000 steps with 4000 atoms
+Loop time of 8.26731 on 1 procs for 3000 steps with 4000 atoms
 
-Performance: 26763.820 tau/day, 309.766 timesteps/s, 1.239 Matom-step/s
+Performance: 31352.411 tau/day, 362.875 timesteps/s, 1.452 Matom-step/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 3.2753     | 3.2753     | 3.2753     |   0.0 | 33.82
+Pair    | 2.9751     | 2.9751     | 2.9751     |   0.0 | 35.99
-Neigh   | 2.2272     | 2.2272     | 2.2272     |   0.0 | 23.00
+Neigh   | 2.0918     | 2.0918     | 2.0918     |   0.0 | 25.30
-Comm    | 0.068198   | 0.068198   | 0.068198   |   0.0 |  0.70
+Comm    | 0.059511   | 0.059511   | 0.059511   |   0.0 |  0.72
-Output  | 0.0008788  | 0.0008788  | 0.0008788  |   0.0 |  0.01
+Output  | 0.0007014  | 0.0007014  | 0.0007014  |   0.0 |  0.01
-Modify  | 4.0327     | 4.0327     | 4.0327     |   0.0 | 41.64
+Modify  | 3.0819     | 3.0819     | 3.0819     |   0.0 | 37.28
-Other   |            | 0.08047    |            |       |  0.83
+Other   |            | 0.05826    |            |       |  0.70
 
 Nlocal:           4000 ave        4000 max        4000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:            364 ave         364 max         364 min
+Nghost:            353 ave         353 max         353 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          12973 ave       12973 max       12973 min
+Neighs:          12970 ave       12970 max       12970 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 12973
+Total # of neighbors = 12970
-Ave neighs/atom = 3.24325
+Ave neighs/atom = 3.2425
-Neighbor list builds = 1274
+Neighbor list builds = 1236
 Dangerous builds = 130
-Total wall time: 0:00:12
+Total wall time: 0:00:10