Merge branch 'develop' into pair_style_tutorial

cmake/CMakeLists.txt

@@ -841,8 +841,7 @@ if(BUILD_SHARED_LIBS)
   set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
   if(Python_EXECUTABLE)
     add_custom_target(
-      install-python ${CMAKE_COMMAND} -E remove_directory build
+      install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
               -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()
@@ -856,35 +855,6 @@ else()
     ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
 endif()
 
-###############################################################################
-# Add LAMMPS python module to "install" target. This is taylored for building
-# LAMMPS for package managers and with different prefix settings.
-# This requires either a shared library or that the PYTHON package is included.
-###############################################################################
-if(BUILD_SHARED_LIBS OR PKG_PYTHON)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-  else()
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
-  if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
-    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
-  endif()
-endif()
-
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)

cmake/Modules/Packages/GPU.cmake

@@ -177,8 +177,6 @@ if(GPU_API STREQUAL "CUDA")
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
   endif()
 
-  target_link_libraries(lammps PRIVATE gpu)
-
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
   target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@@ -251,12 +249,12 @@ elseif(GPU_API STREQUAL "OPENCL")
   else()
     target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   endif()
-  target_link_libraries(lammps PRIVATE gpu)
 
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
   add_dependencies(ocl_get_devices OpenCL::OpenCL)
+
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
@@ -475,10 +473,14 @@ elseif(GPU_API STREQUAL "HIP")
     target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   endif()
-
-  target_link_libraries(lammps PRIVATE gpu)
 endif()
 
+if(BUILD_OMP)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
+  target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
+endif()
+target_link_libraries(lammps PRIVATE gpu)
+
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
 # detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)

cmake/Modules/Packages/MSCG.cmake

@@ -7,8 +7,8 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
-  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
-  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
   mark_as_advanced(MSCG_URL)
   mark_as_advanced(MSCG_MD5)
 

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)

cmake/Modules/StyleHeaderUtils.cmake

@@ -95,73 +95,76 @@ function(RegisterIntegrateStyle path)
 endfunction(RegisterIntegrateStyle)
 
 function(RegisterStyles search_path)
-    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
+    FindStyleHeaders(${search_path} ANGLE_CLASS        angle_        ANGLE        ) # angle        ) # force
-    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} ATOM_CLASS         atom_vec_     ATOM_VEC     ) # atom         ) # atom      atom_vec_hybrid
-    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
+    FindStyleHeaders(${search_path} BODY_CLASS         body_         BODY         ) # body         ) # atom_vec_body
-    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
+    FindStyleHeaders(${search_path} BOND_CLASS         bond_         BOND         ) # bond         ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
+    FindStyleHeaders(${search_path} COMMAND_CLASS      "[^.]"        COMMAND      ) # command      ) # input
-    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
+    FindStyleHeaders(${search_path} COMPUTE_CLASS      compute_      COMPUTE      ) # compute      ) # modify
-    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS     dihedral_     DIHEDRAL     ) # dihedral     ) # force
-    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
+    FindStyleHeaders(${search_path} DUMP_CLASS         dump_         DUMP         ) # dump         ) # output    write_dump
-    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
+    FindStyleHeaders(${search_path} FIX_CLASS          fix_          FIX          ) # fix          ) # modify
-    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
+    FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
+    FindStyleHeaders(${search_path} IMPROPER_CLASS     improper_     IMPROPER     ) # improper     ) # force
-    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS    "[^.]"        INTEGRATE    ) # integrate    ) # update
-    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS       "[^.]"        KSPACE       ) # kspace       ) # force
-    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS     min_          MINIMIZE     ) # minimize     ) # update
-    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+    FindStyleHeaders(${search_path} NBIN_CLASS         nbin_         NBIN         ) # nbin         ) # neighbor
-    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS        npair_        NPAIR        ) # npair        ) # neighbor
-    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS     nstencil_     NSTENCIL     ) # nstencil     ) # neighbor
-    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
+    FindStyleHeaders(${search_path} NTOPO_CLASS        ntopo_        NTOPO        ) # ntopo        ) # neighbor
-    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
+    FindStyleHeaders(${search_path} PAIR_CLASS         pair_         PAIR         ) # pair         ) # force
-    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+    FindStyleHeaders(${search_path} READER_CLASS       reader_       READER       ) # reader       ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS       region_       REGION       ) # region       ) # domain
 endfunction(RegisterStyles)
 
 function(RegisterStylesExt search_path extension sources)
-    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS        ${extension}  ANGLE        ${sources})
-    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS         ${extension}  ATOM_VEC     ${sources})
-    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS         ${extension}  BODY         ${sources})
-    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS         ${extension}  BOND         ${sources})
-    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS      ${extension}  COMMAND      ${sources})
-    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS      ${extension}  COMPUTE      ${sources})
-    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS     ${extension}  DIHEDRAL     ${sources})
-    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS         ${extension}  DUMP         ${sources})
-    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS          ${extension}  FIX          ${sources})
-    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
+    FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension}  GRAN_SUB_MOD ${sources})
-    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS     ${extension}  IMPROPER     ${sources})
-    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS    ${extension}  INTEGRATE    ${sources})
-    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS       ${extension}  KSPACE       ${sources})
-    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS     ${extension}  MINIMIZE     ${sources})
-    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS         ${extension}  NBIN         ${sources})
-    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS        ${extension}  NPAIR        ${sources})
-    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS     ${extension}  NSTENCIL     ${sources})
-    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS        ${extension}  NTOPO        ${sources})
-    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS         ${extension}  PAIR         ${sources})
-    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS       ${extension}  READER       ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS       ${extension}  REGION       ${sources})
 endfunction(RegisterStylesExt)
 
 function(GenerateStyleHeaders output_path)
     message(STATUS "Generating style headers...")
-    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
+    GenerateStyleHeader(${output_path} ANGLE        angle        ) # force
-    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} ATOM_VEC     atom         ) # atom      atom_vec_hybrid
-    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BODY         body         ) # atom_vec_body
-    GenerateStyleHeader(${output_path} BOND       bond      ) # force
+    GenerateStyleHeader(${output_path} BOND         bond         ) # force
-    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
+    GenerateStyleHeader(${output_path} COMMAND      command      ) # input
-    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
+    GenerateStyleHeader(${output_path} COMPUTE      compute      ) # modify
-    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
+    GenerateStyleHeader(${output_path} DIHEDRAL     dihedral     ) # force
-    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
+    GenerateStyleHeader(${output_path} DUMP         dump         ) # output    write_dump
-    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
+    GenerateStyleHeader(${output_path} FIX          fix          ) # modify
-    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
+    GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
-    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
+    GenerateStyleHeader(${output_path} IMPROPER     improper     ) # force
-    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE    integrate    ) # update
-    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
+    GenerateStyleHeader(${output_path} KSPACE       kspace       ) # force
-    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
+    GenerateStyleHeader(${output_path} MINIMIZE     minimize     ) # update
-    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
+    GenerateStyleHeader(${output_path} NBIN         nbin         ) # neighbor
-    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR        npair        ) # neighbor
-    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL     nstencil     ) # neighbor
-    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
+    GenerateStyleHeader(${output_path} NTOPO        ntopo        ) # neighbor
-    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
+    GenerateStyleHeader(${output_path} PAIR         pair         ) # force
-    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+    GenerateStyleHeader(${output_path} READER       reader       ) # read_dump
+    GenerateStyleHeader(${output_path} REGION       region       ) # domain
 endfunction(GenerateStyleHeaders)
 
 function(DetectBuildSystemConflict lammps_src_dir)

doc/github-development-workflow.md

@@ -123,7 +123,7 @@ request is merged.  The template for pull requests includes a header
 where connections between pull requests and issues can be listed, and
 thus where this comment should be placed.
 
-## Milestones and Release Planning
+## Release Planning
 
 LAMMPS uses a continuous release development model with incremental
 changes, i.e. significant effort is made -- including automated pre-merge
@@ -132,24 +132,28 @@ broken.  These tests are run after every update to a pull request.  More
 extensive and time-consuming tests (including regression testing) are
 performed after code is merged to the "develop" branch.  There are feature
 releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
-developers feel, that a sufficient number of changes has been included
+developers feel, that a sufficient number of changes have been included
 and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch
 follows only these versions with fast-forward merges.  While "develop" may
 be temporarily broken through issues only detected by the post-merge tests,
 The "release" branch is always supposed to be of production quality.
 
-About once each year, there is a "stable" release of LAMMPS.
+About once each year, there is a "stable" release of LAMMPS.  These have
-These have seen additional, manual testing and review of
+seen additional, manual testing and review of results from testing with
-results from testing with instrumented code and static code analysis.
+instrumented code and static code analysis.  Also, the last few feature
-Also, the last few feature releases before a stable release are "release
+releases before a stable release are "release candidate" versions which
-candidate" versions which only contain bug fixes, feature additions to
+only contain bug fixes, feature additions to peripheral functionality,
-peripheral functionality, and documentation updates.  In between stable
+and documentation updates.  In between stable releases, bug fixes and
-releases, bug fixes and infrastructure updates are back-ported from the
+infrastructure updates are back-ported from the "develop" branch to the
-"develop" branch to the "maintenance" branch and occasionally merged
+"maintenance" branch and occasionally merged into "stable" and published
-into "stable" and published as update releases.
+as update releases.
+
+## Project Management
 
 For release planning and the information of code contributors, issues
-and pull requests being actively worked on are assigned a "milestone",
+and pull requests are being managed with GitHub Project Boards.  There
-which corresponds to the next stable release or the stable release after
+are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
-that, with a tentative release date.
+and LAMMPS Pull Requests.  Each board is organized in columns where
+submissions are categorized.  Within each column the entries are
+(manually) sorted according their priority.

doc/src/Build_extras.rst

@@ -181,6 +181,9 @@ way no local OpenCL development headers or library needs to be present and only
 OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
 desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
+The GPU library has some multi-thread support using OpenMP.  If LAMMPS is built
+with ``-D BUILD_OMP=on`` this will also be enabled.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@@ -278,6 +281,9 @@ To support the CUDA multiprocessor server you can set the define
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
+The GPU library has some multi-thread support using OpenMP.  You need to add
+the compiler flag that enables OpenMP to the ``CUDR_OPTS`` Makefile variable.
+
 If the library build is successful, 3 files should be created:
 ``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
 ``lib/gpu/Makefile.lammps``\ .  The latter has settings that enable LAMMPS

doc/src/Commands_bond.rst

@@ -42,6 +42,7 @@ OPT.
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/restrain <bond_harmonic_restrain>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
    * :doc:`lepton (o) <bond_lepton>`

doc/src/Commands_compute.rst

@@ -52,6 +52,8 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`dilatation/atom <compute_dilatation_atom>`
    * :doc:`dipole <compute_dipole>`
    * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`dipole/tip4p <compute_dipole>`
+   * :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
    * :doc:`displace/atom <compute_displace_atom>`
    * :doc:`dpd <compute_dpd>`
    * :doc:`dpd/atom <compute_dpd_atom>`

doc/src/Commands_fix.rst

@@ -70,6 +70,7 @@ OPT.
    * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
+   * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electrode/conp (i) <fix_electrode>`
    * :doc:`electrode/conq (i) <fix_electrode>`
@@ -93,6 +94,7 @@ OPT.
    * :doc:`grem <fix_grem>`
    * :doc:`halt <fix_halt>`
    * :doc:`heat <fix_heat>`
+   * :doc:`heat/flow <fix_heat_flow>`
    * :doc:`hyper/global <fix_hyper_global>`
    * :doc:`hyper/local <fix_hyper_local>`
    * :doc:`imd <fix_imd>`

doc/src/Developer_notes.rst

@@ -11,6 +11,7 @@ Available topics are:
 
 - `Reading and parsing of text and text files`_
 - `Requesting and accessing neighbor lists`_
+- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
 - `Fix contributions to instantaneous energy, virial, and cumulative energy`_
 - `KSpace PPPM FFT grids`_
 
@@ -216,6 +217,30 @@ command:
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
+Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are multiple ways to manage per-atom data within LAMMPS.  Often
+the per-atom storage is only used locally and managed by the class that
+uses it.  If the data has to persist between multiple time steps and
+migrate with atoms when they move from sub-domain to sub-domain or
+across periodic boundaries, then using a custom atom style, or :doc:`fix
+property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
+possible options.
+
+- Using the atom style is usually the most programming effort and mostly
+  needed when the per-atom data is an integral part of the model like a
+  per-atom charge or diameter and thus should be part of the Atoms
+  section of a :doc:`data file <read_data>`.
+
+- Fix property/atom is useful if the data is optional or should be
+  entered by the user, or accessed as a (named) custom property. In this
+  case the fix should be entered as part of the input (and not
+  internally) which allows to enter and store its content with data files.
+
+- Fix STORE/ATOM should be used when the data should be accessed internally
+  only and thus the fix can be created internally.
+
 Fix contributions to instantaneous energy, virial, and cumulative energy
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_updating.rst

@@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
 - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
+- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
 - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
 
@@ -385,6 +386,34 @@ New:
 
 This change is **required** or else the code will not compile.
 
+Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: TBD
+
+The available functionality of the internal fix to store per-atom
+properties was expanded to enable storing data with ghost atoms and to
+support binary restart files.  With those changes, the fix was renamed
+to fix STORE/ATOM and the number and order of (required) arguments has
+changed.
+
+Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
+
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
+- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
+- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
+
+New syntax:  ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
+
+- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
+- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
+- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
+- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+
+Since this is an internal fix, there is no user visible change.
+
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Howto_granular.rst

@@ -43,6 +43,15 @@ The fix style *freeze* zeroes both the force and torque of frozen
 atoms, and should be used for granular system instead of the fix style
 *setforce*\ .
 
+To model heat conduction, one must add the temperature and heatflow
+atom variables with:
+* :doc:`fix property/atom <fix_property_atom>`
+a temperature integration fix
+* :doc:`fix heat/flow <fix_heat_flow>`
+and a heat conduction option defined in both
+* :doc:`pair_style granular <pair_granular>`
+* :doc:`fix wall/gran <fix_wall_gran>`
+
 For computational efficiency, you can eliminate needless pairwise
 computations between frozen atoms by using this command:
 
@@ -55,3 +64,6 @@ computations between frozen atoms by using this command:
    will be the same as in 3d.  If you wish to model granular particles in
    2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
    doc page, where 2d simulations are discussed.
+
+To add custom granular contact models, see the
+:doc:`modifying granular sub-models page <Modify_gran_sub_mod>`.

doc/src/Install_linux.rst

@@ -172,7 +172,7 @@ Pre-built EPEL Linux executable
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Pre-built LAMMPS (and KIM) packages for stable releases are available
-in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
+in the `Extra Packages for Enterprise Linux (EPEL) repository <https://docs.fedoraproject.org/en-US/epel/>`_
 for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
 and compatible Linux distributions. Names of packages, executable,
 and content are the same as described above for Fedora Linux.

doc/src/Modify.rst

@@ -34,5 +34,6 @@ style requirements and recommendations <Modify_style>`.
    Modify_min
    Modify_region
    Modify_body
+   Modify_gran_sub_mod
    Modify_thermo
    Modify_variable

doc/src/Modify_gran_sub_mod.rst

@@ -0,0 +1,177 @@
+Granular Sub-Model styles
+===============================
+
+In granular models, particles are spheres with a finite radius and rotational
+degrees of freedom as further described in the
+:doc:`Howto granular page <Howto_granular>`. Interactions between pair of
+particles or particles and walls may therefore depend on many different modes
+of motion as described in :doc:`pair granular <pair_granular>` and
+:doc:`fix wall/gran <fix_wall_gran>`. In both cases, the exchange of forces,
+torques, and heat flow between two types of bodies is defined using a
+GranularModel class. The GranularModel class organizes the details of an
+interaction using a series of granular sub-models each of which describe a
+particular interaction mode (e.g. normal forces or rolling friction). From a
+parent GranSubMod class, several types of sub-model classes are derived:
+
+* GranSubModNormal: normal force sub-model
+* GranSubModDamping: normal damping sub-model
+* GranSubModTangential: tangential forces and sliding friction sub-model
+* GranSubModRolling: rolling friction sub-model
+* GranSubModTwisting: twisting friction sub-model
+* GranSubModHeat: heat conduction sub-model
+
+For each type of sub-model, more classes are further derived, each describing a
+specific implementation. For instance, from the GranSubModNormal class the
+GranSubModNormalHooke, GranSubModNormalHertz, and GranSubModNormalJKR classes
+are derived which calculate Hookean, Hertzian, or JKR normal forces,
+respectively.  This modular structure simplifies the addition of new granular
+contact models as as one only needs to create a new GranSubMod class without
+having to modify the more complex PairGranular, FixGranWall, and GranularModel
+classes. Most GranSubMod methods are also already defined by the parent classes
+so new contact models typically only require edits to a few relevant methods
+(e.g. methods that define coefficients and calculate forces).
+
+Each GranSubMod class has a pointer to both the LAMMPS class and the GranularModel
+class which owns it, ``lmp`` and ``gm``, respectively. The GranularModel class
+includes several public variables that describe the geometry/dynamics of the
+contact such as
+
+.. list-table::
+
+   * - ``xi`` and ``xj``
+     - Positions of the two contacting bodies
+   * - ``vi`` and ``vj``
+     - Velocities of the two contacting bodies
+   * - ``omegai`` and ``omegaj``
+     - Angular velocities of the two contacting bodies
+   * - ``dx`` and ``nx``
+     - The displacement and normalized displacement vectors
+   * - ``r``, ``rsq``, and ``rinv``
+     - The distance, distance squared, and inverse distance
+   * - ``radsum``
+     - The sum of particle radii
+   * - ``vr``, ``vn``, and ``vt``
+     - The relative velocity vector and its normal and tangential components
+   * - ``wr``
+     - The relative rotational velocity
+
+These quantities, among others, are calculated in the ``GranularModel->check_contact()``
+and ``GranularModel->calculate_forces()`` methods which can be referred to for more
+details.
+
+To create a new GranSubMod class, it is recommended that one first looks at similar
+GranSubMod classes. All GranSubMod classes share several general methods which may
+need to be defined
+
+.. list-table::
+
+   * - ``GranSubMod->mix_coeff()``
+     - Optional method to define how coefficients are mixed for different atom types. By default, coefficients are mixed using a geometric mean.
+   * - ``GranSubMod->coeffs_to_local()``
+     - Parses coefficients to define local variables. Run once at model construction.
+   * - ``GranSubMod->init()``
+     - Optional method to define local variables after other GranSubMod types were created. For instance, this method may be used by a tangential model that derives parameters from the normal model.
+
+There are also several type-specific methods
+
+.. list-table::
+
+   * - ``GranSubModNormal->touch()``
+     - Optional method to test when particles are in contact. By default, this is when particles overlap.
+   * - ``GranSubModNormal->pulloff_distance()``
+     - Optional method to return the distance at which particles stop interacting. By default, this is when particles no longer overlap.
+   * - ``GranSubModNormal->calculate_area()``
+     - Optional method to return the surface area of the contact. By default, this returns the geometric cross section.
+   * - ``GranSubModNormal->set_fncrit()``
+     - Optional method that defines the critical force to break the contact used by some tangential, rolling, and twisting sub-models. By default, this is the current total normal force including damping.
+   * - ``GranSubModNormal->calculate_forces()``
+     - Required method that returns the normal contact force
+   * - ``GranSubModDamping->calculate_forces()``
+     - Required method that returns the normal damping force
+   * - ``GranSubModTangential->calculate_forces()``
+     - Required method that calculates tangential forces/torques
+   * - ``GranSubModTwisting->calculate_forces()``
+     - Required method that calculates twisting friction forces/torques
+   * - ``GranSubModRolling->calculate_forces()``
+     - Required method that calculates rolling friction forces/torques
+   * - ``GranSubModHeat->calculate_heat()``
+     - Required method that returns the rate of heat flow
+
+As an example, say one wanted to create a new normal force option that consisted
+of a Hookean force with a piecewise stiffness. This could be done by adding a new
+set of files ``gran_sub_mod_custom.h``:
+
+.. code-block:: c++
+
+   #ifdef GranSubMod_CLASS
+   // clang-format off
+   GranSubModStyle(hooke/piecewise,
+            GranSubModNormalHookePiecewise,
+            NORMAL);
+   // clang-format on
+   #else
+
+   #ifndef GRAN_SUB_MOD_CUSTOM_H_
+   #define GRAN_SUB_MOD_CUSTOM_H_
+
+   #include "gran_sub_mod.h"
+   #include "gran_sub_mod_normal.h"
+
+   namespace LAMMPS_NS {
+   namespace Granular_NS {
+
+   class GranSubModNormalHookePiecewise : public GranSubModNormal {
+    public:
+     GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
+     void coeffs_to_local() override;
+     double calculate_forces();
+    protected:
+     double k1, k2, delta_switch;
+   };
+
+   }    // namespace Granular_NS
+   }    // namespace LAMMPS_NS
+
+   #endif /*GRAN_SUB_MOD_CUSTOM_H_ */
+   #endif /*GRAN_SUB_MOD_CLASS_H_ */
+
+
+and ``gran_sub_mod_custom.cpp``
+
+.. code-block:: c++
+
+   #include "gran_sub_mod_custom.h"
+   #include "gran_sub_mod_normal.h"
+   #include "granular_model.h"
+
+   using namespace LAMMPS_NS;
+   using namespace Granular_NS;
+
+   GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) :  GranSubModNormal(gm, lmp)
+   {
+     num_coeffs = 4;
+   }
+
+   /* ---------------------------------------------------------------------- */
+
+   void GranSubModNormalHookePiecewise::coeffs_to_local()
+   {
+     k1 = coeffs[0];
+     k2 = coeffs[1];
+     damp = coeffs[2];
+     delta_switch = coeffs[3];
+   }
+
+   /* ---------------------------------------------------------------------- */
+
+   double GranSubModNormalHookePiecewise::calculate_forces()
+   {
+     double Fne;
+     if (gm->delta >= delta_switch) {
+       Fne = k1 * delta_switch + k2 * (gm->delta - delta_switch);
+     } else {
+       Fne = k1 * gm->delta;
+     }
+     return Fne;
+   }
+

doc/src/Python_install.rst

@@ -27,124 +27,19 @@ interpreter can find it and installing the LAMMPS shared library into a
 folder that the dynamic loader searches or inside of the installed
 ``lammps`` package folder.  There are multiple ways to achieve this.
 
-#. Do a full LAMMPS installation of libraries, executables, selected
-   headers, documentation (if enabled), and supporting files (only
-   available via CMake), which can also be either system-wide or into
-   user specific folders.
-
 #. Install both components into a Python ``site-packages`` folder, either
    system-wide or in the corresponding user-specific folder. This way no
    additional environment variables need to be set, but the shared
    library is otherwise not accessible.
 
-#. Do an installation into a virtual environment. This can either be an
+#. Do an installation into a virtual environment.
-   installation of the Python package only or a full installation of LAMMPS.
 
 #. Leave the files where they are in the source/development tree and
    adjust some environment variables.
 
 .. tabs::
 
-   .. tab:: Full install (CMake-only)
+   .. tab:: Python package
-
-      :ref:`Build the LAMMPS executable and library <library>` with
-      ``-DBUILD_SHARED_LIBS=on``, ``-DLAMMPS_EXCEPTIONS=on`` and
-      ``-DPKG_PYTHON=on`` (The first option is required, the other two
-      are optional by recommended).  The exact file name of the shared
-      library depends on the platform (Unix/Linux, macOS, Windows) and
-      the build configuration being used.  The installation base folder
-      is already set by default to the ``$HOME/.local`` directory, but
-      it can be changed to a custom location defined by the
-      ``CMAKE_INSTALL_PREFIX`` CMake variable.  This uses a folder
-      called ``build`` to store files generated during compilation.
-
-      .. code-block:: bash
-
-         # create build folder
-         mkdir build
-         cd build
-
-         # configure LAMMPS compilation
-         cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \
-               -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
-
-         # compile LAMMPS
-         cmake --build .
-
-         # install LAMMPS into $HOME/.local
-         cmake --install .
-
-
-      This leads to an installation to the following locations:
-
-      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                        | Notes                                                       |
-      +========================+=================================================================+=============================================================+
-      | LAMMPS Python package  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$HOME/.local/lib/`` (32bit)                                 | Set shared loader environment variable to this path         |
-      |                        | * ``$HOME/.local/lib64/`` (64bit)                               | (see below for more info on this)                           |
-      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$HOME/.local/bin/``                                         |                                                             |
-      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/``                     | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
-      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
-
-      For a system-wide installation you need to set
-      ``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
-      ``/usr/local``); the default is ``${HOME}/.local``.  The
-      installation step for a system folder installation (**not** the
-      configuration/compilation) needs to be done with superuser
-      privilege, e.g. by using ``sudo cmake --install .``.  The
-      installation folders will then be changed to (assuming ``/usr`` as
-      prefix):
-
-      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                | Notes                                                       |
-      +========================+=========================================================+=============================================================+
-      | LAMMPS Python package  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``/usr/lib/`` (32bit)                                 |                                                             |
-      |                        | * ``/usr/lib64/`` (64bit)                               |                                                             |
-      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``/usr/bin/``                                         |                                                             |
-      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``/usr/share/lammps/potentials/``                     |                                                             |
-      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
-
-      To be able to use the "user" installation you have to ensure that
-      the folder containing the LAMMPS shared library is either included
-      in a path searched by the shared linker (e.g. like
-      ``/usr/lib64/``) or part of the ``LD_LIBRARY_PATH`` environment
-      variable (or ``DYLD_LIBRARY_PATH`` on macOS).  Otherwise you will
-      get an error when trying to create a LAMMPS object through the
-      Python module.
-
-      .. code-block:: bash
-
-         # Unix/Linux
-         export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
-
-         # macOS
-         export DYLD_LIBRARY_PATH=$HOME/.local/lib:$DYLD_LIBRARY_PATH
-
-      If you plan to use the LAMMPS executable (e.g., ``lmp``), you may
-      also need to adjust the ``PATH`` environment variable (but many
-      newer Linux distributions already have ``$HOME/.local/bin``
-      included). Example:
-
-      .. code-block:: bash
-
-         export PATH=$HOME/.local/bin:$PATH
-
-      To make those changes permanent, you can add the commands to your
-      ``$HOME/.bashrc`` file.  For a system-wide installation is is not
-      necessary due to files installed in system folders that are loaded
-      automatically when a login shell is started.
-
-   .. tab:: Python package only
 
       Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
       :doc:`traditional make <Build_make>` procedure in :ref:`shared
@@ -272,38 +167,6 @@ folder that the dynamic loader searches or inside of the installed
       | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps``  | ``X.Y`` depends on the installed Python version             |
       +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
 
-      If you do a full installation (CMake only) with "install", this
-      leads to the following installation locations:
-
-      +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                               | Notes                                                       |
-      +========================+========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps``  | ``X.Y`` depends on the installed Python version             |
-      +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/`` (32bit)                        | Set shared loader environment variable to this path         |
-      |                        | * ``$VIRTUAL_ENV/lib64/`` (64bit)                      | (see below for more info on this)                           |
-      +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$VIRTUAL_ENV/bin/``                                |                                                             |
-      +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/``            | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
-      +------------------------+--------------------------------------------------------+-------------------------------------------------------------+
-
-      In that case you need to modify the ``$HOME/myenv/bin/activate``
-      script in a similar fashion you need to update your
-      ``$HOME/.bashrc`` file to include the shared library and
-      executable locations in ``LD_LIBRARY_PATH`` (or
-      ``DYLD_LIBRARY_PATH`` on macOS) and ``PATH``, respectively.
-
-      For example with:
-
-      .. code-block:: bash
-
-         # Unix/Linux
-         echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
-
-         # macOS
-         echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
-
    .. tab:: In place usage
 
       You can also :doc:`compile LAMMPS <Build>` as usual in

doc/src/atom_style.rst

@@ -161,15 +161,14 @@ and each stores a per-particle diameter and mass.  If the diameter >
 0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
 is a point particle.  Note that by use of the *disc* keyword with the
 :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
-<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
+<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
-npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
+:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
-can be effectively treated as 2d discs for a 2d simulation if desired.
+spheres can be effectively treated as 2d discs for a 2d simulation if
-See also the :doc:`set density/disc <set>` command.  The *sphere* and
+desired.  See also the :doc:`set density/disc <set>` command.  These
-*bpm/sphere* styles take an optional 0 or 1 argument.  A value of 0
+styles take an optional 0 or 1 argument.  A value of 0 means the
-means the radius of each sphere is constant for the duration of the
+radius of each sphere is constant for the duration of the simulation.
-simulation.  A value of 1 means the radii may vary dynamically during
+A value of 1 means the radii may vary dynamically during the simulation,
-the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
+e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
-command.
 
 For the *ellipsoid* style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or

doc/src/bond_harmonic_restrain.rst

@@ -0,0 +1,90 @@
+.. index:: bond_style harmonic/restrain
+
+bond_style harmonic/restrain command
+====================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/restrain
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic
+   bond_coeff 5 80.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *harmonic/restrain* bond style uses the potential
+
+.. math::
+
+   E = K (r - r_{t=0})^2
+
+where :math:`r_{t=0}` is the distance between the bonded atoms at the
+beginning of the first :doc:`run <run>` or :doc:`minimize <minimize>`
+command after the bond style has been defined (*t=0*).  Note that the
+usual 1/2 factor is included in :math:`K`.  This will effectively
+restrain bonds to their initial length, whatever that is.  This is where
+this bond style differs from :doc:`bond style harmonic <bond_harmonic>`
+where the bond length is set through the per bond type coefficients.
+
+The following coefficient 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` (energy/distance\^2)
+
+This bond style differs from other options to add harmonic restraints
+like :doc:`fix restrain <fix_restrain>` or :doc:`pair style list
+<pair_list>` or :doc:`fix colvars <fix_colvars>` in that it requires a
+bond topology, and thus the defined bonds will trigger exclusion of
+special neighbors from the neighbor list according to the
+:doc:`special_bonds <special_bonds>` settings.
+
+Restart info
+""""""""""""
+
+This bond style supports the :doc:`write_restart <write_restart>` and
+:doc:`read_restart <read_restart>` commands. The state of the initial
+bond lengths is stored with restart files and read back.
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>`
+page for more info.
+
+This bond style maintains internal data to determine the original bond
+lengths :math:`r_{t=0}`.  This information will be written to
+:doc:`binary restart files <write_restart>` but **not** to :doc:`data
+files <write_data>`.  Thus, continuing a simulation is *only* possible
+with :doc:`read_restart <read_restart>`.  When using the :doc:`read_data
+command <read_data>`, the reference bond lengths :math:`r_{t=0}` will be
+re-initialized from the current geometry.
+
+This bond style cannot be used with :doc:`fix shake or fix rattle
+<fix_shake>`, with :doc:`fix filter/corotate <fix_filter_corotate>`, or
+any :doc:`tip4p pair style <pair_lj_cut_tip4p>` since there is no specific
+equilibrium distance for a given bond type.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`,  :doc:`bond_harmonic <bond_harmonic>`,
+:doc:`fix restrain <fix_restrain>`, :doc:`pair style list <pair_list>`
+
+Default
+"""""""
+
+none

doc/src/bond_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style style args
 
-* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
+* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
 
 * args = none for any style except *hybrid*
 
@@ -93,6 +93,7 @@ accelerated styles exist.
 * :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
 * :doc:`gromos <bond_gromos>` - GROMOS force field bond
 * :doc:`harmonic <bond_harmonic>` - harmonic bond
+* :doc:`harmonic/restrain <bond_harmonic_restrain>` - harmonic bond to restrain to original bond distance
 * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
 * :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
 * :doc:`lepton <bond_lepton>` - bond potential from evaluating a string

doc/src/compute.rst

@@ -206,6 +206,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`dilatation/atom <compute_dilatation_atom>` - Peridynamic dilatation for each atom
 * :doc:`dipole <compute_dipole>` - dipole vector and total dipole
 * :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
+* :doc:`dipole/tip4p <compute_dipole>` - dipole vector and total dipole with TIP4P pair style
+* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk with TIP4P pair style
 * :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
 * :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
 * :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature

doc/src/compute_dipole.rst

@@ -1,6 +1,10 @@
 .. index:: compute dipole
+.. index:: compute dipole/tip4p
 
 compute dipole command
+======================
+
+compute dipole/tip4p command
 ============================
 
 Syntax
@@ -8,10 +12,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID dipole arg
+   compute ID group-ID style arg
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* dipole = style name of this compute command
+* style = *dipole* or *dipole/tip4p*
 * arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
 
 Examples
@@ -21,6 +25,7 @@ Examples
 
    compute 1 fluid dipole
    compute dw water dipole geometry
+   compute dw water dipole/tip4p
 
 Description
 """""""""""
@@ -28,13 +33,20 @@ Description
 Define a computation that calculates the dipole vector and total dipole
 for a group of atoms.
 
-This compute calculates the x,y,z coordinates of the dipole vector
+These computes calculate the x,y,z coordinates of the dipole vector and
-and the total dipole moment for the atoms in the compute group.
+the total dipole moment for the atoms in the compute group.  This
-This includes all effects due to atoms passing through periodic boundaries.
+includes all effects due to atoms passing through periodic boundaries.
-For a group with a net charge the resulting dipole is made position independent
+For a group with a net charge the resulting dipole is made position
-by subtracting the position vector of the center of mass or geometric center
+independent by subtracting the position vector of the center of mass or
-times the net charge from the computed dipole vector. Both per-atom charges
+geometric center times the net charge from the computed dipole
-and per-atom dipole moments, if present, contribute to the computed dipole.
+vector.  Both per-atom charges and per-atom dipole moments, if present,
+contribute to the computed dipole.
+
+.. versionadded:: TBD
+
+Compute *dipole/tip4p* includes adjustments for the charge carrying
+point M in molecules with TIP4P water geometry.  The corresponding
+parameters are extracted from the pair style.
 
 .. note::
 
@@ -49,10 +61,10 @@ and per-atom dipole moments, if present, contribute to the computed dipole.
 Output info
 """""""""""
 
-This compute calculations a global scalar containing the magnitude of
+These computes calculate a global scalar containing the magnitude of the
-the computed dipole moment and a global vector of length 3 with the
+computed dipole moment and a global vector of length 3 with the dipole
-dipole vector.  See the :doc:`Howto output <Howto_output>` page for
+vector.  See the :doc:`Howto output <Howto_output>` page for an overview
-an overview of LAMMPS output options.
+of LAMMPS output options.
 
 The computed values are "intensive".  The array values will be in
 dipole units (i.e., charge :doc:`units <units>` times distance
@@ -60,7 +72,12 @@ dipole units (i.e., charge :doc:`units <units>` times distance
 
 Restrictions
 """"""""""""
- none
+
+Compute style *dipole/tip4p* is part of the EXTRA-COMPUTE package. It is
+only enabled if LAMMPS was built with that package.  See the :doc:`Build
+package <Build_package>` page for more info.
+
+Compute style *dipole/tip4p* can only be used with tip4p pair styles.
 
 Related commands
 """"""""""""""""

doc/src/compute_dipole_chunk.rst

@@ -1,17 +1,21 @@
 .. index:: compute dipole/chunk
+.. index:: compute dipole/tip4p/chunk
 
 compute dipole/chunk command
 ============================
 
+compute dipole/tip4p/chunk command
+==================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID dipole/chunk chunkID arg
+   compute ID group-ID style chunkID arg
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* dipole/chunk = style name of this compute command
+* style = *dipole/chunk* or *dipole/tip4p/chunk*
 * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
 * arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
 
@@ -38,13 +42,20 @@ or atoms in a spatial bin.  See the :doc:`compute chunk/atom
 details of how chunks can be defined and examples of how they can be
 used to measure properties of a system.
 
-This compute calculates the :math:`(x,y,z)` coordinates of the dipole vector
+These computes calculate the :math:`(x,y,z)` coordinates of the dipole
-and the total dipole moment for each chunk, which includes all effects due
+vector and the total dipole moment for each chunk, which includes all
-to atoms passing through periodic boundaries. For chunks with a net
+effects due to atoms passing through periodic boundaries.  For chunks
-charge the resulting dipole is made position independent by subtracting
+with a net charge the resulting dipole is made position independent by
-the position vector of the center of mass or geometric center times the
+subtracting the position vector of the center of mass or geometric
-net charge from the computed dipole vector. Both per-atom charges and
+center times the net charge from the computed dipole vector.  Both
-per-atom dipole moments, if present, contribute to the computed dipole.
+per-atom charges and per-atom dipole moments, if present, contribute to
+the computed dipole.
+
+.. versionadded:: TBD
+
+Compute *dipole/tip4p/chunk* includes adjustments for the charge
+carrying point M in molecules with TIP4P water geometry.  The
+corresponding parameters are extracted from the pair style.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
@@ -78,12 +89,12 @@ command, for example:
 Output info
 """""""""""
 
-This compute calculates a global array where the number of rows = the
+These computes calculate a global array where the number of rows = the
 number of chunks *Nchunk* as calculated by the specified :doc:`compute
-chunk/atom <compute_chunk_atom>` command.  The number of columns is 4 for
+chunk/atom <compute_chunk_atom>` command.  The number of columns is 4
-the :math:`(x,y,z)` dipole vector components and the total dipole of each
+for the :math:`(x,y,z)` dipole vector components and the total dipole of
-chunk. These values can be accessed by any command that uses global
+each chunk.  These values can be accessed by any command that uses
-array values from a compute as input.  See the :doc:`Howto output
+global array values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
 The array values are "intensive".  The array values will be in
@@ -92,7 +103,13 @@ dipole units (i.e., charge :doc:`units <units>` times distance
 
 Restrictions
 """"""""""""
- none
+
+Compute style *dipole/tip4p/chunk* is part of the EXTRA-COMPUTE
+package. It is only enabled if LAMMPS was built with that package.  See
+the :doc:`Build package <Build_package>` page for more info.
+
+Compute style *dipole/tip4p/chunk* can only be used with tip4p pair
+styles.
 
 Related commands
 """"""""""""""""

doc/src/dump.rst

@@ -111,6 +111,7 @@ Syntax
                                q, mux, muy, muz, mu,
                                radius, diameter, omegax, omegay, omegaz,
                                angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                               heatflow, temperature,
                                c_ID, c_ID[I], f_ID, f_ID[I], v_name,
                                i_name, d_name, i2_name[I], d2_name[I]
 
@@ -133,10 +134,12 @@ Syntax
            q = atom charge
            mux,muy,muz = orientation of dipole moment of atom
            mu = magnitude of dipole moment of atom
-           radius,diameter = radius,diameter of spherical particle
+           radius,diameter = radius, diameter of spherical particle
            omegax,omegay,omegaz = angular velocity of spherical particle
            angmomx,angmomy,angmomz = angular momentum of aspherical particle
            tqx,tqy,tqz = torque on finite-size particles
+           heatflow = rate of heat flow into particle
+           temperature = temperature of particle
            c_ID = per-atom vector calculated by a compute with ID
            c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
            f_ID = per-atom vector calculated by a fix with ID

doc/src/fix.rst

@@ -222,6 +222,7 @@ accelerated styles exist.
 * :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
 * :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
 * :doc:`efield <fix_efield>` - impose electric field on system
+* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
 * :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
 * :doc:`electrode/conp <fix_electrode>` - impose electric potential
 * :doc:`electrode/conq <fix_electrode>` - impose total electric charge
@@ -245,6 +246,7 @@ accelerated styles exist.
 * :doc:`grem <fix_grem>` - implements the generalized replica exchange method
 * :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
 * :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
+* :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
 * :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
 * :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
 * :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol

doc/src/fix_efield.rst

@@ -1,17 +1,21 @@
 .. index:: fix efield
+.. index:: fix efield/tip4p
 
 fix efield command
 ==================
 
+fix efield/tip4p command
+========================
+
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID efield ex ey ez keyword value ...
+   fix ID group-ID style ex ey ez keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* efield = style name of this fix command
+* style = *efield* or *efield/tip4p*
 * ex,ey,ez = E-field component values (electric field units)
 * any of ex,ey,ez can be a variable (see below)
 * zero or more keyword/value pairs may be appended to args
@@ -31,27 +35,36 @@ Examples
 
    fix kick external-field efield 1.0 0.0 0.0
    fix kick external-field efield 0.0 0.0 v_oscillate
+   fix kick external-field efield/tip4p 1.0 0.0 0.0
 
 Description
 """""""""""
 
-Add a force F = qE to each charged atom in the group due to an
+Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
 external electric field being applied to the system.  If the system
 contains point-dipoles, also add a torque on the dipoles due to the
 external electric field.
 
-For charges, any of the 3 quantities defining the E-field components
+.. versionadded:: TBD
-can be specified as an equal-style or atom-style
+
-:doc:`variable <variable>`, namely *ex*, *ey*, *ez*\ .  If the value is a
+When the *efield/tip4p* style is used, the E-field will be applied to
-variable, it should be specified as v_name, where name is the variable
+the position of the virtual charge site M of a TIP4P molecule instead of
-name.  In this case, the variable will be evaluated each timestep, and
+the oxygen position as it is defined by a corresponding :doc:`TIP4P pair
-its value used to determine the E-field component.
+style <pair_lj_cut_tip4p>`.  The forces on the M site due to the
+external field are projected on the oxygen and hydrogen atoms of the
+TIP4P molecules.
+
+For charges, any of the 3 quantities defining the E-field components can
+be specified as an equal-style or atom-style :doc:`variable <variable>`,
+namely *ex*, *ey*, *ez*\ .  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each timestep, and its value used to
+determine the E-field component.
 
 For point-dipoles, equal-style variables can be used, but atom-style
 variables are not currently supported, since they imply a spatial
 gradient in the electric field which means additional terms with
-gradients of the field are required for the force and torque on
+gradients of the field are required for the force and torque on dipoles.
-dipoles.
 
 Equal-style variables can specify formulas with various mathematical
 functions, and include :doc:`thermo_style <thermo_style>` command
@@ -81,10 +94,18 @@ self-consistent minimization problem (see below).
 The *energy* keyword is not allowed if the added field is a constant
 vector (ex,ey,ez), with all components defined as numeric constants
 and not as variables.  This is because LAMMPS can compute the energy
-for each charged particle directly as E = -x dot qE = -q (x\*ex + y\*ey
+for each charged particle directly as
-+ z\*ez), so that -Grad(E) = F.  Similarly for point-dipole particles
+
-the energy can be computed as E = -mu dot E = -(mux\*ex + muy\*ey +
+.. math::
-muz\*ez).
+
+   U_{efield} = -\vec{x} \cdot q\vec{E} = -q (x\cdot E_x + y\cdot E_y + z\cdot Ez),
+
+so that :math:`-\nabla U_{efield} = \vec{F}`.  Similarly for point-dipole particles
+the energy can be computed as
+
+.. math::
+
+   U_{efield} = -\vec{\mu} \cdot \vec{E} = -\mu_x\cdot E_x + \mu_y\cdot E_y + \mu_z\cdot E_z
 
 The *energy* keyword is optional if the added force is defined with
 one or more variables, and if you are performing dynamics via the
@@ -120,29 +141,28 @@ Restart, fix_modify, output, run start/stop, minimize info
 No information about this fix is written to :doc:`binary restart files
 <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
-this fix to add the potential energy inferred by the added force due
+fix to add the potential energy inferred by the added force due to the
-to the electric field to the global potential energy of the system as
+electric field to the global potential energy of the system as part of
-part of :doc:`thermodynamic output <thermo_style>`.  The default
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
+this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
-Note that this energy is a fictitious quantity but is needed so that
+energy is a fictitious quantity but is needed so that the :doc:`minimize
-the :doc:`minimize <minimize>` command can include the forces added by
+<minimize>` command can include the forces added by this fix in a
-this fix in a consistent manner.  I.e. there is a decrease in
+consistent manner.  I.e. there is a decrease in potential energy when
-potential energy when atoms move in the direction of the added force
+atoms move in the direction of the added force due to the electric
-due to the electric field.
+field.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
-this fix to add the contribution due to the added forces on atoms to
+fix to add the contribution due to the added forces on atoms to both the
-both the global pressure and per-atom stress of the system via the
+global pressure and per-atom stress of the system via the :doc:`compute
-:doc:`compute pressure <compute_pressure>` and :doc:`compute
+pressure <compute_pressure>` and :doc:`compute stress/atom
-stress/atom <compute_stress_atom>` commands.  The former can be
+<compute_stress_atom>` commands.  The former can be accessed by
-accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
+this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
-<run_style>` integrator the fix adding its forces. Default is the
+integrator the fix adding its forces. Default is the outermost level.
-outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
 which can be accessed by various :doc:`output commands
@@ -169,7 +189,11 @@ the iteration count during the minimization.
 Restrictions
 """"""""""""
 
-None
+Fix style *efield/tip4p* 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.
+
+Fix style *efield/tip4p* can only be used with tip4p pair styles.
 
 Related commands
 """"""""""""""""

doc/src/fix_heat_flow.rst

@@ -0,0 +1,70 @@
+.. index:: fix heat/flow
+
+fix heat/flow command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID heat/flow style values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* heat/flow = style name of this fix command
+* one style with corresponding value(s) needs to be listed
+
+  .. parsed-literal::
+
+     style = *constant* or *type*
+       *constant* = cp
+         cp = value of specifc heat (energy/(mass * temperature) units)
+       *type* = cp1 ... cpN
+         cpN = value of specifc heat for type N (energy/(mass * temperature) units)
+
+*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all heat/flow constant 1.0
+   fix 1 all heat/flow type 1.0 0.5
+
+Description
+"""""""""""
+
+Perform plain time integration to update temperature for atoms in the
+group each timestep. The specific heat of atoms can be defined using either
+the *constant* or *type* keywords. For style *constant*, the specific heat
+is a constant value *cp* for all atoms. For style *type*, *N* different values
+of the specific heat are defined, one for each of the *N* types of atoms.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+No global or per-atom quantities are stored by this fix for access by various
+:doc:`output commands <Howto_output>`. No parameter of this fix can be used
+with the *start/stop* keywords of the :doc:`run <run>` command.  This fix is
+not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+This fix requires that atoms store temperature and heat flow
+as defined by the :doc:`fix property/atom <fix_property_atom>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
+
+Default
+"""""""
+
+none

doc/src/fix_wall_gran.rst

@@ -46,7 +46,7 @@ Syntax
          radius = cylinder radius (distance units)
 
 * zero or more keyword/value pairs may be appended to args
-* keyword = *wiggle* or *shear* or *contacts*
+* keyword = *wiggle* or *shear* or *contacts* or *temperature*
 
   .. parsed-literal::
 
@@ -59,6 +59,8 @@ Syntax
          vshear = magnitude of shear velocity (velocity units)
       *contacts* value = none
          generate contact information for each particle
+      *temperature* value = temperature
+         specify temperature of wall
 
 
 Examples
@@ -71,7 +73,7 @@ Examples
    fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
-   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji heat 10 region myCone temperature 1.0
    fix 6 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
 
 Description
@@ -177,6 +179,16 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
 *vshear* < 0.  In this case, *vshear* is the tangential velocity of
 the wall at whatever *radius* has been defined.
 
+The *temperature* keyword is used to assign a temperature to the wall.
+The following value can either be a numeric value or an equal-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each timestep, and its value used to determine
+the temperature. This option must be used in conjunction with a heat
+conduction model defined in :doc:`pair_style granular <pair_granular>`,
+:doc:`fix property/atom <fix_property_atom>` to store temperature and a
+heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
+flow.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

doc/src/fix_wall_gran_region.rst

@@ -36,12 +36,14 @@ Syntax
 
 * wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
 * region-ID = region whose boundary will act as wall
-* keyword = *contacts*
+* keyword = *contacts* or *temperature*
 
   .. parsed-literal::
 
       *contacts* value = none
          generate contact information for each particle
+      *temperature* value = temperature
+         specify temperature of wall
 
 Examples
 """"""""
@@ -200,6 +202,17 @@ values for the 6 wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
 material.
 
+The *temperature* keyword is used to assign a temperature to the wall.
+The following value can either be a numeric value or an equal-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each timestep, and its value used to determine
+the temperature. This option must be used in conjunction with a heat
+conduction model defined in :doc:`pair_style granular <pair_granular>`,
+:doc:`fix property/atom <fix_property_atom>` to store temperature and a
+heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
+flow.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_gran.rst

@@ -279,6 +279,11 @@ statistically similar results.  This is because the forces they
 compute depend on atom velocities.  See the
 :doc:`read_restart <read_restart>` command for more details.
 
+Accumulated values for individual contacts are saved to to restart
+files but are not saved to data files. Therefore, forces may
+differ significantly when a system is reloaded using A
+:doc:`read_data <read_data>` command.
+
 Related commands
 """"""""""""""""
 

doc/src/pair_granular.rst

@@ -37,6 +37,9 @@ Examples
    pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
    pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
 
+   pair_style granular
+   pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 heat area 0.1
+
 Description
 """""""""""
 
@@ -223,16 +226,19 @@ for all models except *jkr*, for which it is given implicitly according
 to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`.  For *damping viscoelastic*,
 :math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
 
-The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`. Here, the damping coefficient specified as part of
+The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`.
-the normal model is interpreted as a restitution coefficient
+Here, the damping coefficient specified as part of the normal model is interpreted
-:math:`e`. The damping constant :math:`\eta_n` is given by:
+as a restitution coefficient :math:`e`. The damping constant :math:`\eta_n` is
+given by:
 
 .. math::
 
    \eta_n = \alpha (m_{eff}k_n)^{1/2}
 
-For normal contact models based on material parameters, :math:`k_n = 4/3Ea`.  The parameter :math:`\alpha` is related to the restitution
+For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. This
-coefficient *e* according to:
+damping model is not compatible with cohesive normal models such as *JKR* or *DMT*.
+The parameter :math:`\alpha` is related to the restitution coefficient *e*
+according to:
 
 .. math::
 
@@ -631,6 +637,34 @@ attractive force. This keyword cannot be used with the JKR or DMT models.
 
 ----------
 
+The optional *heat* keyword enables heat conduction. The options currently
+supported are:
+
+1. *none*
+2. *area* : :math:`k_{s}`
+
+If the *heat* keyword is not specified, the model defaults to *none*.
+
+For *heat* *area*, the heat
+:math:`Q` conducted between two particles is given by
+
+.. math::
+
+   Q = k_{s} a \Delta T
+
+
+
+where :math:`\Delta T` is the difference in the two particles' temperature,
+:math:`k_{s}` is a non-negative numeric value for the conductivity, and
+:math:`a` is the area of the contact and depends on the normal force model.
+
+Note that the option *none* must either be used in all or none of of the
+*pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and
+:doc:`fix property/atom <fix_property_atom>` for more information on this
+option.
+
+----------
+
 The *granular* pair style can reproduce the behavior of the
 *pair gran/\** styles with the appropriate settings (some very
 minor differences can be expected due to corrections in
@@ -641,7 +675,7 @@ is equivalent to *pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1*\ .
 The second example is equivalent to
 *pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
 The third example is equivalent to
-*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
+*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1 limit_damping*\ .
 
 ----------
 
@@ -733,22 +767,30 @@ These extra quantities can be accessed by the :doc:`compute pair/local <compute_
 Restrictions
 """"""""""""
 
-All the granular pair styles are part of the GRANULAR package.  It is
+This pair style is part of the GRANULAR package.  It is
-only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
 
-These pair styles require that atoms store torque and angular velocity
+This pair style requires that atoms store per-particle radius,
-(omega) as defined by the :doc:`atom_style <atom_style>`.  They also
+torque, and angular velocity (omega) as defined by the
-require a per-particle radius is stored.  The *sphere* atom style does
+:doc:`atom_style sphere <atom_style>`.
-all of this.
 
-This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost
+This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>`
-atoms.
+command so that velocities are stored by ghost atoms.
 
-These pair styles will not restart exactly when using the
+This pair style will not restart exactly when using the
-:doc:`read_restart <read_restart>` command, though they should provide
+:doc:`read_restart <read_restart>` command, though it should provide
-statistically similar results.  This is because the forces they
+statistically similar results.  This is because the forces it
-compute depend on atom velocities.  See the
+computes depend on atom velocities and the atom velocities have
-:doc:`read_restart <read_restart>` command for more details.
+been propagated half a timestep between the force computation and
+when the restart is written, due to using Velocity Verlet time
+integration. See the :doc:`read_restart <read_restart>` command
+for more details.
+
+Accumulated values for individual contacts are saved to restart
+files but are not saved to data files. Therefore, forces may
+differ significantly when a system is reloaded using the
+:doc:`read_data <read_data>` command.
 
 Related commands
 """"""""""""""""

doc/src/set.rst

@@ -19,7 +19,7 @@ Syntax
   *spin/electron* or *radius/electron* or
   *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
   *theta* or *theta/random* or *angmom* or *omega* or
-  *mass* or *density* or *density/disc* or
+  *mass* or *density* or *density/disc* or *temperature* or
   *volume* or *image* or *bond* or *angle* or *dihedral* or
   *improper* or *sph/e* or *sph/cv* or *sph/rho* or
   *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
@@ -100,6 +100,8 @@ Syntax
          value can be an atom-style variable (see below)
        *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
          value can be an atom-style variable (see below)
+       *temperature* value = temperature for finite-size particles (temperature units)
+         value can be an atom-style variable (see below)
        *volume* value = particle volume for Peridynamic particle (distance\^3 units)
          value can be an atom-style variable (see below)
        *image* nx ny nz
@@ -429,6 +431,12 @@ assumed to be in mass/distance\^2 units).
 If none of these cases are valid, then the mass is set to the density
 value directly (the input density is assumed to be in mass units).
 
+Keyword *temperature* sets the temperature of a finite-size particle.
+Currently, only the GRANULAR package supports this attribute. The
+temperature must be added using an instance of
+:doc:`fix property/atom <fix_property_atom>` The values for the
+temperature must be positive.
+
 Keyword *volume* sets the volume of all selected particles.  Currently,
 only the :doc:`atom_style peri <atom_style>` command defines particles
 with a volume attribute.  Note that this command does not adjust the

doc/utils/requirements.txt

@@ -1,5 +1,6 @@
-Sphinx<6.0.0
+Sphinx < 7.0.0
 sphinxcontrib-spelling
+sphinxcontrib-jquery >=3.0.0
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs
 breathe

doc/utils/sphinx-config/conf.py.in

@@ -47,6 +47,7 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.imgmath',
     'sphinx.ext.autodoc',
+    'sphinxcontrib.jquery',
     'sphinxfortran.fortran_domain',
     'sphinx_tabs.tabs',
     'table_from_list',

doc/utils/sphinx-config/false_positives.txt

@@ -1376,6 +1376,7 @@ hdnnp
 HDNNP
 Hearn
 heatconduction
+heatflow
 Hebbeker
 Hebenstreit
 Hecht
@@ -2473,6 +2474,7 @@ nodeless
 nodeset
 nodesets
 Noehring
+nofix
 Noffset
 noforce
 noguess

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

@@ -0,0 +1,484 @@
+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

@@ -0,0 +1,484 @@
+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

@@ -0,0 +1,635 @@
+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

@@ -0,0 +1,635 @@
+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

@@ -0,0 +1,634 @@
+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

@@ -0,0 +1,634 @@
+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.27Nov18.granregion.box.g++.1

@@ -1,475 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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
-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/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.5855 | 0.5855 | 0.5855 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-       0        0            0            0            0            0 
-     100       21   0.54270729   0.54270729   0.26473526 0.0013567682 
-     200       21   0.87606961   0.87606961   0.42735103  0.002190174 
-     300       21    1.1428374    1.1428374   0.55748167 0.0028570936 
-     400       21    1.3543103    1.3543103   0.66829516 0.0033857758 
-     500       21    1.0677786    1.0677786   0.53582407 0.0045048164 
-     600       56    0.6744286    0.6744286    0.3502938 0.0047464584 
-     700       56   0.75569283   0.75569283   0.39779462 0.0051953882 
-     800       56   0.61597505   0.61597505   0.32943642 0.0086022783 
-     900       56   0.65260802   0.65260802   0.34474044 0.0059298996 
-    1000       56   0.51624952   0.51624952   0.28326898 0.0067827337 
-    1100       56   0.46050076   0.46050076   0.25656319 0.0061891094 
-    1200       81   0.39112346   0.39112346   0.21690172 0.0086559316 
-    1300       81   0.33302617   0.33302617   0.19109398 0.0033381104 
-    1400       81    0.3933533    0.3933533   0.21221692  0.004135078 
-    1500       81   0.35495297   0.35495297   0.19925984 0.0037374946 
-    1600       81   0.34150606   0.34150606   0.19025811 0.0053492835 
-    1700      100    0.2561647    0.2561647   0.14186278 0.0090767057 
-    1800      100   0.21124278   0.21124278   0.12154878 0.0028545759 
-    1900      100   0.21793955   0.21793955   0.12173867 0.0029049155 
-    2000      100   0.25530858   0.25530858   0.13892272 0.0035528009 
-    2100      100   0.24671808   0.24671808   0.13687783 0.0076812435 
-    2200      100   0.22465216   0.22465216   0.12513603 0.0042528715 
-    2300      100   0.19362854   0.19362854   0.10914305 0.0061173739 
-    2400      100  0.061627608  0.061627608  0.045907717 0.0010422721 
-    2500      100  0.052700901  0.052700901  0.038883014 0.0019341647 
-    2600      100  0.037332018  0.037332018  0.028357146 0.0028364476 
-    2700      100  0.033526602  0.033526602  0.024609055 0.00044524562 
-    2800      100    0.0194148    0.0194148  0.014491377 0.00056526591 
-    2900      100  0.012346108  0.012346108  0.009857017 0.00081855699 
-    3000      100    0.0107344    0.0107344  0.008669364 0.00040371396 
-    3100      100 0.0092678291 0.0092678291 0.0073003108 0.00033287397 
-    3200      100 0.0085847001 0.0085847001 0.0064045591 0.00023253547 
-    3300      100 0.0049475182 0.0049475182 0.0041173627 0.00019876269 
-    3400      100 0.0030471097 0.0030471097 0.0026940466 0.00013462604 
-    3500      100 0.0031188371 0.0031188371  0.002612223 0.00026148578 
-    3600      100 0.0017616584 0.0017616584 0.0017464137 0.00019049724 
-    3700      100 0.0015475923 0.0015475923 0.0015560356 0.00025062814 
-    3800      100 0.0012547887 0.0012547887 0.0012622678 0.00014132236 
-    3900      100 0.0010047282 0.0010047282 0.0010379262 9.7665594e-05 
-    4000      100 0.00080895307 0.00080895307 0.00088263027 8.1278842e-05 
-    4100      100 0.00079078739 0.00079078739 0.00085810727 8.1271694e-05 
-    4200      100 0.00075192318 0.00075192318 0.00083085046 8.9352453e-05 
-    4300      100 0.00063546457 0.00063546457 0.00073222177 8.9264255e-05 
-    4400      100 0.00062398391 0.00062398391 0.00071312118 8.4200615e-05 
-    4500      100 0.00056464934 0.00056464934 0.00066087801 9.2097641e-05 
-    4600      100 0.00066951894 0.00066951894 0.00071633313 8.2457941e-05 
-    4700      100  0.001128837  0.001128837 0.00095293877 0.00011716361 
-    4800      100 0.00049580391 0.00049580391 0.00056710488 0.00010718794 
-    4900      100 0.00054374371 0.00054374371 0.00058671699 5.6580257e-05 
-    5000      100 0.00043016232 0.00043016232 0.00050264172 2.8640786e-05 
-Loop time of 0.0807264 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 26757050.955 tau/day, 61937.618 timesteps/s
-97.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0089066  | 0.0089066  | 0.0089066  |   0.0 | 11.03
-Neigh   | 0.017107   | 0.017107   | 0.017107   |   0.0 | 21.19
-Comm    | 0.00091505 | 0.00091505 | 0.00091505 |   0.0 |  1.13
-Output  | 0.00051451 | 0.00051451 | 0.00051451 |   0.0 |  0.64
-Modify  | 0.047671   | 0.047671   | 0.047671   |   0.0 | 59.05
-Other   |            | 0.005612   |            |       |  6.95
-
-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
-
-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
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-    5000      100 0.00043016232 0.00043016232 0.00050264172 2.8677624e-05 
-    5100      100   0.56489668   0.56489668   0.31137762  0.011848041 
-    5200      100   0.66068288   0.66068288   0.35915482  0.010199755 
-    5300      100   0.74068022   0.74068022   0.39643217  0.010806409 
-    5400      100   0.80913562   0.80913562   0.42748505   0.01190892 
-    5500      100   0.89409135   0.89409135   0.46135116  0.013093474 
-    5600      100   0.97585093   0.97585093   0.50021126  0.013588886 
-    5700      100    1.0151954    1.0151954    0.5174624   0.01601347 
-    5800      100    1.0452728    1.0452728   0.53122496   0.01879329 
-    5900      100    1.0881689    1.0881689   0.55152229  0.017120714 
-    6000      100    1.1133186    1.1133186    0.5638022  0.017284617 
-    6100      100    1.1532099    1.1532099   0.58310076  0.017031384 
-    6200      100    1.1798849    1.1798849    0.5959516  0.017971323 
-    6300      100      1.19387      1.19387   0.60173877  0.020140984 
-    6400      100    1.2126705    1.2126705   0.61086899  0.018426638 
-    6500      100    1.2137646    1.2137646   0.61284198  0.019127381 
-    6600      100    1.2339012    1.2339012   0.62199324  0.019378799 
-    6700      100    1.2439326    1.2439326   0.62488425  0.021049447 
-    6800      100    1.2489549    1.2489549    0.6278167  0.019552409 
-    6900      100    1.2733303    1.2733303   0.63898149  0.020237284 
-    7000      100    1.2835029    1.2835029    0.6440245  0.020798586 
-    7100      100    1.2866111    1.2866111   0.64522896  0.020355019 
-    7200      100    1.2886381    1.2886381    0.6467497   0.02062322 
-    7300      100    1.2885085    1.2885085   0.64617988  0.020350755 
-    7400      100    1.2912349    1.2912349   0.64691898  0.020197503 
-    7500      100    1.2963062    1.2963062   0.64926335  0.020349791 
-    7600      100    1.3016488    1.3016488   0.65150178  0.021001457 
-    7700      100    1.3009311    1.3009311   0.65106234  0.021546471 
-    7800      100    1.3016987    1.3016987   0.65143099  0.020994967 
-    7900      100    1.3028811    1.3028811   0.65164558  0.022200425 
-    8000      100    1.3087855    1.3087855   0.65439023  0.021310808 
-    8100      100    1.3102001    1.3102001   0.65514941  0.021177764 
-    8200      100    1.3133931    1.3133931   0.65681861  0.021591267 
-    8300      100    1.3148898    1.3148898   0.65775353  0.021335384 
-    8400      100    1.3160355    1.3160355   0.65845913  0.021238095 
-    8500      100    1.3171797    1.3171797   0.65934185  0.021172983 
-    8600      100    1.3176785    1.3176785   0.65964311  0.020747457 
-    8700      100    1.3180425    1.3180425   0.66019624  0.021275913 
-    8800      100    1.3287501    1.3287501   0.66444242  0.021832635 
-    8900      100    1.3249847    1.3249847    0.6625848  0.021337451 
-    9000      100     1.326216     1.326216   0.66297827  0.021470663 
-    9100      100    1.3261662    1.3261662   0.66303852  0.021423573 
-    9200      100    1.3312132    1.3312132    0.6653609  0.021385943 
-    9300      100    1.3300976    1.3300976   0.66504574  0.021489888 
-    9400      100    1.3377335    1.3377335   0.66820989  0.021565001 
-    9500      100    1.3421956    1.3421956   0.67027168  0.022402346 
-    9600      100    1.3464217    1.3464217   0.67228206  0.021991922 
-    9700      100    1.3470623    1.3470623   0.67258349  0.022035729 
-    9800      100    1.3446725    1.3446725   0.67135725  0.022295251 
-    9900      100     1.343146     1.343146   0.67066672  0.022049041 
-   10000      100    1.3435397    1.3435397   0.67093067  0.022451365 
-Loop time of 0.247549 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 8725560.044 tau/day, 20198.056 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.031783   | 0.031783   | 0.031783   |   0.0 | 12.84
-Neigh   | 0.038383   | 0.038383   | 0.038383   |   0.0 | 15.51
-Comm    | 0.0012343  | 0.0012343  | 0.0012343  |   0.0 |  0.50
-Output  | 0.00056028 | 0.00056028 | 0.00056028 |   0.0 |  0.23
-Modify  | 0.1687     | 0.1687     | 0.1687     |   0.0 | 68.15
-Other   |            | 0.00689    |            |       |  2.78
-
-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:    199 ave 199 max 199 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 199
-Ave neighs/atom = 1.99
-Neighbor list builds = 621
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   10000      100    1.3435397    1.3435397   0.67093067  0.022411116 
-   10100      100   0.31352763   0.31352763   0.18877908   0.01321582 
-   10200      100   0.13367611   0.13367611  0.090010637 0.0074171016 
-   10300      100  0.068195658  0.068195658  0.052632714 0.0019696287 
-   10400      100  0.053814936  0.053814936  0.043037586 0.0017121584 
-   10500      100   0.04032072   0.04032072  0.032944572 0.0011809154 
-   10600      100  0.029178161  0.029178161  0.023951873 0.0007804529 
-   10700      100  0.025978206  0.025978206  0.021045025 0.00099531465 
-   10800      100  0.023205036  0.023205036   0.01898502 0.00040036401 
-   10900      100  0.019994638  0.019994638  0.016451227 0.00027385559 
-   11000      100  0.017838131  0.017838131  0.014730762 0.00040399762 
-   11100      100  0.014863196  0.014863196  0.012314308 0.00019097464 
-   11200      100  0.012131256  0.012131256  0.010102122 0.00018514926 
-   11300      100  0.010881385  0.010881385 0.0090013541 0.00016579157 
-   11400      100 0.0076519814 0.0076519814 0.0064604568 0.00035399997 
-   11500      100 0.0067507315 0.0067507315 0.0057378868 0.00049116726 
-   11600      100 0.0053146649 0.0053146649 0.0047005938 0.00019625233 
-   11700      100 0.0044162463 0.0044162463 0.0039534657 0.00012548039 
-   11800      100 0.0037025387 0.0037025387 0.0033604103 6.2969827e-05 
-   11900      100 0.0032632211 0.0032632211 0.0030406641 8.1600622e-05 
-   12000      100 0.0028944057 0.0028944057 0.0026875858 6.6435833e-05 
-   12100      100 0.0027644728 0.0027644728 0.0025859762 5.5899271e-05 
-   12200      100  0.002480367  0.002480367 0.0023685117 6.0201418e-05 
-   12300      100 0.0024136475 0.0024136475 0.0023107986 4.4386874e-05 
-   12400      100 0.0021911567 0.0021911567 0.0021413262 5.0213175e-05 
-   12500      100 0.0019775905 0.0019775905 0.0019927698 0.00035250097 
-   12600      100 0.0017410363 0.0017410363  0.001830428 5.7885177e-05 
-   12700      100 0.0015749276 0.0015749276 0.0016816771 4.5530192e-05 
-   12800      100 0.0015187705 0.0015187705 0.0016218625 4.0589413e-05 
-   12900      100 0.0014778376 0.0014778376  0.001580232 4.0085455e-05 
-   13000      100 0.0014693491 0.0014693491 0.0015681809 4.0407656e-05 
-   13100      100 0.0014434495 0.0014434495 0.0015356278 5.7849212e-05 
-   13200      100 0.0014121959 0.0014121959 0.0015058758 3.2720737e-05 
-   13300      100 0.0012876041 0.0012876041 0.0013838998 3.7725702e-05 
-   13400      100 0.0012304951 0.0012304951 0.0013373457 3.6784546e-05 
-   13500      100 0.0011954303 0.0011954303 0.0012877627 3.6584963e-05 
-   13600      100 0.0011028947 0.0011028947 0.0011955404 2.3767582e-05 
-   13700      100 0.0010611762 0.0010611762 0.0011504675 3.485879e-05 
-   13800      100 0.0010080835 0.0010080835 0.0010997919 3.7905404e-05 
-   13900      100 0.00096495712 0.00096495712 0.0010530767 3.5273885e-05 
-   14000      100 0.00094945029 0.00094945029 0.0010409175 3.3718395e-05 
-   14100      100 0.00092386757 0.00092386757 0.0010217415 3.3313256e-05 
-   14200      100 0.00088928389 0.00088928389  0.000983023 3.290941e-05 
-   14300      100 0.00082696485 0.00082696485 0.00092690771 3.1651431e-05 
-   14400      100 0.00081086188 0.00081086188 0.00091681096 3.1845632e-05 
-   14500      100 0.00077732305 0.00077732305 0.00087592983 4.8087361e-05 
-   14600      100 0.00073386005 0.00073386005 0.00082546873 3.0892065e-05 
-   14700      100 0.00068701098 0.00068701098 0.00075953521 0.00010208859 
-   14800      100 0.00065860451 0.00065860451 0.00073738846 2.9272912e-05 
-   14900      100 0.00064706564 0.00064706564 0.00072748391 2.9817955e-05 
-   15000      100 0.00064227996 0.00064227996 0.00070964586 3.2547768e-05 
-Loop time of 0.0840213 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 25707757.817 tau/day, 59508.699 timesteps/s
-98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.01004    | 0.01004    | 0.01004    |   0.0 | 11.95
-Neigh   | 0.0057366  | 0.0057366  | 0.0057366  |   0.0 |  6.83
-Comm    | 0.00086808 | 0.00086808 | 0.00086808 |   0.0 |  1.03
-Output  | 0.00049472 | 0.00049472 | 0.00049472 |   0.0 |  0.59
-Modify  | 0.060893   | 0.060893   | 0.060893   |   0.0 | 72.47
-Other   |            | 0.005989   |            |       |  7.13
-
-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:    151 ave 151 max 151 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 151
-Ave neighs/atom = 1.51
-Neighbor list builds = 92
-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
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   15000      100 0.00064227996 0.00064227996 0.00070964586 3.2291286e-05 
-   15100      100   0.81230775   0.81230775   0.53266834  0.010948517 
-   15200      100   0.87957637   0.87957637   0.57559572  0.012401402 
-   15300      100    1.0262431    1.0262431   0.66535656  0.015239294 
-   15400      100    1.2863564    1.2863564   0.82026439  0.020115365 
-   15500      100    1.4721549    1.4721549   0.92138954  0.022400442 
-   15600      100    1.7140429    1.7140429    1.0103822   0.02558084 
-   15700      100    1.8963287    1.8963287    1.0916756  0.032032318 
-   15800      100    2.0741177    2.0741177    1.1706233  0.034251942 
-   15900      100    2.1434733    2.1434733    1.2054242  0.030132271 
-   16000      100    2.1409892    2.1409892    1.2019761  0.030914205 
-   16100      100    2.2496058    2.2496058    1.2476438  0.030939743 
-   16200      100     2.233356     2.233356    1.2499888  0.030097445 
-   16300      100    2.2673491    2.2673491     1.272321  0.030968524 
-   16400      100    2.3735648    2.3735648    1.3126117  0.034532377 
-   16500      100    2.4510087    2.4510087    1.3588349  0.036685351 
-   16600      100     2.497406     2.497406    1.3811443  0.032019982 
-   16700      100    2.6800518    2.6800518    1.4661941  0.037455527 
-   16800      100    2.8673997    2.8673997    1.5558303   0.03606532 
-   16900      100    3.1229488    3.1229488    1.6918439  0.039753213 
-   17000      100     3.117815     3.117815    1.6996841  0.046210837 
-   17100      100    3.3336225    3.3336225    1.7834517  0.047865361 
-   17200      100    3.1773164    3.1773164    1.7113961  0.047778334 
-   17300      100    3.4336759    3.4336759    1.8343073  0.049673718 
-   17400      100    3.3142326    3.3142326    1.7796613  0.055329946 
-   17500      100    3.3205493    3.3205493    1.7853946  0.043558145 
-   17600      100    3.2764553    3.2764553    1.7640702  0.051463316 
-   17700      100    3.1909643    3.1909643    1.7407995  0.043248948 
-   17800      100    3.1958324    3.1958324     1.735056  0.050123145 
-   17900      100    3.2431806    3.2431806    1.7380638  0.050838878 
-   18000      100    3.2967417    3.2967417    1.7705821  0.042176084 
-   18100      100    3.4270672    3.4270672    1.8459819  0.043589925 
-   18200      100    3.3638494    3.3638494    1.8159436  0.048949648 
-   18300      100    3.3192279    3.3192279    1.8122198  0.043629595 
-   18400      100    3.2627211    3.2627211     1.796316  0.045504529 
-   18500      100    3.5669172    3.5669172    1.9257062  0.048460393 
-   18600      100    3.5546411    3.5546411    1.9154318  0.046890968 
-   18700      100    3.7288485    3.7288485     2.011106  0.046906531 
-   18800      100    3.6800347    3.6800347    1.9936406  0.049985172 
-   18900      100    3.7151898    3.7151898     2.007659  0.050394561 
-   19000      100    3.9693368    3.9693368    2.1311549  0.053710204 
-   19100      100    3.6907732    3.6907732    1.9939387   0.05480136 
-   19200      100    3.8808777    3.8808777    2.0790125  0.055093552 
-   19300      100    3.8422142    3.8422142    2.0756951  0.058090774 
-   19400      100    3.7836875    3.7836875    2.0399805   0.06965907 
-   19500      100    4.0480195    4.0480195     2.169214  0.053420651 
-   19600      100     3.965917     3.965917    2.1245227  0.059077084 
-   19700      100    3.8980869    3.8980869    2.0956306  0.050857062 
-   19800      100     4.008079     4.008079    2.1501421  0.054938689 
-   19900      100    3.7244506    3.7244506    2.0080877  0.055481507 
-   20000      100    3.8146094    3.8146094    2.0541416  0.053187111 
-Loop time of 0.210396 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 10266363.999 tau/day, 23764.731 timesteps/s
-98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.013991   | 0.013991   | 0.013991   |   0.0 |  6.65
-Neigh   | 0.056947   | 0.056947   | 0.056947   |   0.0 | 27.07
-Comm    | 0.0013928  | 0.0013928  | 0.0013928  |   0.0 |  0.66
-Output  | 0.00054646 | 0.00054646 | 0.00054646 |   0.0 |  0.26
-Modify  | 0.13027    | 0.13027    | 0.13027    |   0.0 | 61.92
-Other   |            | 0.007249   |            |       |  3.45
-
-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 = 910
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   20000      100    3.8146094    3.8146094    2.0541416  0.052956687 
-   20100      100    1.3848453    1.3848453   0.82244153  0.017544632 
-   20200      100   0.89469578   0.89469578   0.55929611    0.0111604 
-   20300      100   0.83962013   0.83962013   0.52665461  0.010396174 
-   20400      100   0.77264252   0.77264252   0.48961142 0.0095493901 
-   20500      100   0.78613208   0.78613208   0.48683715  0.012166835 
-   20600      100   0.88411633   0.88411633   0.52854942  0.011725323 
-   20700      100   0.89833225   0.89833225   0.52549693  0.012193413 
-   20800      100   0.90216089   0.90216089   0.51167019  0.014289685 
-   20900      100   0.98665057   0.98665057    0.5468893  0.013794318 
-   21000      100    0.7576342    0.7576342   0.42758791  0.011720156 
-   21100      100    0.3821563    0.3821563   0.23426423  0.005324458 
-   21200      100   0.17486973   0.17486973   0.12876582 0.0029726352 
-   21300      100   0.17940562   0.17940562   0.12400155 0.0026179917 
-   21400      100   0.15526876   0.15526876   0.10526802  0.002341177 
-   21500      100  0.079493361  0.079493361  0.062289324 0.0017379534 
-   21600      100  0.057299519  0.057299519  0.047939171 0.0020095941 
-   21700      100  0.056900097  0.056900097  0.045799124 0.0017782068 
-   21800      100  0.039847861  0.039847861  0.035138066 0.0018265057 
-   21900      100   0.03919167   0.03919167  0.031815619 0.0012160098 
-   22000      100  0.025499317  0.025499317  0.022126202 0.0010056809 
-   22100      100  0.018956113  0.018956113  0.017843095 0.0016109368 
-   22200      100  0.017337018  0.017337018  0.016063068 0.00042537508 
-   22300      100  0.014785686  0.014785686  0.013007571 0.00049466367 
-   22400      100  0.011754087  0.011754087  0.010399793 0.00042349151 
-   22500      100  0.010362474  0.010362474  0.009077435 0.00025198478 
-   22600      100 0.0089484896 0.0089484896 0.0079474121 0.00035239475 
-   22700      100 0.0089936432 0.0089936432 0.0077908763 0.00018548371 
-   22800      100 0.0068663718 0.0068663718 0.0064061667 0.00025641972 
-   22900      100 0.0050272392 0.0050272392 0.0046676214 0.00040466013 
-   23000      100 0.0049250142 0.0049250142 0.0044849467 0.00035704909 
-   23100      100 0.0050508148 0.0050508148 0.0043117775 0.00030051828 
-   23200      100 0.0037293467 0.0037293467 0.0033592517 0.00038108923 
-   23300      100 0.0032823722 0.0032823722 0.0030511575 0.00040421775 
-   23400      100 0.0026913866 0.0026913866 0.0025493429 9.2813733e-05 
-   23500      100 0.0025590632 0.0025590632 0.0024466447 8.4695125e-05 
-   23600      100 0.0025270441 0.0025270441 0.0024236554 8.4237376e-05 
-   23700      100 0.0026406527 0.0026406527 0.0024501963 0.00015009901 
-   23800      100 0.0024633391 0.0024633391 0.0023470594 3.8990761e-05 
-   23900      100 0.0029505606 0.0029505606 0.0025122613 4.9810757e-05 
-   24000      100 0.0019535519 0.0019535519 0.0019112421 3.5804751e-05 
-   24100      100 0.0017505151 0.0017505151  0.001726233 2.380737e-05 
-   24200      100 0.0015864857 0.0015864857 0.0015479949 1.963276e-05 
-   24300      100 0.0014535898 0.0014535898 0.0014221262 3.6607862e-05 
-   24400      100 0.0013744934 0.0013744934 0.0013523293 1.4522467e-05 
-   24500      100 0.0013286378 0.0013286378 0.0013097089 3.2389792e-05 
-   24600      100 0.0012093624 0.0012093624 0.0011617482 4.848694e-05 
-   24700      100 0.0011817062 0.0011817062 0.0011409092 3.8898899e-05 
-   24800      100 0.0011142524 0.0011142524 0.0010877723 1.4560662e-05 
-   24900      100 0.0010941199 0.0010941199 0.0010614415 7.0209336e-05 
-   25000      100 0.0010773559 0.0010773559 0.0010389783 1.3332279e-05 
-Loop time of 0.0912137 on 1 procs for 5000 steps with 100 atoms
-
-Performance: 23680652.416 tau/day, 54816.325 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.010053   | 0.010053   | 0.010053   |   0.0 | 11.02
-Neigh   | 0.017597   | 0.017597   | 0.017597   |   0.0 | 19.29
-Comm    | 0.00092912 | 0.00092912 | 0.00092912 |   0.0 |  1.02
-Output  | 0.00049806 | 0.00049806 | 0.00049806 |   0.0 |  0.55
-Modify  | 0.056085   | 0.056085   | 0.056085   |   0.0 | 61.49
-Other   |            | 0.006052   |            |       |  6.63
-
-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:    143 ave 143 max 143 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 143
-Ave neighs/atom = 1.43
-Neighbor list builds = 289
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.27Nov18.granregion.box.g++.4

@@ -1,475 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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
-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/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.4834 | 0.4834 | 0.4834 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-       0        0            0            0            0            0 
-     100       21   0.54270729   0.54270729   0.26473526 0.0013567682 
-     200       21   0.87606961   0.87606961   0.42735103  0.002190174 
-     300       21    1.1428374    1.1428374   0.55748167 0.0028570936 
-     400       21    1.3543103    1.3543103   0.66829516 0.0033857758 
-     500       21    1.0677786    1.0677786   0.53582407 0.0045048164 
-     600       56    0.6744286    0.6744286    0.3502938 0.0047464584 
-     700       56   0.75569283   0.75569283   0.39779462 0.0051953882 
-     800       56   0.61597505   0.61597505   0.32943642 0.0086022783 
-     900       56   0.65260802   0.65260802   0.34474044 0.0059298996 
-    1000       56   0.51624952   0.51624952   0.28326898 0.0067827337 
-    1100       56   0.46050076   0.46050076   0.25656319 0.0061891094 
-    1200       81   0.39112346   0.39112346   0.21690172 0.0086559316 
-    1300       81   0.33302617   0.33302617   0.19109398 0.0033381104 
-    1400       81    0.3933533    0.3933533   0.21221692  0.004135078 
-    1500       81   0.35495297   0.35495297   0.19925984 0.0037374946 
-    1600       81   0.34150606   0.34150606   0.19025811 0.0053492835 
-    1700      100    0.2561647    0.2561647   0.14186278 0.0090767057 
-    1800      100   0.21124278   0.21124278   0.12154878  0.002854576 
-    1900      100   0.21793955   0.21793955   0.12173867 0.0029049175 
-    2000      100   0.25530858   0.25530858   0.13892272 0.0035528022 
-    2100      100   0.24671805   0.24671805   0.13687782 0.0076812357 
-    2200      100   0.22465212   0.22465212   0.12513612 0.0042526344 
-    2300      100   0.19362805   0.19362805   0.10914275 0.0061175383 
-    2400      100  0.061626039  0.061626039  0.045905953 0.0010393593 
-    2500      100  0.052690575  0.052690575  0.038879745 0.0018543933 
-    2600      100  0.037256691  0.037256691   0.02833916 0.0027683815 
-    2700      100  0.033416362  0.033416362  0.024551243 0.00046725913 
-    2800      100  0.019617758  0.019617758  0.014619416 0.00064550316 
-    2900      100  0.012313874  0.012313874 0.0098188153 0.00033470181 
-    3000      100  0.010948455  0.010948455 0.0087981878 0.00034401243 
-    3100      100  0.009359431  0.009359431 0.0073642412 0.00045497356 
-    3200      100  0.008129885  0.008129885 0.0061460516 0.00029944201 
-    3300      100 0.0050682533 0.0050682533 0.0042692811 0.00026543293 
-    3400      100 0.0031539312 0.0031539312 0.0027256511 0.00012475748 
-    3500      100 0.0023621311 0.0023621311 0.0021691817 0.0001186392 
-    3600      100 0.0018305354 0.0018305354 0.0018004128 0.00015926282 
-    3700      100 0.0016522492 0.0016522492 0.0017231072 0.0002193159 
-    3800      100 0.0011715102 0.0011715102 0.0012739973 0.0001747857 
-    3900      100 0.0010607606 0.0010607606 0.0010974725 0.00012476088 
-    4000      100 0.00087570802 0.00087570802 0.00095828935 6.5544103e-05 
-    4100      100 0.00078598203 0.00078598203 0.00088068743 9.4560761e-05 
-    4200      100 0.00088317454 0.00088317454 0.00092784605 8.1108122e-05 
-    4300      100 0.0015013254 0.0015013254 0.0012069505 8.8289686e-05 
-    4400      100 0.00070054041 0.00070054041 0.00079451193 5.195712e-05 
-    4500      100 0.00096259073 0.00096259073 0.00091232511 3.4895669e-05 
-    4600      100 0.00056641848 0.00056641848 0.00069083146 3.9657253e-05 
-    4700      100 0.0005455099 0.0005455099 0.00064816699 2.8131762e-05 
-    4800      100 0.00048254366 0.00048254366 0.00057192255 4.7914432e-05 
-    4900      100 0.00037108125 0.00037108125 0.00048035333 6.4711817e-05 
-    5000      100 0.00031290399 0.00031290399 0.00042398478 4.6025975e-05 
-Loop time of 0.075416 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 28641126.336 tau/day, 66298.904 timesteps/s
-93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0022948  | 0.0041364  | 0.0061705  |   2.8 |  5.48
-Neigh   | 0.0043123  | 0.0057145  | 0.0070784  |   1.8 |  7.58
-Comm    | 0.014259   | 0.018658   | 0.024313   |   3.3 | 24.74
-Output  | 0.0011525  | 0.001404   | 0.0015383  |   0.4 |  1.86
-Modify  | 0.0030508  | 0.014543   | 0.026602   |   9.5 | 19.28
-Other   |            | 0.03096    |            |       | 41.05
-
-Nlocal:    25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    5.5 ave 12 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:    39.75 ave 84 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 159
-Ave neighs/atom = 1.59
-Neighbor list builds = 310
-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
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-    5000      100 0.00031290399 0.00031290399 0.00042398478 4.4282259e-05 
-    5100      100   0.62661084   0.62661084   0.33840611  0.012020153 
-    5200      100   0.67371678   0.67371678   0.36218522 0.0093514044 
-    5300      100   0.75892331   0.75892331    0.4000747  0.010693252 
-    5400      100   0.86207426   0.86207426   0.44630388  0.013540097 
-    5500      100   0.96205334   0.96205334   0.49432848  0.017375079 
-    5600      100    1.0261194    1.0261194   0.52203912  0.016045333 
-    5700      100    1.0584366    1.0584366   0.53794336  0.018621676 
-    5800      100    1.0881674    1.0881674   0.55300469   0.01930602 
-    5900      100    1.1214233    1.1214233   0.56613492  0.021141141 
-    6000      100    1.1666836    1.1666836   0.58759377  0.017655361 
-    6100      100    1.1785775    1.1785775   0.59365148   0.01829443 
-    6200      100    1.2092305    1.2092305   0.60798809  0.018752443 
-    6300      100    1.2331787    1.2331787   0.62003386  0.020291021 
-    6400      100    1.2561616    1.2561616   0.63143643  0.019899235 
-    6500      100     1.284432     1.284432    0.6460504   0.02083284 
-    6600      100    1.2678801    1.2678801   0.63882384  0.019456553 
-    6700      100    1.2662641    1.2662641   0.63676836  0.020235578 
-    6800      100    1.2785484    1.2785484   0.64129093  0.020335162 
-    6900      100    1.2916608    1.2916608   0.64764298  0.020154225 
-    7000      100    1.2907774    1.2907774   0.64724849  0.020550885 
-    7100      100    1.3074473    1.3074473   0.65460147  0.020847362 
-    7200      100    1.3124592    1.3124592   0.65641332  0.020897348 
-    7300      100    1.3206191    1.3206191   0.66011491  0.021444077 
-    7400      100    1.3273988    1.3273988   0.66350669   0.02129418 
-    7500      100    1.3343911    1.3343911   0.66707269  0.021337376 
-    7600      100    1.3368998    1.3368998   0.66869327  0.021415901 
-    7700      100     1.330658     1.330658   0.66535295  0.021500761 
-    7800      100     1.330801     1.330801   0.66555123  0.022806058 
-    7900      100    1.3392828    1.3392828   0.66926796   0.02194009 
-    8000      100    1.3432728    1.3432728   0.67142337  0.022393719 
-    8100      100    1.3411612    1.3411612   0.66989302  0.022366895 
-    8200      100    1.3427451    1.3427451   0.67054285  0.021966329 
-    8300      100    1.3418147    1.3418147   0.67023132  0.022513459 
-    8400      100     1.346493     1.346493   0.67247837  0.022705366 
-    8500      100    1.3513958    1.3513958    0.6749092  0.022834077 
-    8600      100    1.3520297    1.3520297   0.67506261  0.023227676 
-    8700      100    1.3517157    1.3517157   0.67485073  0.023043414 
-    8800      100    1.3530071    1.3530071   0.67547212  0.022933766 
-    8900      100    1.3550454    1.3550454   0.67657277  0.022744182 
-    9000      100    1.3554069    1.3554069   0.67673505  0.022802134 
-    9100      100    1.3556675    1.3556675   0.67698335  0.022868449 
-    9200      100    1.3534709    1.3534709   0.67600677  0.022537792 
-    9300      100    1.3525103    1.3525103   0.67569499  0.022687849 
-    9400      100    1.3612673    1.3612673   0.67967213  0.022703588 
-    9500      100    1.3649439    1.3649439   0.68147385  0.023498539 
-    9600      100    1.3629376    1.3629376   0.68063814  0.023515579 
-    9700      100    1.3648924    1.3648924   0.68137104  0.023641856 
-    9800      100    1.3662063    1.3662063   0.68196538  0.023576884 
-    9900      100    1.3689695    1.3689695   0.68326751  0.023572622 
-   10000      100    1.3701139    1.3701139   0.68383343  0.023720885 
-Loop time of 0.174251 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 12395939.906 tau/day, 28694.305 timesteps/s
-96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0024631  | 0.010709   | 0.020461   |   8.0 |  6.15
-Neigh   | 0.0078361  | 0.012368   | 0.016955   |   4.0 |  7.10
-Comm    | 0.0059071  | 0.013641   | 0.023547   |   6.6 |  7.83
-Output  | 0.0011749  | 0.0021775  | 0.0030091  |   1.4 |  1.25
-Modify  | 0.015055   | 0.055709   | 0.097013   |  17.2 | 31.97
-Other   |            | 0.07965    |            |       | 45.71
-
-Nlocal:    25 ave 51 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    4.5 ave 10 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:    49.25 ave 101 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 197
-Ave neighs/atom = 1.97
-Neighbor list builds = 627
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   10000      100    1.3701139    1.3701139   0.68383343  0.023895921 
-   10100      100   0.25960098   0.25960098   0.15183967 0.0049554084 
-   10200      100   0.15017576   0.15017576   0.10081112 0.0045433238 
-   10300      100   0.10129671   0.10129671  0.078049099 0.0014012658 
-   10400      100   0.06742425   0.06742425  0.055603816 0.0010184792 
-   10500      100  0.053446366  0.053446366  0.045338293 0.00089291689 
-   10600      100  0.041898231  0.041898231  0.036081995 0.00060703885 
-   10700      100   0.03580041   0.03580041  0.031118724 0.00067731964 
-   10800      100  0.030933755  0.030933755  0.026372348 0.00039362325 
-   10900      100  0.027278004  0.027278004  0.022868898 0.0003680788 
-   11000      100  0.021566952  0.021566952  0.017994879 0.0013056062 
-   11100      100  0.019143625  0.019143625  0.015833865 0.00050998112 
-   11200      100  0.015659868  0.015659868  0.013119379 0.00012755696 
-   11300      100  0.013554605  0.013554605   0.01147808 0.00027393437 
-   11400      100   0.01204033   0.01204033  0.010273026 0.00033430792 
-   11500      100  0.010958991  0.010958991 0.0093924566 0.00049023273 
-   11600      100   0.01012553   0.01012553 0.0084556996 0.00021457333 
-   11700      100 0.0083584131 0.0083584131 0.0071118766 7.7149089e-05 
-   11800      100  0.007044883  0.007044883 0.0058675523 0.00036165381 
-   11900      100 0.0059875106 0.0059875106 0.0050610372 7.4095443e-05 
-   12000      100 0.0045180275 0.0045180275 0.0039006565 0.00014607704 
-   12100      100 0.0036631356 0.0036631356 0.0031154279 7.031064e-05 
-   12200      100 0.0034443424 0.0034443424 0.0029190637 0.00020974475 
-   12300      100 0.0030853504 0.0030853504 0.0026315266 3.4873541e-05 
-   12400      100 0.0025451749 0.0025451749 0.0022290833 0.00041551536 
-   12500      100 0.0021624857 0.0021624857 0.0019127734 2.6760761e-05 
-   12600      100 0.0020637862 0.0020637862 0.0018186641 4.9446655e-05 
-   12700      100 0.0019889538 0.0019889538 0.0017604689 3.326943e-05 
-   12800      100 0.0018706349 0.0018706349 0.0016669237 2.3327318e-05 
-   12900      100 0.0017472824 0.0017472824  0.001579469 8.816765e-05 
-   13000      100 0.0016034824 0.0016034824 0.0014549852 3.5407524e-05 
-   13100      100   0.00151798   0.00151798 0.0013826659 1.8754149e-05 
-   13200      100 0.0013049781 0.0013049781 0.0012137907 0.00015263775 
-   13300      100 0.0012270536 0.0012270536 0.0011590841  4.77636e-06 
-   13400      100 0.0011395128 0.0011395128 0.0010860297 2.5606328e-05 
-   13500      100 0.0010858414 0.0010858414 0.0010486713 5.8563931e-05 
-   13600      100 0.0010474389 0.0010474389  0.001015904 1.4319658e-05 
-   13700      100 0.00099241549 0.00099241549 0.00097825038 1.2281142e-05 
-   13800      100 0.00084449252 0.00084449252 0.00084141963 1.0451215e-05 
-   13900      100 0.00084004792 0.00084004792 0.00083755495 3.7174162e-05 
-   14000      100 0.00082183505 0.00082183505 0.00082027058 1.0170209e-05 
-   14100      100 0.00082377076 0.00082377076 0.00080489795 1.181976e-05 
-   14200      100 0.00076903208 0.00076903208 0.00076216608 4.4590341e-05 
-   14300      100 0.00075173269 0.00075173269 0.00074828209 2.2134371e-05 
-   14400      100 0.00074379148 0.00074379148 0.00074072001 1.5746014e-05 
-   14500      100 0.00072454029 0.00072454029 0.0007174429 8.9830398e-06 
-   14600      100 0.00072372648 0.00072372648 0.00071678769 9.1111512e-06 
-   14700      100 0.00071541587 0.00071541587 0.00070893868 7.8446375e-05 
-   14800      100 0.0006820307 0.0006820307 0.00066675502 8.4401299e-06 
-   14900      100 0.00067050627 0.00067050627 0.00065751846 0.0001228548 
-   15000      100 0.00064977132 0.00064977132 0.00062305247 7.8887775e-06 
-Loop time of 0.0746691 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 28927619.905 tau/day, 66962.083 timesteps/s
-96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0021737  | 0.0042608  | 0.0063519  |   3.2 |  5.71
-Neigh   | 0.0012126  | 0.0019009  | 0.0026193  |   1.6 |  2.55
-Comm    | 0.0023425  | 0.0092477  | 0.016876   |   7.2 | 12.38
-Output  | 0.0010619  | 0.0017995  | 0.0030522  |   1.8 |  2.41
-Modify  | 0.00097013 | 0.017151   | 0.03415    |  12.3 | 22.97
-Other   |            | 0.04031    |            |       | 53.98
-
-Nlocal:    25 ave 55 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    3.75 ave 9 max 0 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs:    42.5 ave 88 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 170
-Ave neighs/atom = 1.7
-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
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   15000      100 0.00064977132 0.00064977132 0.00062305247 7.9405607e-06 
-   15100      100    1.0123899    1.0123899   0.66185504  0.014587215 
-   15200      100    1.0332828    1.0332828   0.67443308  0.014002815 
-   15300      100    1.0804076    1.0804076   0.72450056  0.016985272 
-   15400      100    1.2868163    1.2868163    0.8708132  0.022190597 
-   15500      100    1.5180471    1.5180471   0.99613124  0.026761866 
-   15600      100    1.5422016    1.5422016    1.0021746  0.024490139 
-   15700      100    1.7142241    1.7142241    1.0611146    0.0301368 
-   15800      100    1.8747057    1.8747057    1.1207858  0.027612699 
-   15900      100    1.9294819    1.9294819    1.1289025  0.027270228 
-   16000      100     1.953275     1.953275    1.1264475  0.031568811 
-   16100      100    2.0434228    2.0434228    1.1665365  0.026358952 
-   16200      100    2.2129393    2.2129393    1.2448327  0.029613382 
-   16300      100    2.2558224    2.2558224    1.2373264  0.028306021 
-   16400      100     2.367398     2.367398     1.293448  0.029659303 
-   16500      100    2.4221549    2.4221549    1.3198966  0.032541712 
-   16600      100     2.510283     2.510283    1.3618001  0.034740544 
-   16700      100    2.6776293    2.6776293    1.4508262  0.034556341 
-   16800      100    2.8095841    2.8095841    1.5190571  0.035183782 
-   16900      100    2.8485646    2.8485646    1.5344387  0.037153336 
-   17000      100    3.0298285    3.0298285    1.6321623  0.040745906 
-   17100      100    3.0218054    3.0218054    1.6187189  0.042082135 
-   17200      100    3.1981705    3.1981705    1.7090597  0.041770208 
-   17300      100    3.3178559    3.3178559    1.7723201  0.044604756 
-   17400      100    3.3940903    3.3940903    1.8229846  0.049231759 
-   17500      100    3.3274817    3.3274817    1.7870996  0.051649102 
-   17600      100    3.3204358    3.3204358     1.791527  0.043875639 
-   17700      100    3.2185649    3.2185649    1.7480866  0.049941218 
-   17800      100    3.2507826    3.2507826    1.7727758  0.048622479 
-   17900      100    3.2432767    3.2432767    1.7796296  0.044343902 
-   18000      100    3.0841272    3.0841272    1.6978832  0.045344433 
-   18100      100    3.0953909    3.0953909     1.699898  0.040070963 
-   18200      100    3.1405704    3.1405704    1.7316463  0.042528194 
-   18300      100    3.1904871    3.1904871    1.7555188  0.041141165 
-   18400      100    3.3256779    3.3256779    1.8243767  0.043908318 
-   18500      100    3.5161823    3.5161823    1.9150861  0.045165166 
-   18600      100    3.5668273    3.5668273    1.9217975  0.048127705 
-   18700      100    3.6648305    3.6648305    1.9685241  0.051205352 
-   18800      100    3.9000502    3.9000502    2.0886668   0.05262835 
-   18900      100    4.0217758    4.0217758    2.1465498  0.054502839 
-   19000      100    3.8431174    3.8431174    2.0581611  0.054852333 
-   19100      100    4.1721454    4.1721454    2.2221193  0.053831555 
-   19200      100    3.9061181    3.9061181     2.096323  0.058077678 
-   19300      100    4.0191085    4.0191085    2.1408069   0.05475437 
-   19400      100    3.8840871    3.8840871    2.0887677  0.061905092 
-   19500      100    3.8388062    3.8388062    2.0567095  0.051076414 
-   19600      100    3.6331742    3.6331742    1.9574769   0.04748008 
-   19700      100    3.6996954    3.6996954    1.9887285  0.053305043 
-   19800      100    3.8649872    3.8649872    2.0827424  0.060484008 
-   19900      100    3.8305733    3.8305733    2.0700281  0.052926584 
-   20000      100    3.7948463    3.7948463    2.0657301  0.048516953 
-Loop time of 0.156359 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 13814330.011 tau/day, 31977.616 timesteps/s
-94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0040646  | 0.0058124  | 0.0074518  |   1.6 |  3.72
-Neigh   | 0.014813   | 0.018389   | 0.020829   |   1.6 | 11.76
-Comm    | 0.031892   | 0.034103   | 0.036658   |   1.0 | 21.81
-Output  | 0.0013497  | 0.0019822  | 0.003484   |   2.0 |  1.27
-Modify  | 0.031006   | 0.046878   | 0.056364   |   4.5 | 29.98
-Other   |            | 0.0492     |            |       | 31.46
-
-Nlocal:    25 ave 37 max 10 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    3.75 ave 6 max 2 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-Neighs:    36.25 ave 57 max 9 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-
-Total # of neighbors = 145
-Ave neighs/atom = 1.45
-Neighbor list builds = 921
-Dangerous builds = 0
-
-region          container delete
-region          container block -6 6 -6 6 -6 6 units box
-run             5000
-Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.734 | 5.734 Mbytes
-Step Atoms Temp c_1 c_2 Press 
-   20000      100    3.7948463    3.7948463    2.0657301  0.048381317 
-   20100      100    1.1359931    1.1359931   0.70170151  0.015300556 
-   20200      100   0.87354617   0.87354617   0.55969299  0.012181983 
-   20300      100   0.84424484   0.84424484   0.52849351  0.017724782 
-   20400      100   0.82422562   0.82422562   0.50175766 0.0098154181 
-   20500      100   0.83731289   0.83731289   0.49814627  0.010465327 
-   20600      100   0.93125924   0.93125924   0.53803834  0.011624902 
-   20700      100    1.0810919    1.0810919   0.60974741   0.01425935 
-   20800      100    1.0646343    1.0646343   0.60037545  0.013418132 
-   20900      100    1.0608055    1.0608055   0.58353908  0.015119612 
-   21000      100   0.68173094   0.68173094    0.3941588 0.0099947535 
-   21100      100   0.35407592   0.35407592   0.21306735 0.0043859494 
-   21200      100   0.19247432   0.19247432   0.12989264 0.0031808422 
-   21300      100   0.13493768   0.13493768  0.093987634 0.0025990872 
-   21400      100  0.085735857  0.085735857  0.062091707  0.001434207 
-   21500      100  0.074307566  0.074307566   0.05224051 0.0022163094 
-   21600      100  0.069932382  0.069932382  0.045388838 0.0020296572 
-   21700      100  0.041749712  0.041749712  0.031422931  0.001211155 
-   21800      100   0.03378055   0.03378055  0.026248846 0.0020596463 
-   21900      100  0.030608528  0.030608528  0.022868294 0.0016282878 
-   22000      100  0.025632448  0.025632448  0.019606402 0.0011659657 
-   22100      100  0.013785062  0.013785062  0.011561769 0.00069006322 
-   22200      100  0.013139066  0.013139066  0.010559726 0.00038424576 
-   22300      100   0.01455318   0.01455318  0.011094558 0.00054735929 
-   22400      100 0.0096885414 0.0096885414  0.008012617 0.00055875777 
-   22500      100 0.0081193116 0.0081193116  0.006802973 0.00052914932 
-   22600      100 0.0057159621 0.0057159621 0.0048680253 0.00054864875 
-   22700      100 0.0052344376 0.0052344376 0.0045511708 0.00026333033 
-   22800      100 0.0054554177 0.0054554177 0.0045005479 0.0002085972 
-   22900      100 0.0039455776 0.0039455776 0.0035287888 0.00022514017 
-   23000      100 0.0042620461 0.0042620461 0.0035747729 0.00020030999 
-   23100      100 0.0035303095 0.0035303095 0.0031995108 0.00016007298 
-   23200      100 0.0029747457 0.0029747457 0.0027095904 0.00029775807 
-   23300      100 0.0032404433 0.0032404433  0.002769389 0.00019627995 
-   23400      100 0.0024965262 0.0024965262 0.0022343473 0.00018870133 
-   23500      100   0.00251617   0.00251617 0.0022533604 0.0002661237 
-   23600      100 0.0025923653 0.0025923653 0.0022887204 0.00018475201 
-   23700      100 0.0023016545 0.0023016545 0.0019829032 0.00014888334 
-   23800      100 0.0028358441 0.0028358441 0.0021790504 0.00064613131 
-   23900      100 0.0016682403 0.0016682403 0.0014930521 8.8407075e-05 
-   24000      100 0.0016341577 0.0016341577 0.0014597606 0.00011262081 
-   24100      100 0.0015433636 0.0015433636 0.0013981581 8.364568e-05 
-   24200      100 0.0015033978 0.0015033978 0.0013582013 8.4539006e-05 
-   24300      100 0.0014513098 0.0014513098 0.0012943981 0.00010546194 
-   24400      100 0.0013293352 0.0013293352  0.001206366 8.4967509e-05 
-   24500      100 0.0013732518 0.0013732518  0.001202532 0.00014787559 
-   24600      100 0.00091890041 0.00091890041 0.00084499923 0.00010080638 
-   24700      100 0.00083467915 0.00083467915 0.00077071316 5.3934025e-05 
-   24800      100 0.00080701934 0.00080701934 0.0007477161 5.3982095e-05 
-   24900      100 0.00080620771 0.00080620771 0.0007471026 5.3581294e-05 
-   25000      100 0.00080568604 0.00080568604 0.00074625735 5.3574637e-05 
-Loop time of 0.0792506 on 4 procs for 5000 steps with 100 atoms
-
-Performance: 27255302.560 tau/day, 63090.978 timesteps/s
-95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0023611  | 0.0047854  | 0.0077851  |   3.4 |  6.04
-Neigh   | 0.0042653  | 0.005571   | 0.0067258  |   1.5 |  7.03
-Comm    | 0.0077977  | 0.013373   | 0.019515   |   4.4 | 16.87
-Output  | 0.0010924  | 0.0017727  | 0.0030222  |   1.8 |  2.24
-Modify  | 0.0023608  | 0.015964   | 0.030545   |  10.5 | 20.14
-Other   |            | 0.03778    |            |       | 47.68
-
-Nlocal:    25 ave 50 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    5 ave 10 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    35.75 ave 78 max 0 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 143
-Ave neighs/atom = 1.43
-Neighbor list builds = 287
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/granregion/log.27Nov18.granregion.funnel.g++.1

@@ -1,601 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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} bin
-neighbor        0.5 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 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/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-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:705)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes
-Step CPU Atoms KinEng 
-       0            0        0           -0 
-    1000   0.63593698     2000           -0 
-    2000    1.0282419     2000           -0 
-    3000    1.4184453     2000           -0 
-    4000    1.8055785     2000           -0 
-    5000    2.1941335     2000           -0 
-    6000    2.5804653     2000           -0 
-    7000    2.9660621     2000           -0 
-    8000    3.3506265     2000           -0 
-    9000    3.7344413     2000           -0 
-   10000    4.1212304     2000           -0 
-   11000    4.5044594     2000           -0 
-   12000    4.8875456     2000           -0 
-   13000    5.2698007     2000           -0 
-   14000    5.6527214     2000           -0 
-   15000    6.0349295     2000           -0 
-   16000    6.4172938     2000           -0 
-   17000    6.8001184     2000           -0 
-   18000    7.1826644     2000           -0 
-   19000    7.5654378     2000           -0 
-   20000    7.9511659     2000           -0 
-Loop time of 7.95118 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    | 0.6189     | 0.6189     | 0.6189     |   0.0 |  7.78
-Neigh   | 0.09361    | 0.09361    | 0.09361    |   0.0 |  1.18
-Comm    | 0.016098   | 0.016098   | 0.016098   |   0.0 |  0.20
-Output  | 0.00048828 | 0.00048828 | 0.00048828 |   0.0 |  0.01
-Modify  | 6.9973     | 6.9973     | 6.9973     |   0.0 | 88.00
-Other   |            | 0.2248     |            |       |  2.83
-
-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:    1537 ave 1537 max 1537 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1537
-Ave neighs/atom = 0.7685
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Per MPI rank memory allocation (min/avg/max) = 12.77 | 12.77 | 12.77 Mbytes
-Step CPU Atoms KinEng 
-   20000            0     2000    6443.7665 
-   21000    0.3826313     2000    6572.3531 
-   22000   0.76688981     2000    6723.8376 
-   23000    1.1534231     2000    6853.1812 
-   24000    1.5391715     2000    6976.0209 
-   25000    1.9263508     2000    7096.9955 
-   26000    2.3168406     2000    7215.5795 
-   27000    2.7065961     2000    7349.2382 
-   28000     3.096664     2000    7471.8719 
-   29000    3.4905531     2000    7574.8228 
-   30000    3.8877606     2000    7659.3836 
-   31000    4.2839894     2000    7703.6856 
-   32000    4.6859732     2000     7644.279 
-   33000    5.0932801     2000    7526.6944 
-   34000    5.5045564     2000    7370.0821 
-   35000    5.9206297     2000    7193.0457 
-   36000     6.343729     2000    6990.9899 
-   37000    6.7719142     2000    6849.2841 
-   38000    7.2016783     2000    6701.7433 
-   39000    7.6354482     2000    6538.9557 
-   40000     8.078445     2000    6381.9346 
-   41000    8.5191586     2000    6217.5253 
-   42000    8.9630713     2000    6093.5344 
-   43000    9.4097741     2000    5943.0479 
-   44000    9.8652256     2000    5841.0782 
-   45000    10.331057     2000    5652.8319 
-   46000    10.803253     2000    5476.1466 
-   47000    11.278766     2000    5267.7855 
-   48000    11.759121     2000    5131.4036 
-   49000    12.248896     2000    4972.7696 
-   50000    12.747719     2000    4867.0868 
-   51000    13.246704     2000     4681.897 
-   52000    13.757842     2000    4506.8185 
-   53000    14.276078     2000    4346.8045 
-   54000    14.795933     2000    4193.8194 
-   55000    15.311241     2000    4058.2049 
-   56000    15.828737     2000    3879.0325 
-   57000    16.359453     2000    3696.3154 
-   58000    16.905406     2000    3504.0399 
-   59000    17.460454     2000    3284.6522 
-   60000    18.027276     2000    3061.0727 
-   61000    18.586931     2000    2874.2926 
-   62000    19.158563     2000    2653.0722 
-   63000    19.738442     2000    2437.4941 
-   64000    20.331411     2000    2124.1876 
-   65000    20.936204     2000    1864.5661 
-   66000    21.547443     2000    1610.2335 
-   67000    22.166888     2000    1390.0428 
-   68000    22.789106     2000    1163.7679 
-   69000    23.416016     2000     933.0928 
-   70000    24.038879     2000    745.66667 
-   71000    24.663115     2000    605.58458 
-   72000    25.294193     2000    444.31183 
-   73000    25.932019     2000    357.19162 
-   74000    26.568184     2000    291.16762 
-   75000    27.203393     2000    230.58362 
-   76000    27.836079     2000    197.59502 
-   77000    28.467344     2000    166.55702 
-   78000    29.099997     2000    139.89052 
-   79000    29.741694     2000     117.1145 
-   80000    30.388097     2000    100.12353 
-   81000    31.036193     2000    85.233155 
-   82000    31.688463     2000    71.145302 
-   83000    32.343411     2000    61.545348 
-   84000    32.999346     2000    54.099358 
-   85000    33.652976     2000    46.922028 
-   86000    34.306931     2000    41.606645 
-   87000    34.967787     2000    37.462793 
-   88000    35.633721     2000    33.698298 
-   89000    36.310035     2000    29.340455 
-   90000    36.995441     2000    26.072122 
-   91000     37.67904     2000     23.20848 
-   92000    38.367699     2000    21.015862 
-   93000    39.058641     2000    20.134175 
-   94000    39.749342     2000    19.196075 
-   95000    40.442651     2000    18.285127 
-   96000    41.140177     2000    17.476411 
-   97000    41.840761     2000     16.55882 
-   98000    42.543845     2000    15.444541 
-   99000    43.256415     2000     14.41642 
-  100000     43.97382     2000    13.818738 
-  101000    44.684596     2000    12.878373 
-  102000    45.401082     2000     12.11804 
-  103000    46.120936     2000    11.016885 
-  104000     46.83935     2000    10.531044 
-  105000    47.559419     2000     10.46735 
-  106000    48.286016     2000    10.246007 
-  107000    49.012266     2000    9.6423041 
-  108000     49.74013     2000    9.3948808 
-  109000    50.471961     2000    9.5178141 
-  110000    51.206152     2000    9.4143884 
-  111000    51.939123     2000    9.5058226 
-  112000    52.673443     2000    9.6911516 
-  113000    53.410485     2000    9.7756849 
-  114000    54.152537     2000    9.3876232 
-  115000    54.891784     2000    8.6725333 
-  116000    55.631474     2000    8.6691065 
-  117000    56.371762     2000    8.0156055 
-  118000    57.110131     2000    7.9150786 
-  119000      57.8533     2000    7.5310892 
-  120000    58.599064     2000    7.2940498 
-  121000    59.340753     2000    6.8347898 
-  122000    60.084676     2000     6.696484 
-  123000    60.826952     2000    6.7799146 
-  124000    61.569413     2000    6.7901567 
-  125000    62.316334     2000    6.7532108 
-  126000    63.061374     2000     6.762162 
-  127000    63.806385     2000    6.6317366 
-  128000    64.555969     2000    6.8246399 
-  129000    65.308131     2000    6.9130358 
-  130000    66.060967     2000    7.1750566 
-  131000    66.809725     2000    6.9507379 
-  132000    67.559796     2000    6.7987445 
-  133000    68.314249     2000    6.8535775 
-  134000    69.065513     2000    7.0255144 
-  135000    69.817604     2000    6.7381064 
-  136000    70.572079     2000    6.5567748 
-  137000    71.324444     2000    6.2655395 
-  138000    72.079147     2000    6.1923013 
-  139000    72.831323     2000    6.0958081 
-  140000     73.59117     2000    5.9185709 
-  141000    74.343753     2000    5.9151241 
-  142000    75.096509     2000    5.4743035 
-  143000    75.852151     2000     5.438642 
-  144000    76.605005     2000    4.6646664 
-  145000    77.357571     2000    4.6899837 
-  146000    78.113125     2000    4.5357917 
-  147000    78.867751     2000    4.5993842 
-  148000    79.625344     2000    4.7076884 
-  149000     80.37992     2000    4.8306642 
-  150000    81.143175     2000    4.8282147 
-  151000    81.899326     2000     4.546308 
-  152000    82.658645     2000    4.6700755 
-  153000     83.41837     2000    4.7557633 
-  154000     84.17509     2000    4.9004538 
-  155000    84.934161     2000    5.0552949 
-  156000    85.695466     2000    4.0672495 
-  157000    86.453115     2000    3.5819543 
-  158000    87.212663     2000    3.3533477 
-  159000    87.967768     2000    3.3281001 
-  160000    88.729631     2000    3.0831743 
-  161000    89.498983     2000    3.0519269 
-  162000    90.259424     2000    3.0951675 
-  163000    91.019656     2000    2.9868352 
-  164000    91.776359     2000    2.9195788 
-  165000    92.536374     2000    2.5637813 
-  166000    93.296332     2000    2.5553272 
-  167000     94.05653     2000    2.0752912 
-  168000    94.814559     2000    1.9689845 
-  169000    95.576005     2000    1.9117916 
-  170000    96.337863     2000    1.8568914 
-Loop time of 96.3379 on 1 procs for 150000 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    | 37.121     | 37.121     | 37.121     |   0.0 | 38.53
-Neigh   | 0.8454     | 0.8454     | 0.8454     |   0.0 |  0.88
-Comm    | 0.11506    | 0.11506    | 0.11506    |   0.0 |  0.12
-Output  | 0.004431   | 0.004431   | 0.004431   |   0.0 |  0.00
-Modify  | 56.517     | 56.517     | 56.517     |   0.0 | 58.67
-Other   |            | 1.735      |            |       |  1.80
-
-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:    15524 ave 15524 max 15524 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 15524
-Ave neighs/atom = 7.762
-Neighbor list builds = 388
-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
-Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes
-Step CPU Atoms KinEng 
-  170000            0     2000    1.8568914 
-  171000   0.75704765     2000    2.4011583 
-  172000    1.5101345     2000     3.176628 
-  173000    2.2556529     2000    4.5364486 
-  174000    2.9946566     2000    6.5494125 
-  175000    3.7253478     2000    9.1934319 
-  176000    4.4570525     2000     12.25765 
-  177000    5.1876664     2000    15.799657 
-  178000    5.9178619     2000    19.982558 
-  179000    6.6439464     2000    24.927165 
-  180000    7.3749168     2000    30.428362 
-  181000    8.1011977     2000     36.74232 
-  182000    8.8207343     2000    43.820448 
-  183000    9.5397925     2000    50.903222 
-  184000    10.253098     2000    59.425781 
-  185000    10.965505     2000    69.143119 
-  186000    11.673319     2000    79.210705 
-  187000    12.373966     2000    90.411346 
-  188000    13.075475     2000    102.35389 
-  189000    13.770632     2000    114.93888 
-  190000    14.469445     2000    128.63341 
-  191000    15.158381     2000    143.44526 
-  192000    15.846267     2000    159.04574 
-  193000    16.527754     2000     174.3114 
-  194000    17.204808     2000    190.42123 
-  195000    17.881059     2000    207.70459 
-  196000    18.556555     2000    224.90931 
-  197000    19.229818     2000    242.64914 
-  198000    19.905086     2000    261.48312 
-  199000    20.578518     2000    281.28308 
-  200000     21.25632     2000    302.95108 
-  201000    21.921347     2000    325.95534 
-  202000    22.583873     2000     350.6874 
-  203000    23.244724     2000    376.31773 
-  204000    23.904842     2000    404.21947 
-  205000    24.562788     2000    432.96116 
-  206000    25.217762     2000     462.4113 
-  207000    25.875814     2000    491.91207 
-  208000    26.531285     2000    522.15395 
-  209000    27.184766     2000     553.1024 
-  210000    27.842961     2000     585.7133 
-  211000    28.489339     2000    619.96357 
-  212000    29.139612     2000    653.96189 
-  213000    29.783866     2000     689.8027 
-  214000    30.426881     2000    727.28401 
-  215000     31.06706     2000    766.40354 
-  216000    31.706399     2000    805.65433 
-  217000    32.343033     2000    845.40981 
-  218000    32.989384     2000    884.24637 
-  219000    33.633664     2000     923.5998 
-  220000    34.285172     2000    965.01779 
-  221000    34.931959     2000    1009.1763 
-  222000    35.571624     2000    1054.7789 
-  223000    36.207868     2000    1101.9922 
-  224000    36.836062     2000    1151.1205 
-  225000    37.464514     2000    1201.3979 
-  226000     38.09746     2000    1252.4054 
-  227000    38.732507     1999    1296.6784 
-  228000    39.371367     1997    1342.3466 
-  229000    40.012553     1992    1368.8559 
-  230000    40.652111     1977    1360.2259 
-  231000    41.275478     1965    1340.3793 
-  232000    41.892734     1953    1318.8318 
-  233000     42.50588     1938    1295.5667 
-  234000    43.121427     1924    1270.0641 
-  235000    43.740727     1914     1258.296 
-  236000    44.359241     1902    1224.3945 
-  237000    44.979463     1899    1248.3905 
-  238000    45.597358     1885    1206.9229 
-  239000    46.210114     1875    1195.5429 
-  240000    46.818148     1861    1142.6591 
-  241000    47.411079     1851    1131.5523 
-  242000    48.002522     1841    1116.8741 
-  243000    48.594254     1830    1099.9978 
-  244000    49.191798     1822    1078.6068 
-  245000    49.791332     1814    1072.1498 
-  246000    50.389728     1803    1020.7842 
-  247000    50.984212     1794    1000.1936 
-  248000    51.571047     1781    942.02462 
-  249000    52.149428     1772    916.83697 
-  250000    52.726202     1758    825.10751 
-  251000     53.29913     1748    789.06351 
-  252000    53.871912     1739    753.92258 
-  253000    54.441009     1729    697.83686 
-  254000    55.010203     1718    648.98541 
-  255000    55.573602     1710    620.38129 
-  256000    56.134709     1705    622.43466 
-  257000    56.701827     1700    595.79102 
-  258000    57.264463     1698    608.49223 
-  259000    57.827817     1695     614.0119 
-  260000    58.398994     1690    601.50438 
-  261000    58.964611     1687     608.5892 
-  262000    59.526765     1683    597.07884 
-  263000    60.082729     1682    618.65041 
-  264000    60.640105     1678    615.47784 
-  265000    61.195717     1675    605.27658 
-  266000    61.751087     1671    583.69853 
-  267000    62.305546     1669    600.11043 
-  268000     62.86105     1666    598.79807 
-  269000    63.417551     1663    588.40338 
-  270000    63.974486     1660    579.59387 
-Loop time of 63.9745 on 1 procs for 100000 steps with 1660 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    | 26.514     | 26.514     | 26.514     |   0.0 | 41.44
-Neigh   | 0.60324    | 0.60324    | 0.60324    |   0.0 |  0.94
-Comm    | 0.075881   | 0.075881   | 0.075881   |   0.0 |  0.12
-Output  | 0.0029137  | 0.0029137  | 0.0029137  |   0.0 |  0.00
-Modify  | 35.686     | 35.686     | 35.686     |   0.0 | 55.78
-Other   |            | 1.092      |            |       |  1.71
-
-Nlocal:    1660 ave 1660 max 1660 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:    11681 ave 11681 max 11681 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 11681
-Ave neighs/atom = 7.03675
-Neighbor list builds = 249
-Dangerous builds = 0
-Total wall time: 0:02:48

examples/granregion/log.27Nov18.granregion.funnel.g++.4

@@ -1,601 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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} bin
-neighbor        0.5 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 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/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-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:705)
-thermo_modify	flush yes lost warn
-
-# Initial run to fill up the cone
-
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 6.05 | 6.05 | 6.05 Mbytes
-Step CPU Atoms KinEng 
-       0            0        0           -0 
-    1000   0.63366675     2000           -0 
-    2000    1.0221362     2000           -0 
-    3000    1.3905275     2000           -0 
-    4000    1.7514329     2000           -0 
-    5000    2.1040537     2000           -0 
-    6000    2.4468088     2000           -0 
-    7000    2.7853072     2000           -0 
-    8000    3.1109948     2000           -0 
-    9000    3.4281557     2000           -0 
-   10000    3.7435207     2000           -0 
-   11000    3.8612552     2000           -0 
-   12000    3.9786677     2000           -0 
-   13000    4.0988154     2000           -0 
-   14000    4.2249811     2000           -0 
-   15000    4.3562138     2000           -0 
-   16000    4.4940333     2000           -0 
-   17000    4.6394637     2000           -0 
-   18000    4.7909062     2000           -0 
-   19000    4.9482198     2000           -0 
-   20000    5.1116607     2000           -0 
-Loop time of 5.11176 on 4 procs for 20000 steps with 2000 atoms
-
-97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.050997   | 0.14884    | 0.36048    |  32.0 |  2.91
-Neigh   | 0.01374    | 0.025199   | 0.043743   |   7.0 |  0.49
-Comm    | 0.063387   | 0.1781     | 0.29748    |  22.6 |  3.48
-Output  | 0.0016627  | 0.0060938  | 0.015082   |   6.8 |  0.12
-Modify  | 1.1198     | 1.987      | 3.7195     |  72.6 | 38.87
-Other   |            | 2.767      |            |       | 54.12
-
-Nlocal:    500 ave 505 max 493 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Nghost:    159.25 ave 254 max 71 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    397.5 ave 616 max 214 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 1590
-Ave neighs/atom = 0.795
-Neighbor list builds = 69
-Dangerous builds = 0
-unfix 		ins
-run		150000
-Per MPI rank memory allocation (min/avg/max) = 12.37 | 12.51 | 12.7 Mbytes
-Step CPU Atoms KinEng 
-   20000            0     2000    6443.7665 
-   21000   0.11261106     2000    6572.3531 
-   22000   0.23091817     2000    6723.8376 
-   23000   0.35577631     2000    6853.1812 
-   24000   0.48790455     2000    6976.0209 
-   25000   0.63509274     2000    7096.9955 
-   26000   0.78251743     2000    7215.5795 
-   27000   0.93707466     2000    7349.2382 
-   28000    1.1032445     2000    7471.8719 
-   29000    1.2721858     2000    7574.8228 
-   30000     1.449265     2000    7659.3836 
-   31000    1.5742557     2000    7703.6856 
-   32000    1.7076068     2000     7644.279 
-   33000    1.8527873     2000    7526.6944 
-   34000     2.009855     2000    7370.0821 
-   35000    2.1766446     2000    7193.0459 
-   36000    2.3557482     2000    6990.9912 
-   37000    2.5468907     2000     6849.286 
-   38000    2.7480681     2000    6701.7548 
-   39000    2.9574037     2000    6538.6915 
-   40000    3.1807711     2000    6382.3209 
-   41000    3.3486595     2000     6216.424 
-   42000    3.5162592     2000      6091.29 
-   43000     3.687057     2000    5945.3256 
-   44000    3.8662596     2000     5840.875 
-   45000    4.0557241     2000     5649.763 
-   46000    4.2541051     2000    5476.2837 
-   47000    4.4571214     2000    5277.0701 
-   48000    4.6628008     2000    5123.9796 
-   49000    4.8686502     2000    4968.3344 
-   50000    5.0788848     2000    4869.5754 
-   51000    5.2552598     2000    4704.8517 
-   52000    5.4428713     2000    4522.8978 
-   53000    5.6520596     2000    4393.8047 
-   54000    5.8613031     2000     4235.438 
-   55000    6.0776098     2000    4082.3073 
-   56000    6.2998042     2000    3901.0483 
-   57000    6.5321434     2000    3718.0882 
-   58000    6.7745438     2000     3504.621 
-   59000    7.0237701     2000    3285.7484 
-   60000    7.2791855     2000    3047.3386 
-   61000     7.489058     2000    2875.4032 
-   62000    7.7044094     2000      2647.83 
-   63000    7.9194827     2000    2396.5343 
-   64000    8.1429474     2000    2107.2113 
-   65000    8.3745618     2000    1858.1977 
-   66000     8.610673     2000    1615.8096 
-   67000    8.8505244     2000    1416.5065 
-   68000    9.0955915     2000    1206.8534 
-   69000    9.3609676     2000    953.93974 
-   70000    9.6382594     2000     766.9148 
-   71000    9.8719468     2000    611.45063 
-   72000    10.095534     2000    464.94805 
-   73000    10.317962     2000    364.31415 
-   74000    10.547287     2000    298.77524 
-   75000    10.764052     2000    245.73022 
-   76000    10.978769     2000     207.8035 
-   77000    11.199921     2000     179.1305 
-   78000    11.410296     2000    151.21032 
-   79000    11.624499     2000    124.49675 
-   80000    11.849562     2000    106.71504 
-   81000    12.077449     2000    93.299034 
-   82000    12.306904     2000    81.220408 
-   83000    12.539016     2000    67.383955 
-   84000    12.773108     2000    57.287165 
-   85000    13.009487     2000    49.255887 
-   86000    13.252544     2000    44.082536 
-   87000    13.502564     2000    40.193574 
-   88000    13.747198     2000    36.903867 
-   89000    13.993028     2000     33.55332 
-   90000    14.240036     2000    30.730912 
-   91000    14.472719     2000    28.650574 
-   92000    14.708542     2000    26.377609 
-   93000    14.948106     2000    24.433165 
-   94000    15.186653     2000    22.933076 
-   95000    15.428022     2000     22.31788 
-   96000    15.676323     2000    20.829124 
-   97000    15.916326     2000    19.401354 
-   98000    16.160197     2000    18.943699 
-   99000    16.404796     2000    17.690599 
-  100000    16.659731     2000    17.215943 
-  101000    16.904498     2000    15.948087 
-  102000    17.150993     2000    15.140324 
-  103000     17.39584     2000    14.885674 
-  104000    17.643707     2000    14.414752 
-  105000    17.889343     2000    14.270676 
-  106000    18.136159     2000    13.943799 
-  107000    18.383653     2000    13.840145 
-  108000    18.630952     2000    12.826341 
-  109000    18.878218     2000    12.209012 
-  110000    19.125558     2000    11.916194 
-  111000      19.3726     2000    11.970849 
-  112000    19.621494     2000     11.56909 
-  113000    19.869978     2000    11.390562 
-  114000    20.123402     2000    11.276545 
-  115000    20.370963     2000    11.171298 
-  116000    20.619975     2000    11.686225 
-  117000    20.869585     2000    11.379805 
-  118000    21.118875     2000    10.539511 
-  119000     21.36837     2000    10.064595 
-  120000    21.629511     2000    10.003722 
-  121000    21.877867     2000    9.6974586 
-  122000    22.127922     2000    9.7156209 
-  123000    22.378215     2000     9.615256 
-  124000    22.630463     2000    8.8979008 
-  125000    22.882154     2000    8.2220003 
-  126000    23.135763     2000    8.3153866 
-  127000    23.392389     2000    8.0945497 
-  128000    23.645521     2000    7.8942467 
-  129000     23.89965     2000    7.4794776 
-  130000    24.153195     2000    7.3635341 
-  131000    24.406239     2000    7.5757743 
-  132000     24.66016     2000    7.7047492 
-  133000    24.914093     2000    8.0142133 
-  134000    25.173429     2000    8.1716714 
-  135000    25.433318     2000    7.7803343 
-  136000    25.692997     2000    6.3545482 
-  137000    25.947787     2000     6.313769 
-  138000    26.200427     2000    6.4948596 
-  139000    26.452514     2000    6.6183259 
-  140000    26.714963     2000    6.7922281 
-  141000    26.968235     2000    7.0752448 
-  142000    27.220962     2000    7.2328717 
-  143000    27.474819     2000     7.626453 
-  144000    27.728029     2000    7.4576787 
-  145000    27.981958     2000     7.124435 
-  146000    28.236591     2000    7.2581589 
-  147000    28.489842     2000    7.0622049 
-  148000    28.744432     2000    7.1672801 
-  149000    28.998739     2000    7.3248363 
-  150000    29.253511     2000    7.0092266 
-  151000     29.50567     2000    6.8124438 
-  152000    29.759836     2000    6.9808705 
-  153000    30.015359     2000    7.1516731 
-  154000    30.275488     2000    6.6245443 
-  155000    30.533407     2000    5.5867165 
-  156000    30.788683     2000     5.318949 
-  157000    31.043126     2000    5.1195805 
-  158000    31.297011     2000    5.2045485 
-  159000    31.551327     2000      5.24992 
-  160000    31.807728     2000    5.3270577 
-  161000    32.061371     2000     4.995281 
-  162000    32.315467     2000    5.0755874 
-  163000     32.57628     2000    5.0788135 
-  164000     32.83119     2000    4.5917317 
-  165000    33.085634     2000    4.6255452 
-  166000    33.344148     2000    4.2563299 
-  167000    33.599342     2000    3.3808566 
-  168000    33.853488     2000     3.218931 
-  169000    34.121464     2000    3.0839289 
-  170000    34.378727     2000    3.0358838 
-Loop time of 34.3788 on 4 procs for 150000 steps with 2000 atoms
-
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.5861     | 10.058     | 12.152     |  68.4 | 29.26
-Neigh   | 0.17612    | 0.25274    | 0.30005    |   9.2 |  0.74
-Comm    | 1.5024     | 2.6626     | 3.4174     |  44.9 |  7.74
-Output  | 0.006542   | 0.019532   | 0.046425   |  11.5 |  0.06
-Modify  | 11.945     | 14.674     | 16.29      |  42.7 | 42.68
-Other   |            | 6.711      |            |       | 19.52
-
-Nlocal:    500 ave 508 max 489 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Nghost:    446.75 ave 708 max 191 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    4498 ave 5441 max 3786 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 17992
-Ave neighs/atom = 8.996
-Neighbor list builds = 403
-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
-Per MPI rank memory allocation (min/avg/max) = 13.68 | 15.35 | 16.59 Mbytes
-Step CPU Atoms KinEng 
-  170000            0     2000    3.0358838 
-  171000   0.25455499     2000    3.7725185 
-  172000   0.50768304     2000     4.727285 
-  173000   0.76122355     2000    5.9840449 
-  174000    1.0141416     2000    8.0335022 
-  175000    1.2750733     2000    10.177259 
-  176000    1.5277736     2000    13.655163 
-  177000    1.7810826     2000    17.987975 
-  178000    2.0348532     2000    23.266471 
-  179000    2.2915859     2000    29.266364 
-  180000     2.547174     2000     35.84089 
-  181000    2.8009758     2000    43.130989 
-  182000    3.0531759     2000    51.177142 
-  183000    3.3130636     2000    60.031831 
-  184000    3.5651338     2000     69.52374 
-  185000    3.8185399     2000    79.941907 
-  186000     4.070199     2000    91.195382 
-  187000    4.3204038     2000     102.1696 
-  188000    4.5699775     2000    112.73657 
-  189000    4.8184452     2000    123.57252 
-  190000    5.0653601     2000    135.59942 
-  191000    5.3119307     2000    147.37757 
-  192000    5.5574484     2000    159.12931 
-  193000    5.8029084     2000    170.90271 
-  194000    6.0463562     2000    185.71189 
-  195000    6.2883332     2000    201.83733 
-  196000    6.5281694     2000    218.30785 
-  197000    6.7682493     2000    236.05694 
-  198000    7.0084231     2000    255.23099 
-  199000    7.2519951     2000    273.94566 
-  200000    7.5010133     2000    293.91107 
-  201000    7.7396591     2000    316.52142 
-  202000    7.9784184     2000    340.91391 
-  203000     8.224021     2000    364.81801 
-  204000    8.4597676     2000    390.06478 
-  205000    8.6934731     2000    415.90918 
-  206000    8.9342225     2000     441.0995 
-  207000    9.1714027     2000    467.40314 
-  208000    9.4081488     2000    494.93631 
-  209000    9.6457636     2000    524.70539 
-  210000    9.8831718     2000    556.52058 
-  211000    10.118018     2000    589.36821 
-  212000      10.3541     2000     622.6887 
-  213000    10.587226     2000    657.05888 
-  214000    10.820744     2000    691.14292 
-  215000    11.055785     2000    726.94959 
-  216000    11.298702     2000    762.92802 
-  217000    11.534793     2000    801.23648 
-  218000    11.769849     2000     841.1559 
-  219000    12.000917     2000     882.4342 
-  220000    12.232812     2000     924.8466 
-  221000    12.461166     2000    968.86229 
-  222000    12.698451     2000    1013.1381 
-  223000    12.930287     2000    1058.2988 
-  224000    13.172862     2000    1105.2911 
-  225000    13.405001     2000    1152.8617 
-  226000    13.633187     1999    1197.6777 
-  227000    13.857126     1998    1243.1211 
-  228000    14.079622     1992    1262.1402 
-  229000    14.303362     1987    1281.9162 
-  230000    14.530392     1973    1264.0674 
-  231000    14.756486     1964    1277.8347 
-  232000    14.984495     1953    1266.7926 
-  233000    15.213102     1940    1244.0038 
-  234000    15.441666     1925    1206.4472 
-  235000    15.667547     1914      1193.33 
-  236000    15.895047     1901    1160.4096 
-  237000    16.120833     1890    1141.6816 
-  238000    16.346628     1883    1149.1584 
-  239000    16.573303     1877    1141.7514 
-  240000    16.801035     1871    1146.8662 
-  241000    17.024775     1866     1152.561 
-  242000    17.248651     1858    1148.2529 
-  243000     17.47241     1847    1114.7239 
-  244000     17.70222     1832    1070.9996 
-  245000    17.926477     1824    1066.7549 
-  246000    18.157588     1813    1027.1865 
-  247000    18.378868     1804    1011.5024 
-  248000    18.599988     1797    993.10451 
-  249000    18.819007     1787    951.89778 
-  250000    19.044634     1777    926.30475 
-  251000    19.254408     1764    875.07091 
-  252000    19.465788     1755    824.89358 
-  253000    19.676327     1742    742.51957 
-  254000    19.887648     1731    708.30958 
-  255000    20.094912     1722    690.09761 
-  256000    20.299963     1713    638.00218 
-  257000    20.506153     1705    596.86839 
-  258000    20.713994     1701    583.71937 
-  259000    20.919755     1691     549.0049 
-  260000    21.123122     1688     549.4278 
-  261000    21.332215     1684    535.35719 
-  262000    21.533673     1682    546.74031 
-  263000    21.737042     1678    532.69324 
-  264000    21.941306     1676    537.89254 
-  265000     22.15135     1676    559.50898 
-  266000    22.358371     1670    540.21452 
-  267000    22.563236     1668    557.19857 
-  268000    22.764648     1665    569.52869 
-  269000     22.96391     1658    543.77057 
-  270000    23.172415     1656    550.23716 
-Loop time of 23.1725 on 4 procs for 100000 steps with 1656 atoms
-
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.3849     | 7.3002     | 10.192     |  91.3 | 31.50
-Neigh   | 0.14271    | 0.16781    | 0.19054    |   4.5 |  0.72
-Comm    | 1.086      | 1.9721     | 2.6157     |  42.7 |  8.51
-Output  | 0.0018437  | 0.013918   | 0.041359   |  13.5 |  0.06
-Modify  | 8.6598     | 9.3198     | 9.8874     |  16.6 | 40.22
-Other   |            | 4.399      |            |       | 18.98
-
-Nlocal:    414 ave 454 max 385 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Nghost:    395.25 ave 645 max 157 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    3498.5 ave 4524 max 2034 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 13994
-Ave neighs/atom = 8.45048
-Neighbor list builds = 240
-Dangerous builds = 0
-Total wall time: 0:01:02

examples/granregion/log.27Nov18.granregion.mixer.g++.1

@@ -1,602 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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} bin
-neighbor        0.6 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 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/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-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:705)
-thermo_modify	flush yes lost warn
-
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes
-Step CPU Atoms KinEng v_theta 
-       0            0        0           -0            0 
-    1000   0.15327144      444           -0  0.015707963 
-    2000   0.30070925      444           -0  0.031415927 
-    3000   0.44653535      444           -0   0.04712389 
-    4000   0.59226131      444           -0  0.062831853 
-    5000   0.73794818      444           -0  0.078539816 
-    6000   0.88327622      444           -0   0.09424778 
-    7000    1.0286083      444           -0   0.10995574 
-    8000    1.1740625      444           -0   0.12566371 
-    9000    1.3224797      444           -0   0.14137167 
-   10000    1.4717772      444           -0   0.15707963 
-   11000    1.6204555      444           -0    0.1727876 
-   12000    1.7690799      444           -0   0.18849556 
-   13000     1.918304      444           -0   0.20420352 
-   14000    2.0670426      444           -0   0.21991149 
-   15000    2.2157068      444           -0   0.23561945 
-   16000    2.3642888      444           -0   0.25132741 
-   17000    2.5129776      444           -0   0.26703538 
-   18000    2.6614521      444           -0   0.28274334 
-   19000    2.8100598      444           -0    0.2984513 
-   20000    2.9591351      444           -0   0.31415927 
-   21000    3.1073661      444           -0   0.32986723 
-   22000    3.2557554      444           -0   0.34557519 
-   23000    3.4041324      444           -0   0.36128316 
-   24000    3.5526814      444           -0   0.37699112 
-   25000     3.700824      444           -0   0.39269908 
-   26000    3.8496137      444           -0   0.40840704 
-   27000    3.9986103      444           -0   0.42411501 
-   28000    4.1475384      444           -0   0.43982297 
-   29000    4.2963772      444           -0   0.45553093 
-   30000    4.4454341      444           -0    0.4712389 
-   31000    4.5942066      444           -0   0.48694686 
-   32000    4.7434044      444           -0   0.50265482 
-   33000     4.893549      444           -0   0.51836279 
-   34000    5.0427935      444           -0   0.53407075 
-   35000    5.1920972      444           -0   0.54977871 
-   36000    5.3411844      444           -0   0.56548668 
-   37000    5.4904606      444           -0   0.58119464 
-   38000    5.6397707      444           -0    0.5969026 
-   39000    5.7900345      444           -0   0.61261057 
-   40000    5.9405882      444           -0   0.62831853 
-   41000     6.089345      444           -0   0.64402649 
-   42000    6.2388933      444           -0   0.65973446 
-   43000    6.3888056      444           -0   0.67544242 
-   44000    6.5379841      444           -0   0.69115038 
-   45000    6.6875141      444           -0   0.70685835 
-   46000    6.8370855      444           -0   0.72256631 
-   47000    6.9866009      444           -0   0.73827427 
-   48000    7.1364653      444           -0   0.75398224 
-   49000    7.2859883      444           -0    0.7696902 
-   50000    7.4368248      444           -0   0.78539816 
-   51000    7.5870779      444           -0   0.80110613 
-   52000    7.7370813      444           -0   0.81681409 
-   53000    7.8879561      444           -0   0.83252205 
-   54000    8.0383027      444           -0   0.84823002 
-   55000    8.1916294      444           -0   0.86393798 
-   56000    8.3458471      444           -0   0.87964594 
-   57000    8.5010631      444           -0   0.89535391 
-   58000    8.6560545      444           -0   0.91106187 
-   59000    8.8110209      444           -0   0.92676983 
-   60000    8.9674675      444           -0    0.9424778 
-   61000    9.1231239      444           -0   0.95818576 
-   62000    9.2785382      444           -0   0.97389372 
-   63000    9.4343674      444           -0   0.98960169 
-   64000    9.5911541      444           -0    1.0053096 
-   65000    9.7477772      444           -0    1.0210176 
-   66000    9.9050307      444           -0    1.0367256 
-   67000    10.063978      444           -0    1.0524335 
-   68000    10.221835      444           -0    1.0681415 
-   69000     10.37944      444           -0    1.0838495 
-   70000    10.537409      444           -0    1.0995574 
-   71000    10.695649      444           -0    1.1152654 
-   72000     10.85453      444           -0    1.1309734 
-   73000    11.013438      444           -0    1.1466813 
-   74000    11.172689      444           -0    1.1623893 
-   75000    11.332172      444           -0    1.1780972 
-   76000    11.492824      444           -0    1.1938052 
-   77000    11.653915      444           -0    1.2095132 
-   78000    11.815798      444           -0    1.2252211 
-   79000     11.97868      444           -0    1.2409291 
-   80000    12.141392      444           -0    1.2566371 
-   81000     12.30536      444           -0     1.272345 
-   82000    12.468797      444           -0     1.288053 
-   83000    12.633028      444           -0     1.303761 
-   84000    12.797936      444           -0    1.3194689 
-   85000    13.019726      888           -0    1.3351769 
-   86000    13.333436      888           -0    1.3508848 
-   87000    13.648179      888           -0    1.3665928 
-   88000    13.962435      888           -0    1.3823008 
-   89000    14.276158      888           -0    1.3980087 
-   90000    14.590669      888           -0    1.4137167 
-   91000    14.904268      888           -0    1.4294247 
-   92000    15.216788      888           -0    1.4451326 
-   93000    15.529868      888           -0    1.4608406 
-   94000    15.843157      888           -0    1.4765485 
-   95000    16.156564      888           -0    1.4922565 
-   96000    16.469569      888           -0    1.5079645 
-   97000    16.784048      888           -0    1.5236724 
-   98000    17.100451      888           -0    1.5393804 
-   99000    17.416338      888           -0    1.5550884 
-  100000    17.733482      888           -0    1.5707963 
-  101000    18.052522      888           -0    1.5865043 
-  102000    18.371428      888           -0    1.6022123 
-  103000    18.690222      888           -0    1.6179202 
-  104000    19.009665      888           -0    1.6336282 
-  105000    19.328189      888           -0    1.6493361 
-  106000    19.647804      888           -0    1.6650441 
-  107000     19.96805      888           -0    1.6807521 
-  108000    20.286857      888           -0      1.69646 
-  109000    20.607965      888           -0     1.712168 
-  110000    20.931749      888           -0     1.727876 
-  111000    21.251903      888           -0    1.7435839 
-  112000    21.572158      888           -0    1.7592919 
-  113000    21.892612      888           -0    1.7749998 
-  114000    22.214408      888           -0    1.7907078 
-  115000    22.535498      888           -0    1.8064158 
-  116000    22.856752      888           -0    1.8221237 
-  117000    23.178885      888           -0    1.8378317 
-  118000    23.501127      888           -0    1.8535397 
-  119000      23.8241      888           -0    1.8692476 
-  120000    24.147258      888           -0    1.8849556 
-  121000    24.472969      888           -0    1.9006636 
-  122000    24.799108      888           -0    1.9163715 
-  123000    25.125275      888           -0    1.9320795 
-  124000    25.453866      888           -0    1.9477874 
-  125000    25.784766      888           -0    1.9634954 
-  126000    26.117013      888           -0    1.9792034 
-  127000    26.448734      888           -0    1.9949113 
-  128000    26.780032      888           -0    2.0106193 
-  129000    27.113678      888           -0    2.0263273 
-  130000    27.450001      888           -0    2.0420352 
-  131000    27.782047      888           -0    2.0577432 
-  132000    28.114287      888           -0    2.0734512 
-  133000    28.446648      888           -0    2.0891591 
-  134000    28.780438      888           -0    2.1048671 
-  135000    29.116443      888           -0     2.120575 
-  136000    29.451848      888           -0     2.136283 
-  137000    29.787778      888           -0     2.151991 
-  138000     30.12804      888           -0    2.1676989 
-  139000     30.46814      888           -0    2.1834069 
-  140000    30.808946      888           -0    2.1991149 
-  141000    31.147584      888           -0    2.2148228 
-  142000    31.486475      888           -0    2.2305308 
-  143000    31.826754      888           -0    2.2462387 
-  144000    32.165796      888           -0    2.2619467 
-  145000    32.506074      888           -0    2.2776547 
-  146000    32.847604      888           -0    2.2933626 
-  147000    33.188988      888           -0    2.3090706 
-  148000    33.532869      888           -0    2.3247786 
-  149000    33.876629      888           -0    2.3404865 
-  150000    34.221172      888           -0    2.3561945 
-  151000    34.562559      888           -0    2.3719025 
-  152000    34.904679      888           -0    2.3876104 
-  153000    35.247727      888           -0    2.4033184 
-  154000    35.591228      888           -0    2.4190263 
-  155000    35.949192      888           -0    2.4347343 
-  156000    36.320157      888           -0    2.4504423 
-  157000    36.693571      888           -0    2.4661502 
-  158000    37.069463      888           -0    2.4818582 
-  159000     37.44221      888           -0    2.4975662 
-  160000     37.81863      888           -0    2.5132741 
-  161000    38.195121      888           -0    2.5289821 
-  162000    38.573424      888           -0      2.54469 
-  163000    38.950044      888           -0     2.560398 
-  164000    39.331977      888           -0     2.576106 
-  165000    39.714367      888           -0    2.5918139 
-  166000    40.097099      888           -0    2.6075219 
-  167000    40.477443      888           -0    2.6232299 
-  168000    40.860404      888           -0    2.6389378 
-  169000    41.244357      888           -0    2.6546458 
-  170000    41.658126     1000           -0    2.6703538 
-  171000    42.082517     1000           -0    2.6860617 
-  172000    42.507502     1000           -0    2.7017697 
-  173000     42.93363     1000           -0    2.7174776 
-  174000    43.361133     1000           -0    2.7331856 
-  175000    43.792381     1000           -0    2.7488936 
-  176000    44.223827     1000           -0    2.7646015 
-  177000    44.656581     1000           -0    2.7803095 
-  178000    45.087615     1000           -0    2.7960175 
-  179000    45.521129     1000           -0    2.8117254 
-  180000    45.957808     1000           -0    2.8274334 
-  181000    46.391451     1000           -0    2.8431414 
-  182000    46.825486     1000           -0    2.8588493 
-  183000     47.26091     1000           -0    2.8745573 
-  184000    47.694263     1000           -0    2.8902652 
-  185000    48.123312     1000           -0    2.9059732 
-  186000    48.554081     1000           -0    2.9216812 
-  187000    48.982617     1000           -0    2.9373891 
-  188000    49.414355     1000           -0    2.9530971 
-  189000     49.84753     1000           -0    2.9688051 
-  190000    50.284462     1000           -0     2.984513 
-  191000     50.71899     1000           -0     3.000221 
-  192000    51.157278     1000           -0    3.0159289 
-  193000    51.586171     1000           -0    3.0316369 
-  194000    52.011691     1000           -0    3.0473449 
-  195000    52.437732     1000           -0    3.0630528 
-  196000    52.863703     1000           -0    3.0787608 
-  197000    53.290403     1000           -0    3.0944688 
-  198000      53.7191     1000           -0    3.1101767 
-  199000    54.147195     1000           -0    3.1258847 
-  200000    54.575967     1000           -0    3.1415927 
-Loop time of 54.576 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 14960.907 tau/day, 3664.615 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.7989     | 3.7989     | 3.7989     |   0.0 |  6.96
-Neigh   | 0.067629   | 0.067629   | 0.067629   |   0.0 |  0.12
-Comm    | 0.63734    | 0.63734    | 0.63734    |   0.0 |  1.17
-Output  | 0.0049303  | 0.0049303  | 0.0049303  |   0.0 |  0.01
-Modify  | 49.1       | 49.1       | 49.1       |   0.0 | 89.97
-Other   |            | 0.9668     |            |       |  1.77
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    196 ave 196 max 196 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    3910 ave 3910 max 3910 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3910
-Ave neighs/atom = 3.91
-Neighbor list builds = 219
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes
-Step CPU Atoms KinEng v_theta 
-  200000            0     1000   0.93873133    3.1415927 
-  201000    0.4261198     1000   0.93239566    3.1573006 
-  202000   0.84928846     1000   0.90333835    3.1730086 
-  203000    1.2720087     1000   0.89351493    3.1887165 
-  204000    1.6929317     1000   0.87648478    3.2044245 
-  205000     2.114043     1000   0.86818482    3.2201325 
-  206000    2.5357664     1000   0.86033251    3.2358404 
-  207000    2.9579847     1000   0.85442625    3.2515484 
-  208000    3.3812878     1000    0.8517451    3.2672564 
-  209000    3.8124611     1000   0.84406987    3.2829643 
-  210000    4.2440236     1000   0.83964642    3.2986723 
-  211000    4.6781921     1000   0.82994066    3.3143802 
-  212000    5.1116509     1000   0.82908369    3.3300882 
-  213000    5.5468135     1000   0.83115482    3.3457962 
-  214000    5.9802556     1000   0.82680518    3.3615041 
-  215000    6.4107294     1000    0.8223909    3.3772121 
-  216000    6.8419023     1000   0.81872537    3.3929201 
-  217000    7.2763367     1000   0.82446065     3.408628 
-  218000    7.7160695     1000   0.82278874     3.424336 
-  219000    8.1540956     1000   0.83017397     3.440044 
-  220000    8.5917952     1000   0.82232305    3.4557519 
-  221000    9.0296218     1000   0.82584132    3.4714599 
-  222000    9.4719794     1000   0.82143909    3.4871678 
-  223000    9.9180939     1000   0.82925587    3.5028758 
-  224000    10.361852     1000   0.84546265    3.5185838 
-  225000    10.803539     1000   0.84436452    3.5342917 
-  226000    11.248456     1000   0.84849375    3.5499997 
-  227000    11.695092     1000    0.8409057    3.5657077 
-  228000    12.136044     1000   0.83139305    3.5814156 
-  229000    12.579807     1000   0.83098473    3.5971236 
-  230000     13.02219     1000   0.81335147    3.6128316 
-  231000    13.463863     1000   0.78946649    3.6285395 
-  232000    13.906293     1000   0.78807613    3.6442475 
-  233000    14.348807     1000   0.79086655    3.6599554 
-  234000    14.793175     1000   0.79358862    3.6756634 
-  235000    15.238316     1000   0.79444252    3.6913714 
-  236000    15.683342     1000   0.79392156    3.7070793 
-  237000     16.12611     1000   0.80416034    3.7227873 
-  238000      16.5711     1000   0.80365093    3.7384953 
-  239000    17.014355     1000   0.80860323    3.7542032 
-  240000    17.454467     1000   0.80245788    3.7699112 
-  241000     17.89162     1000   0.79602568    3.7856191 
-  242000    18.330859     1000   0.79023692    3.8013271 
-  243000    18.769301     1000   0.79066782    3.8170351 
-  244000    19.211293     1000   0.77671368     3.832743 
-  245000    19.651443     1000   0.77121874     3.848451 
-  246000    20.092102     1000   0.74658977     3.864159 
-  247000    20.532732     1000   0.73825017    3.8798669 
-  248000    20.975646     1000    0.7187986    3.8955749 
-  249000    21.418807     1000   0.71707058    3.9112829 
-  250000    21.862497     1000   0.72983635    3.9269908 
-  251000    22.311832     1000    0.7355358    3.9426988 
-  252000     22.75883     1000   0.74427811    3.9584067 
-  253000    23.203455     1000   0.74968093    3.9741147 
-  254000    23.651472     1000   0.75350303    3.9898227 
-  255000    24.102152     1000   0.75617916    4.0055306 
-  256000    24.554236     1000   0.74949839    4.0212386 
-  257000    25.008718     1000   0.73534118    4.0369466 
-  258000    25.461913     1000   0.73761942    4.0526545 
-  259000    25.916674     1000   0.75485851    4.0683625 
-  260000    26.373941     1000   0.77147511    4.0840704 
-  261000    26.832072     1000   0.76658917    4.0997784 
-  262000     27.28741     1000   0.76441563    4.1154864 
-  263000    27.742157     1000   0.74449444    4.1311943 
-  264000    28.192718     1000    0.7403314    4.1469023 
-  265000    28.642541     1000   0.74262656    4.1626103 
-  266000     29.09406     1000   0.74117022    4.1783182 
-  267000    29.547747     1000   0.73877643    4.1940262 
-  268000    29.998243     1000   0.75062626    4.2097342 
-  269000    30.449751     1000   0.74649396    4.2254421 
-  270000    30.901232     1000   0.75371324    4.2411501 
-  271000    31.354755     1000   0.75254842     4.256858 
-  272000    31.810717     1000   0.74245946     4.272566 
-  273000    32.265754     1000   0.73056023     4.288274 
-  274000    32.719719     1000   0.72004393    4.3039819 
-  275000    33.173929     1000   0.70665742    4.3196899 
-  276000    33.628581     1000   0.69417262    4.3353979 
-  277000    34.080936     1000   0.67343474    4.3511058 
-  278000    34.532053     1000   0.66922758    4.3668138 
-  279000    34.985569     1000   0.66239909    4.3825218 
-  280000    35.443496     1000   0.66406486    4.3982297 
-  281000    35.901536     1000   0.67123654    4.4139377 
-  282000    36.357765     1000   0.67660885    4.4296456 
-  283000    36.811956     1000    0.6809288    4.4453536 
-  284000    37.266937     1000   0.69561154    4.4610616 
-  285000    37.720866     1000   0.70874512    4.4767695 
-  286000    38.177032     1000   0.72957833    4.4924775 
-  287000    38.633109     1000   0.72891066    4.5081855 
-  288000    39.086933     1000   0.72673285    4.5238934 
-  289000    39.538699     1000   0.72583062    4.5396014 
-  290000    39.991294     1000    0.7209406    4.5553093 
-  291000    40.437987     1000   0.70642559    4.5710173 
-  292000    40.885753     1000   0.69074151    4.5867253 
-  293000    41.326601     1000   0.68041469    4.6024332 
-  294000    41.763719     1000    0.6712034    4.6181412 
-  295000    42.198532     1000   0.66140336    4.6338492 
-  296000    42.635139     1000   0.65458145    4.6495571 
-  297000    43.071132     1000   0.63884999    4.6652651 
-  298000    43.507309     1000   0.63182296    4.6809731 
-  299000    43.943936     1000    0.6324286     4.696681 
-  300000    44.383148     1000   0.62640427     4.712389 
-  301000    44.819379     1000   0.62138494    4.7280969 
-  302000    45.260834     1000   0.62902694    4.7438049 
-  303000    45.705719     1000   0.63308052    4.7595129 
-  304000     46.14622     1000   0.63266845    4.7752208 
-  305000    46.586693     1000   0.63464534    4.7909288 
-  306000    47.028768     1000   0.62941378    4.8066368 
-  307000    47.470183     1000   0.62801025    4.8223447 
-  308000    47.914518     1000   0.62291875    4.8380527 
-  309000    48.365654     1000   0.62529494    4.8537606 
-  310000    48.817185     1000   0.62504442    4.8694686 
-  311000    49.269423     1000   0.63074915    4.8851766 
-  312000    49.722869     1000   0.64292914    4.9008845 
-  313000    50.175859     1000   0.65319818    4.9165925 
-  314000    50.630132     1000   0.66755513    4.9323005 
-  315000    51.084836     1000   0.67585436    4.9480084 
-  316000    51.539391     1000   0.67676226    4.9637164 
-  317000    51.995233     1000   0.67394312    4.9794244 
-  318000    52.453581     1000   0.67299959    4.9951323 
-  319000    52.906322     1000   0.68074615    5.0108403 
-  320000    53.362206     1000   0.67696004    5.0265482 
-  321000    53.813824     1000   0.67899008    5.0422562 
-  322000    54.264433     1000   0.67901671    5.0579642 
-  323000    54.715627     1000   0.67620354    5.0736721 
-  324000       55.168     1000   0.67165541    5.0893801 
-  325000    55.620891     1000   0.67820953    5.1050881 
-  326000    56.073685     1000   0.67490808     5.120796 
-  327000    56.526012     1000   0.67238149     5.136504 
-  328000    56.977525     1000   0.66885914     5.152212 
-  329000    57.431088     1000   0.66876389    5.1679199 
-  330000    57.886694     1000   0.66879597    5.1836279 
-  331000    58.338381     1000   0.66577546    5.1993358 
-  332000    58.791084     1000    0.6602875    5.2150438 
-  333000    59.242965     1000   0.65879422    5.2307518 
-  334000    59.698559     1000    0.6581474    5.2464597 
-  335000    60.153261     1000    0.6521249    5.2621677 
-  336000    60.605605     1000   0.63371979    5.2778757 
-  337000    61.059824     1000   0.62373279    5.2935836 
-  338000    61.510606     1000    0.6212013    5.3092916 
-  339000    61.962049     1000   0.62303395    5.3249995 
-  340000    62.413564     1000   0.63183785    5.3407075 
-  341000     62.86366     1000   0.64387158    5.3564155 
-  342000    63.317623     1000   0.65045982    5.3721234 
-  343000    63.772034     1000   0.65401192    5.3878314 
-  344000    64.225206     1000   0.65181077    5.4035394 
-  345000    64.681317     1000   0.64098248    5.4192473 
-  346000    65.136483     1000   0.63163559    5.4349553 
-  347000    65.588996     1000   0.64182161    5.4506633 
-  348000    66.042215     1000   0.65528889    5.4663712 
-  349000    66.501687     1000   0.66603277    5.4820792 
-  350000    66.960896     1000   0.67362185    5.4977871 
-  351000    67.417316     1000   0.68867905    5.5134951 
-  352000    67.876742     1000    0.6907547    5.5292031 
-  353000    68.336836     1000   0.69043981     5.544911 
-  354000    68.797396     1000   0.68676964     5.560619 
-  355000    69.255062     1000   0.68019369     5.576327 
-  356000    69.711663     1000   0.66189875    5.5920349 
-  357000    70.172728     1000   0.65275709    5.6077429 
-  358000    70.632655     1000   0.64560617    5.6234508 
-  359000    71.091165     1000   0.63865266    5.6391588 
-  360000    71.548341     1000    0.6366388    5.6548668 
-  361000    72.006137     1000   0.63619567    5.6705747 
-  362000    72.466621     1000   0.63986167    5.6862827 
-  363000    72.928505     1000     0.656198    5.7019907 
-  364000    73.391876     1000   0.66522563    5.7176986 
-  365000    73.852366     1000   0.67330205    5.7334066 
-  366000    74.317924     1000   0.67997811    5.7491146 
-  367000    74.781431     1000   0.67734915    5.7648225 
-  368000     75.24363     1000   0.66811078    5.7805305 
-  369000    75.704319     1000   0.67232161    5.7962384 
-  370000    76.165294     1000   0.67262944    5.8119464 
-  371000    76.624971     1000   0.68614241    5.8276544 
-  372000    77.085918     1000   0.70293842    5.8433623 
-  373000    77.544679     1000   0.71889856    5.8590703 
-  374000    78.007103     1000    0.7170296    5.8747783 
-  375000    78.468913     1000   0.71258031    5.8904862 
-  376000     78.93354     1000   0.70758873    5.9061942 
-  377000     79.39396     1000   0.69486822    5.9219022 
-  378000    79.850685     1000   0.68311194    5.9376101 
-  379000    80.307228     1000   0.67317549    5.9533181 
-  380000    80.767418     1000   0.67691049     5.969026 
-  381000    81.227579     1000   0.69231691     5.984734 
-  382000    81.686924     1000   0.69998609     6.000442 
-  383000    82.145783     1000   0.69328258    6.0161499 
-  384000    82.604827     1000   0.69903908    6.0318579 
-  385000    83.056443     1000   0.69455744    6.0475659 
-  386000    83.507131     1000   0.68865933    6.0632738 
-  387000     83.95695     1000   0.68630439    6.0789818 
-  388000    84.404079     1000    0.6800564    6.0946897 
-  389000    84.851053     1000   0.66747339    6.1103977 
-  390000    85.298614     1000   0.65695883    6.1261057 
-  391000    85.744507     1000   0.65659359    6.1418136 
-  392000    86.191348     1000   0.65933663    6.1575216 
-  393000    86.632782     1000   0.65170236    6.1732296 
-  394000    87.074105     1000   0.65631817    6.1889375 
-  395000      87.5177     1000   0.66205838    6.2046455 
-  396000    87.963111     1000   0.65512694    6.2203535 
-  397000    88.408348     1000   0.65266011    6.2360614 
-  398000    88.854042     1000   0.64593806    6.2517694 
-  399000    89.298754     1000   0.64940473    6.2674773 
-  400000    89.745445     1000   0.66033435    6.2831853 
-Loop time of 89.7455 on 1 procs for 200000 steps with 1000 atoms
-
-Performance: 9098.023 tau/day, 2228.525 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 10.924     | 10.924     | 10.924     |   0.0 | 12.17
-Neigh   | 0.10266    | 0.10266    | 0.10266    |   0.0 |  0.11
-Comm    | 1.9424     | 1.9424     | 1.9424     |   0.0 |  2.16
-Output  | 0.0056458  | 0.0056458  | 0.0056458  |   0.0 |  0.01
-Modify  | 75.442     | 75.442     | 75.442     |   0.0 | 84.06
-Other   |            | 1.329      |            |       |  1.48
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    272 ave 272 max 272 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    4933 ave 4933 max 4933 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4933
-Ave neighs/atom = 4.933
-Neighbor list builds = 171
-Dangerous builds = 0
-Total wall time: 0:02:24

examples/granregion/log.27Nov18.granregion.mixer.g++.4

@@ -1,602 +0,0 @@
-LAMMPS (27 Nov 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  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} bin
-neighbor        0.6 bin
-thermo 		${logfreq}
-thermo 		1000
-
-comm_style	brick
-comm_modify 	mode multi group all vel yes
-balance		1.1 shift xyz 20 1.1
-Neighbor list info ...
-  update every 1 steps, delay 10 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/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-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:705)
-thermo_modify	flush yes lost warn
-
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes
-Step CPU Atoms KinEng v_theta 
-       0            0        0           -0            0 
-    1000  0.096722603      444           -0  0.015707963 
-    2000   0.18796778      444           -0  0.031415927 
-    3000   0.27916241      444           -0   0.04712389 
-    4000   0.37111688      444           -0  0.062831853 
-    5000   0.46224833      444           -0  0.078539816 
-    6000   0.55190682      444           -0   0.09424778 
-    7000   0.64120579      444           -0   0.10995574 
-    8000   0.73025131      444           -0   0.12566371 
-    9000   0.82121348      444           -0   0.14137167 
-   10000   0.91006637      444           -0   0.15707963 
-   11000   0.97034311      444           -0    0.1727876 
-   12000     1.030247      444           -0   0.18849556 
-   13000    1.0894752      444           -0   0.20420352 
-   14000    1.1483686      444           -0   0.21991149 
-   15000    1.2138393      444           -0   0.23561945 
-   16000    1.2744856      444           -0   0.25132741 
-   17000    1.3361425      444           -0   0.26703538 
-   18000    1.3998857      444           -0   0.28274334 
-   19000    1.4625463      444           -0    0.2984513 
-   20000    1.5255082      444           -0   0.31415927 
-   21000    1.5845048      444           -0   0.32986723 
-   22000    1.6437175      444           -0   0.34557519 
-   23000    1.7022173      444           -0   0.36128316 
-   24000    1.7614172      444           -0   0.37699112 
-   25000    1.8209105      444           -0   0.39269908 
-   26000    1.8818901      444           -0   0.40840704 
-   27000    1.9439991      444           -0   0.42411501 
-   28000    2.0067189      444           -0   0.43982297 
-   29000    2.0697014      444           -0   0.45553093 
-   30000    2.1327429      444           -0    0.4712389 
-   31000    2.1904151      444           -0   0.48694686 
-   32000    2.2478669      444           -0   0.50265482 
-   33000    2.3062997      444           -0   0.51836279 
-   34000    2.3723967      444           -0   0.53407075 
-   35000    2.4331915      444           -0   0.54977871 
-   36000    2.4937904      444           -0   0.56548668 
-   37000    2.5550685      444           -0   0.58119464 
-   38000    2.6170652      444           -0    0.5969026 
-   39000    2.6789875      444           -0   0.61261057 
-   40000    2.7414019      444           -0   0.62831853 
-   41000     2.799027      444           -0   0.64402649 
-   42000    2.8570235      444           -0   0.65973446 
-   43000    2.9140713      444           -0   0.67544242 
-   44000    2.9702985      444           -0   0.69115038 
-   45000    3.0274565      444           -0   0.70685835 
-   46000    3.0860338      444           -0   0.72256631 
-   47000    3.1450455      444           -0   0.73827427 
-   48000    3.2057948      444           -0   0.75398224 
-   49000     3.267339      444           -0    0.7696902 
-   50000    3.3300545      444           -0   0.78539816 
-   51000    3.3942592      444           -0   0.80110613 
-   52000    3.4522727      444           -0   0.81681409 
-   53000    3.5117693      444           -0   0.83252205 
-   54000    3.5717957      444           -0   0.84823002 
-   55000    3.6338761      444           -0   0.86393798 
-   56000    3.7006576      444           -0   0.87964594 
-   57000    3.7648654      444           -0   0.89535391 
-   58000     3.829128      444           -0   0.91106187 
-   59000    3.8930187      444           -0   0.92676983 
-   60000    3.9581499      444           -0    0.9424778 
-   61000    4.0213017      444           -0   0.95818576 
-   62000    4.0822632      444           -0   0.97389372 
-   63000    4.1443422      444           -0   0.98960169 
-   64000    4.2072315      444           -0    1.0053096 
-   65000    4.2711387      444           -0    1.0210176 
-   66000    4.3361402      444           -0    1.0367256 
-   67000    4.4031398      444           -0    1.0524335 
-   68000    4.4698064      444           -0    1.0681415 
-   69000    4.5374978      444           -0    1.0838495 
-   70000    4.6051283      444           -0    1.0995574 
-   71000    4.6694169      444           -0    1.1152654 
-   72000    4.7335079      444           -0    1.1309734 
-   73000    4.7967482      444           -0    1.1466813 
-   74000    4.8603547      444           -0    1.1623893 
-   75000    4.9250085      444           -0    1.1780972 
-   76000    4.9909372      444           -0    1.1938052 
-   77000    5.0578024      444           -0    1.2095132 
-   78000    5.1250138      444           -0    1.2252211 
-   79000    5.1929755      444           -0    1.2409291 
-   80000    5.2627637      444           -0    1.2566371 
-   81000    5.3280981      444           -0     1.272345 
-   82000    5.3957336      444           -0     1.288053 
-   83000    5.4648135      444           -0     1.303761 
-   84000    5.5368683      444           -0    1.3194689 
-   85000    5.6352935      888           -0    1.3351769 
-   86000    5.7708502      888           -0    1.3508848 
-   87000    5.9051492      888           -0    1.3665928 
-   88000    6.0384896      888           -0    1.3823008 
-   89000    6.1714747      888           -0    1.3980087 
-   90000    6.3042989      888           -0    1.4137167 
-   91000    6.4114611      888           -0    1.4294247 
-   92000    6.5164247      888           -0    1.4451326 
-   93000    6.6219602      888           -0    1.4608406 
-   94000     6.728405      888           -0    1.4765485 
-   95000    6.8411646      888           -0    1.4922565 
-   96000    6.9479821      888           -0    1.5079645 
-   97000    7.0569239      888           -0    1.5236724 
-   98000    7.1673372      888           -0    1.5393804 
-   99000    7.2778809      888           -0    1.5550884 
-  100000     7.398834      888           -0    1.5707963 
-  101000    7.5066864      888           -0    1.5865043 
-  102000    7.6158357      888           -0    1.6022123 
-  103000     7.725111      888           -0    1.6179202 
-  104000    7.8344197      888           -0    1.6336282 
-  105000    7.9532022      888           -0    1.6493361 
-  106000    8.0643187      888           -0    1.6650441 
-  107000    8.1765473      888           -0    1.6807521 
-  108000    8.2890661      888           -0      1.69646 
-  109000    8.4048562      888           -0     1.712168 
-  110000    8.5208168      888           -0     1.727876 
-  111000    8.6303153      888           -0    1.7435839 
-  112000    8.7401052      888           -0    1.7592919 
-  113000    8.8518219      888           -0    1.7749998 
-  114000    8.9638157      888           -0    1.7907078 
-  115000    9.0766122      888           -0    1.8064158 
-  116000    9.1908746      888           -0    1.8221237 
-  117000     9.306145      888           -0    1.8378317 
-  118000    9.4229569      888           -0    1.8535397 
-  119000    9.5407412      888           -0    1.8692476 
-  120000    9.6574531      888           -0    1.8849556 
-  121000    9.7683234      888           -0    1.9006636 
-  122000    9.8812008      888           -0    1.9163715 
-  123000    9.9952521      888           -0    1.9320795 
-  124000    10.111879      888           -0    1.9477874 
-  125000    10.228812      888           -0    1.9634954 
-  126000    10.347842      888           -0    1.9792034 
-  127000     10.47052      888           -0    1.9949113 
-  128000    10.593136      888           -0    2.0106193 
-  129000    10.718124      888           -0    2.0263273 
-  130000    10.844211      888           -0    2.0420352 
-  131000    10.959177      888           -0    2.0577432 
-  132000    11.075781      888           -0    2.0734512 
-  133000    11.191418      888           -0    2.0891591 
-  134000    11.313376      888           -0    2.1048671 
-  135000    11.432321      888           -0     2.120575 
-  136000    11.551893      888           -0     2.136283 
-  137000    11.672695      888           -0     2.151991 
-  138000    11.793487      888           -0    2.1676989 
-  139000    11.914089      888           -0    2.1834069 
-  140000    12.037441      888           -0    2.1991149 
-  141000    12.161974      888           -0    2.2148228 
-  142000    12.286641      888           -0    2.2305308 
-  143000    12.414012      888           -0    2.2462387 
-  144000    12.540939      888           -0    2.2619467 
-  145000     12.66985      888           -0    2.2776547 
-  146000     12.79975      888           -0    2.2933626 
-  147000    12.932702      888           -0    2.3090706 
-  148000    13.066088      888           -0    2.3247786 
-  149000    13.200814      888           -0    2.3404865 
-  150000     13.33565      888           -0    2.3561945 
-  151000    13.465995      888           -0    2.3719025 
-  152000    13.586622      888           -0    2.3876104 
-  153000    13.711423      888           -0    2.4033184 
-  154000    13.835058      888           -0    2.4190263 
-  155000    13.967661      888           -0    2.4347343 
-  156000    14.100609      888           -0    2.4504423 
-  157000    14.234485      888           -0    2.4661502 
-  158000    14.373325      888           -0    2.4818582 
-  159000    14.510608      888           -0    2.4975662 
-  160000    14.651416      888           -0    2.5132741 
-  161000    14.785767      888           -0    2.5289821 
-  162000    14.921569      888           -0      2.54469 
-  163000    15.058895      888           -0     2.560398 
-  164000    15.198786      888           -0     2.576106 
-  165000    15.341662      888           -0    2.5918139 
-  166000    15.487128      888           -0    2.6075219 
-  167000    15.649383      888           -0    2.6232299 
-  168000    15.795388      888           -0    2.6389378 
-  169000    15.942671      888           -0    2.6546458 
-  170000    16.091824     1000           -0    2.6703538 
-  171000    16.239863     1000           -0    2.6860617 
-  172000    16.391118     1000           -0    2.7017697 
-  173000      16.5417     1000           -0    2.7174776 
-  174000     16.69479     1000           -0    2.7331856 
-  175000    16.847412     1000           -0    2.7488936 
-  176000    17.000374     1000           -0    2.7646015 
-  177000     17.15471     1000           -0    2.7803095 
-  178000     17.31284     1000           -0    2.7960175 
-  179000     17.46991     1000           -0    2.8117254 
-  180000    17.629018     1000           -0    2.8274334 
-  181000    17.787736     1000           -0    2.8431414 
-  182000    17.946197     1000           -0    2.8588493 
-  183000    18.105271     1000           -0    2.8745573 
-  184000    18.263731     1000           -0    2.8902652 
-  185000    18.433277     1000           -0    2.9059732 
-  186000    18.594456     1000           -0    2.9216812 
-  187000    18.755532     1000           -0    2.9373891 
-  188000    18.918447     1000           -0    2.9530971 
-  189000    19.080359     1000           -0    2.9688051 
-  190000    19.243927     1000           -0     2.984513 
-  191000    19.395044     1000           -0     3.000221 
-  192000    19.546837     1000           -0    3.0159289 
-  193000    19.695827     1000           -0    3.0316369 
-  194000    19.843856     1000           -0    3.0473449 
-  195000    19.993821     1000           -0    3.0630528 
-  196000    20.145787     1000           -0    3.0787608 
-  197000    20.298114     1000           -0    3.0944688 
-  198000     20.45074     1000           -0    3.1101767 
-  199000    20.607595     1000           -0    3.1258847 
-  200000    20.760979     1000           -0    3.1415927 
-Loop time of 20.7611 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 39328.699 tau/day, 9633.409 timesteps/s
-98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.57172    | 0.93292    | 1.2995     |  37.1 |  4.49
-Neigh   | 0.015648   | 0.018747   | 0.02175    |   2.1 |  0.09
-Comm    | 3.17       | 3.6151     | 4.0856     |  23.0 | 17.41
-Output  | 0.0051017  | 0.012686   | 0.033359   |  10.6 |  0.06
-Modify  | 12.36      | 13.269     | 14.095     |  21.8 | 63.91
-Other   |            | 2.912      |            |       | 14.03
-
-Nlocal:    250 ave 270 max 230 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost:    297 ave 337 max 234 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    982.5 ave 1580 max 496 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 3930
-Ave neighs/atom = 3.93
-Neighbor list builds = 218
-Dangerous builds = 0
-unfix 		ins
-run		200000
-Per MPI rank memory allocation (min/avg/max) = 12 | 12.19 | 12.35 Mbytes
-Step CPU Atoms KinEng v_theta 
-  200000            0     1000   0.89289812    3.1415927 
-  201000   0.15554476     1000   0.90162438    3.1573006 
-  202000   0.31118774     1000   0.89175077    3.1730086 
-  203000   0.47266722     1000   0.88068523    3.1887165 
-  204000   0.64758801     1000   0.88775074    3.2044245 
-  205000   0.85137105     1000   0.89009449    3.2201325 
-  206000    1.0712745     1000   0.89031724    3.2358404 
-  207000    1.3620427     1000   0.90901476    3.2515484 
-  208000    1.6051998     1000   0.91977358    3.2672564 
-  209000    1.7975032     1000   0.92044257    3.2829643 
-  210000    1.9654117     1000   0.90550844    3.2986723 
-  211000    2.1186137     1000   0.90179135    3.3143802 
-  212000    2.2714169     1000   0.90474936    3.3300882 
-  213000    2.4236252     1000    0.9011002    3.3457962 
-  214000    2.5737655     1000   0.89619815    3.3615041 
-  215000    2.7326233     1000   0.89129064    3.3772121 
-  216000    2.8794787     1000   0.88785486    3.3929201 
-  217000    3.0264313     1000   0.89448821     3.408628 
-  218000    3.1743443     1000   0.89323746     3.424336 
-  219000    3.3225086     1000   0.88176869     3.440044 
-  220000    3.4717121     1000   0.86989815    3.4557519 
-  221000    3.6229391     1000   0.85900389    3.4714599 
-  222000    3.7768724     1000   0.85440461    3.4871678 
-  223000    3.9287963     1000    0.8604449    3.5028758 
-  224000     4.082505     1000   0.84537374    3.5185838 
-  225000     4.234731     1000   0.84526488    3.5342917 
-  226000    4.3872988     1000   0.85877362    3.5499997 
-  227000    4.5396216     1000   0.86762074    3.5657077 
-  228000    4.7092509     1000   0.86460359    3.5814156 
-  229000    4.8631954     1000   0.85409682    3.5971236 
-  230000    5.0194352     1000   0.83902718    3.6128316 
-  231000    5.1765387     1000   0.83908755    3.6285395 
-  232000    5.3335299     1000   0.83178808    3.6442475 
-  233000    5.4917257     1000   0.83369584    3.6599554 
-  234000     5.654233     1000    0.8530074    3.6756634 
-  235000    5.8163757     1000   0.86385009    3.6913714 
-  236000    5.9791231     1000   0.86453337    3.7070793 
-  237000    6.1401029     1000   0.86137572    3.7227873 
-  238000     6.300632     1000    0.8656285    3.7384953 
-  239000    6.4597898     1000   0.85993724    3.7542032 
-  240000    6.6216707     1000    0.8484153    3.7699112 
-  241000    6.7793672     1000   0.84624799    3.7856191 
-  242000     6.939244     1000   0.83739227    3.8013271 
-  243000    7.1013088     1000   0.83026469    3.8170351 
-  244000     7.267416     1000   0.81060567     3.832743 
-  245000    7.4318523     1000   0.81081038     3.848451 
-  246000    7.6077905     1000   0.80857771     3.864159 
-  247000    7.7763391     1000   0.80353315    3.8798669 
-  248000    7.9485247     1000   0.80191903    3.8955749 
-  249000    8.1208956     1000   0.79865102    3.9112829 
-  250000    8.2921841     1000   0.79407385    3.9269908 
-  251000    8.4614651     1000    0.7880275    3.9426988 
-  252000    8.6266186     1000   0.79212521    3.9584067 
-  253000    8.7913449     1000   0.78976714    3.9741147 
-  254000    8.9596558     1000   0.79720779    3.9898227 
-  255000    9.1278918     1000   0.79329363    4.0055306 
-  256000    9.3016815     1000   0.80851295    4.0212386 
-  257000    9.4701304     1000   0.82322071    4.0369466 
-  258000    9.6399531     1000   0.83042211    4.0526545 
-  259000    9.8090186     1000   0.82773068    4.0683625 
-  260000    9.9798045     1000    0.8246773    4.0840704 
-  261000    10.148952     1000   0.81374287    4.0997784 
-  262000    10.318855     1000   0.79936963    4.1154864 
-  263000    10.496092     1000   0.78124408    4.1311943 
-  264000    10.671031     1000   0.77790646    4.1469023 
-  265000    10.843052     1000   0.77212005    4.1626103 
-  266000     11.01867     1000   0.77977752    4.1783182 
-  267000    11.192151     1000   0.79237542    4.1940262 
-  268000    11.362491     1000   0.80631398    4.2097342 
-  269000     11.53223     1000   0.82380407    4.2254421 
-  270000      11.7123     1000   0.82477127    4.2411501 
-  271000    11.883593     1000   0.81655074     4.256858 
-  272000    12.052348     1000   0.80678676     4.272566 
-  273000    12.220196     1000   0.79162789     4.288274 
-  274000    12.395164     1000   0.78896081    4.3039819 
-  275000    12.569757     1000   0.77904648    4.3196899 
-  276000    12.748754     1000   0.78252999    4.3353979 
-  277000     12.91648     1000   0.78293295    4.3511058 
-  278000    13.086087     1000   0.78311337    4.3668138 
-  279000    13.260159     1000   0.77657634    4.3825218 
-  280000    13.428503     1000   0.76835711    4.3982297 
-  281000    13.596094     1000   0.75586438    4.4139377 
-  282000    13.763325     1000   0.74600306    4.4296456 
-  283000    13.932867     1000   0.73228762    4.4453536 
-  284000    14.098865     1000   0.72344939    4.4610616 
-  285000    14.269317     1000   0.72160289    4.4767695 
-  286000    14.441196     1000   0.71321619    4.4924775 
-  287000    14.614458     1000   0.72631772    4.5081855 
-  288000    14.783358     1000   0.74390396    4.5238934 
-  289000    14.953564     1000   0.77320352    4.5396014 
-  290000     15.12428     1000   0.77249469    4.5553093 
-  291000    15.283974     1000    0.7583723    4.5710173 
-  292000    15.449553     1000   0.74568347    4.5867253 
-  293000    15.611965     1000   0.74108034    4.6024332 
-  294000    15.770807     1000   0.72706174    4.6181412 
-  295000    15.927151     1000   0.71122597    4.6338492 
-  296000    16.086734     1000   0.70272297    4.6495571 
-  297000    16.245418     1000    0.6945394    4.6652651 
-  298000    16.406617     1000   0.69541258    4.6809731 
-  299000    16.568989     1000   0.71696092     4.696681 
-  300000    16.754911     1000   0.72939561     4.712389 
-  301000    16.919453     1000   0.73621801    4.7280969 
-  302000     17.07794     1000   0.72052605    4.7438049 
-  303000    17.234397     1000   0.71057318    4.7595129 
-  304000     17.39014     1000   0.70014814    4.7752208 
-  305000    17.550789     1000   0.68855925    4.7909288 
-  306000    17.718802     1000   0.68665019    4.8066368 
-  307000    17.874036     1000    0.6831349    4.8223447 
-  308000    18.029367     1000   0.67929468    4.8380527 
-  309000    18.188065     1000   0.67833006    4.8537606 
-  310000    18.348243     1000   0.67764037    4.8694686 
-  311000    18.512475     1000   0.68271978    4.8851766 
-  312000    18.676519     1000   0.69021026    4.9008845 
-  313000    18.836426     1000   0.68795473    4.9165925 
-  314000    18.997681     1000   0.68308892    4.9323005 
-  315000    19.158794     1000   0.68086977    4.9480084 
-  316000    19.318186     1000   0.67879169    4.9637164 
-  317000    19.479364     1000   0.68128526    4.9794244 
-  318000    19.645085     1000   0.68718719    4.9951323 
-  319000    19.806831     1000   0.68419901    5.0108403 
-  320000     19.97005     1000   0.68045269    5.0265482 
-  321000    20.130643     1000   0.68430036    5.0422562 
-  322000    20.291637     1000   0.68195368    5.0579642 
-  323000    20.457605     1000   0.67964011    5.0736721 
-  324000    20.621699     1000   0.67681293    5.0893801 
-  325000     20.78525     1000   0.67601868    5.1050881 
-  326000    20.950321     1000   0.67600265     5.120796 
-  327000     21.11346     1000   0.68484094     5.136504 
-  328000    21.276964     1000   0.68526189     5.152212 
-  329000    21.440971     1000   0.67602072    5.1679199 
-  330000    21.609791     1000   0.68222852    5.1836279 
-  331000    21.773574     1000   0.68825647    5.1993358 
-  332000     21.93854     1000   0.68168415    5.2150438 
-  333000    22.102281     1000   0.67460357    5.2307518 
-  334000    22.265741     1000   0.67747925    5.2464597 
-  335000    22.436954     1000     0.681763    5.2621677 
-  336000    22.614367     1000   0.67611867    5.2778757 
-  337000    22.779064     1000   0.66903217    5.2935836 
-  338000    22.945739     1000    0.6684293    5.3092916 
-  339000    23.111375     1000   0.66465194    5.3249995 
-  340000    23.278674     1000   0.66226848    5.3407075 
-  341000    23.444642     1000   0.66407188    5.3564155 
-  342000    23.614615     1000   0.65762812    5.3721234 
-  343000    23.785007     1000   0.66936507    5.3878314 
-  344000    23.956265     1000   0.67424224    5.4035394 
-  345000    24.129057     1000     0.684271    5.4192473 
-  346000    24.303073     1000   0.68294352    5.4349553 
-  347000    24.475812     1000   0.69795697    5.4506633 
-  348000    24.652771     1000   0.69818863    5.4663712 
-  349000    24.830973     1000   0.69578798    5.4820792 
-  350000     25.00923     1000   0.69377251    5.4977871 
-  351000    25.185421     1000   0.69638202    5.5134951 
-  352000    25.363647     1000   0.70115823    5.5292031 
-  353000    25.540517     1000   0.70891635     5.544911 
-  354000    25.718709     1000   0.70876639     5.560619 
-  355000    25.893633     1000   0.71130235     5.576327 
-  356000    26.068423     1000   0.69380913    5.5920349 
-  357000    26.243801     1000   0.67934899    5.6077429 
-  358000    26.418883     1000   0.67024516    5.6234508 
-  359000    26.594722     1000   0.66145645    5.6391588 
-  360000    26.770322     1000   0.65335546    5.6548668 
-  361000    26.946396     1000   0.65495192    5.6705747 
-  362000     27.12296     1000   0.64973833    5.6862827 
-  363000    27.298461     1000   0.64532381    5.7019907 
-  364000    27.473586     1000   0.64282855    5.7176986 
-  365000    27.653872     1000   0.64451862    5.7334066 
-  366000    27.830317     1000   0.64366439    5.7491146 
-  367000    28.007037     1000   0.64395479    5.7648225 
-  368000    28.184079     1000   0.65827587    5.7805305 
-  369000    28.376009     1000   0.66311341    5.7962384 
-  370000    28.557287     1000   0.66165026    5.8119464 
-  371000    28.736569     1000   0.66878374    5.8276544 
-  372000     28.91063     1000   0.66944548    5.8433623 
-  373000    29.084648     1000   0.66061945    5.8590703 
-  374000    29.258649     1000   0.65320954    5.8747783 
-  375000    29.433156     1000   0.64641195    5.8904862 
-  376000    29.611781     1000   0.64631388    5.9061942 
-  377000     29.78531     1000   0.64232398    5.9219022 
-  378000    29.955917     1000   0.63805257    5.9376101 
-  379000    30.126378     1000   0.63666047    5.9533181 
-  380000    30.297285     1000   0.63651856     5.969026 
-  381000    30.471635     1000    0.6377374     5.984734 
-  382000    30.644813     1000   0.64750107     6.000442 
-  383000    30.816208     1000   0.65655138    6.0161499 
-  384000    30.986444     1000   0.65408935    6.0318579 
-  385000    31.156501     1000   0.64437236    6.0475659 
-  386000    31.327665     1000   0.63862174    6.0632738 
-  387000     31.49731     1000   0.64133807    6.0789818 
-  388000    31.682031     1000   0.64174374    6.0946897 
-  389000     31.85148     1000   0.64480071    6.1103977 
-  390000    32.020336     1000   0.64982943    6.1261057 
-  391000    32.187634     1000    0.6461109    6.1418136 
-  392000    32.357282     1000   0.64044412    6.1575216 
-  393000    32.527796     1000   0.64662995    6.1732296 
-  394000    32.704323     1000   0.65330527    6.1889375 
-  395000    32.880643     1000   0.66026265    6.2046455 
-  396000    33.048614     1000    0.6718969    6.2203535 
-  397000    33.222059     1000   0.66481385    6.2360614 
-  398000    33.391738     1000   0.66685494    6.2517694 
-  399000    33.560431     1000    0.6612594    6.2674773 
-  400000    33.729715     1000   0.65289572    6.2831853 
-Loop time of 33.7298 on 4 procs for 200000 steps with 1000 atoms
-
-Performance: 24207.249 tau/day, 5929.470 timesteps/s
-97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.6748     | 2.6848     | 3.6646     |  58.4 |  7.96
-Neigh   | 0.021206   | 0.026438   | 0.03191    |   3.1 |  0.08
-Comm    | 6.133      | 7.3745     | 8.6652     |  45.0 | 21.86
-Output  | 0.0053763  | 0.016101   | 0.044719   |  13.0 |  0.05
-Modify  | 18.26      | 20.115     | 22.413     |  39.2 | 59.64
-Other   |            | 3.513      |            |       | 10.42
-
-Nlocal:    250 ave 266 max 230 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Nghost:    401.5 ave 476 max 325 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    1264 ave 1634 max 895 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 5056
-Ave neighs/atom = 5.056
-Neighbor list builds = 160
-Dangerous builds = 0
-Total wall time: 0:00:54

examples/granular/in.pour.drum

@@ -44,7 +44,7 @@ change_box      all boundary p p f
 
 pair_style      granular
 pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall 
 
 variable        theta equal 0
 

examples/granular/in.pour.heat

@@ -0,0 +1,84 @@
+# pour one types of particles into cylinder and oscillate
+# temperature of the bottom plate
+
+variable        name string heat_plate
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 10
+variable        boxy equal 10
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_height equal 30
+
+variable        xc equal 0.5*${boxx}
+variable        yc equal 0.5*${boxx}
+variable        zc equal 0.5*${boxz}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dhi equal 2.0*${rhi}
+
+variable        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box      2 boxreg
+change_box      all boundary p p f
+
+pair_style      granular
+pair_coeff      * * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+
+fix             0 all property/atom temperature heatflow
+fix             1 all balance 100 1.0 shift xy 5 1.1
+fix             2 all nve/sphere
+fix             3 all heat/flow constant 1.0
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 1000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify     vel yes
+
+neighbor        ${skin} bin
+neigh_modify    delay 0 every 1 check yes
+
+variable        oscillate equal 1.0*sin(step*0.0001)
+
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0 region bottom_wall temperature v_oscillate
+
+thermo_style    custom step atoms ke pxx pyy pzz
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 1000 ${name}.dump id type radius mass x y z temperature heatflow
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+group           delgroup dynamic all var zmax every 10000
+
+run             100000
+

examples/granular/log.15Sep22.pour.drum.g++.1

@@ -0,0 +1,272 @@
+LAMMPS (15 Sep 2022)
+# 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.
+
+variable        name string rotating_drum_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 30
+variable        boxy equal 30
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_rad equal 30*0.5
+variable        drum_height equal 20
+
+variable        xc equal 0.5*${boxx}
+variable        xc equal 0.5*30
+variable        yc equal 0.5*${boxx}
+variable        yc equal 0.5*30
+variable        zc equal 0.5*${boxz}
+variable        zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+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        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 30 0 ${boxz}
+region          boxreg block 0 30 0 30 0 50
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  1 by 1 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
+
+variable        theta equal 0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 20 ${boxz}
+region          insreg cylinder z 15 15 14.45 20 50
+
+fix             0 all balance 100 1.0 shift xy 5 1.1
+fix             1 all nve/sphere
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+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
+
+neighbor        ${skin} bin
+neighbor        0.2 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style    custom step atoms ke v_theta
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+variable        zmax atom z+c_1>0.5*20
+group           delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run             2000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  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
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes
+   Step        Atoms        KinEng        v_theta    
+         0           0  -0              0            
+       100        4000  -0              0            
+       200        4000  -0              0            
+       300        4000  -0              0            
+       400        4000  -0              0            
+       500        4000  -0              0            
+       600        4000  -0              0            
+       700        4000  -0              0            
+       800        4000  -0              0            
+       900        4000  -0              0            
+      1000        4000  -0              0            
+      1100        4000  -0              0            
+      1200        4000  -0              0            
+      1300        4000  -0              0            
+      1400        4000  -0              0            
+      1500        4000  -0              0            
+      1600        4000  -0              0            
+      1700        4000  -0              0            
+      1800        4000  -0              0            
+      1900        4000  -0              0            
+      2000        4000  -0              0            
+Loop time of 2.81549 on 1 procs for 2000 steps with 4000 atoms
+
+Performance: 61374.657 tau/day, 710.355 timesteps/s, 2.841 Matom-step/s
+98.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.35362    | 0.35362    | 0.35362    |   0.0 | 12.56
+Neigh   | 1.0852     | 1.0852     | 1.0852     |   0.0 | 38.54
+Comm    | 0.041891   | 0.041891   | 0.041891   |   0.0 |  1.49
+Output  | 0.00059151 | 0.00059151 | 0.00059151 |   0.0 |  0.02
+Modify  | 1.2814     | 1.2814     | 1.2814     |   0.0 | 45.51
+Other   |            | 0.0528     |            |       |  1.88
+
+Nlocal:           4000 ave        4000 max        4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            179 ave         179 max         179 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           7019 ave        7019 max        7019 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7019
+Ave neighs/atom = 1.75475
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms    group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region          top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix           grav
+unfix           ins1
+unfix           ins2
+fix             grav all gravity 10 vector 0 -1 0
+
+variable        theta equal 2*PI*elapsed/20000.0
+run             3000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 22.42 | 22.42 | 22.42 Mbytes
+   Step        Atoms        KinEng        v_theta    
+      2000        4000   59.969827      0            
+      2100        4000   47.251389      0.031415927  
+      2200        4000   33.726755      0.062831853  
+      2300        4000   24.212479      0.09424778   
+      2400        4000   17.366268      0.12566371   
+      2500        4000   18.502318      0.15707963   
+      2600        4000   17.44981       0.18849556   
+      2700        4000   16.068315      0.21991149   
+      2800        4000   14.252644      0.25132741   
+      2900        4000   11.544019      0.28274334   
+      3000        4000   9.0353662      0.31415927   
+      3100        4000   6.9955912      0.34557519   
+      3200        4000   5.955137       0.37699112   
+      3300        4000   5.8947849      0.40840704   
+      3400        4000   6.0544729      0.43982297   
+      3500        4000   6.5326359      0.4712389    
+      3600        4000   6.6047764      0.50265482   
+      3700        4000   6.7073614      0.53407075   
+      3800        4000   6.7367804      0.56548668   
+      3900        4000   6.6178006      0.5969026    
+      4000        4000   6.3834858      0.62831853   
+      4100        4000   5.8660652      0.65973446   
+      4200        4000   5.308513       0.69115038   
+      4300        4000   4.7270842      0.72256631   
+      4400        4000   4.1920733      0.75398224   
+      4500        4000   3.7068814      0.78539816   
+      4600        4000   3.3259615      0.81681409   
+      4700        4000   2.9339231      0.84823002   
+      4800        4000   2.670752       0.87964594   
+      4900        4000   2.4509115      0.91106187   
+      5000        4000   2.2609335      0.9424778    
+Loop time of 9.82178 on 1 procs for 3000 steps with 4000 atoms
+
+Performance: 26390.330 tau/day, 305.444 timesteps/s, 1.222 Matom-step/s
+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    | 3.2932     | 3.2932     | 3.2932     |   0.0 | 33.53
+Neigh   | 2.2872     | 2.2872     | 2.2872     |   0.0 | 23.29
+Comm    | 0.067117   | 0.067117   | 0.067117   |   0.0 |  0.68
+Output  | 0.00093425 | 0.00093425 | 0.00093425 |   0.0 |  0.01
+Modify  | 4.0986     | 4.0986     | 4.0986     |   0.0 | 41.73
+Other   |            | 0.07476    |            |       |  0.76
+
+Nlocal:           4000 ave        4000 max        4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            363 ave         363 max         363 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13089 ave       13089 max       13089 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13089
+Ave neighs/atom = 3.27225
+Neighbor list builds = 1247
+Dangerous builds = 130
+Total wall time: 0:00:12

examples/granular/log.15Sep22.pour.drum.g++.4

@@ -0,0 +1,272 @@
+LAMMPS (15 Sep 2022)
+# 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.
+
+variable        name string rotating_drum_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 30
+variable        boxy equal 30
+variable        boxz equal 50
+
+variable        drum_rad equal ${boxx}*0.5
+variable        drum_rad equal 30*0.5
+variable        drum_height equal 20
+
+variable        xc equal 0.5*${boxx}
+variable        xc equal 0.5*30
+variable        yc equal 0.5*${boxx}
+variable        yc equal 0.5*30
+variable        zc equal 0.5*${boxz}
+variable        zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+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        cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*${rhi}
+variable        cyl_rad_inner equal 15-1.1*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 30 0 30 0 ${boxz}
+region          boxreg block 0 30 0 30 0 50
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  2 by 2 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff      2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
+
+variable        theta equal 0
+
+region          curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region          bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region          insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region          insreg cylinder z 15 15 14.45 20 ${boxz}
+region          insreg cylinder z 15 15 14.45 20 50
+
+fix             0 all balance 100 1.0 shift xy 5 1.1
+fix             1 all nve/sphere
+fix             grav all gravity 10 vector 0 0 -1
+fix             ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+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
+
+neighbor        ${skin} bin
+neighbor        0.2 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix             4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style    custom step atoms ke v_theta
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+#For removal later
+compute         1 all property/atom radius
+variable        zmax atom z+c_1>0.5*${drum_height}
+variable        zmax atom z+c_1>0.5*20
+group           delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run             2000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  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
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.3 | 15.3 | 15.3 Mbytes
+   Step        Atoms        KinEng        v_theta    
+         0           0  -0              0            
+       100        4000  -0              0            
+       200        4000  -0              0            
+       300        4000  -0              0            
+       400        4000  -0              0            
+       500        4000  -0              0            
+       600        4000  -0              0            
+       700        4000  -0              0            
+       800        4000  -0              0            
+       900        4000  -0              0            
+      1000        4000  -0              0            
+      1100        4000  -0              0            
+      1200        4000  -0              0            
+      1300        4000  -0              0            
+      1400        4000  -0              0            
+      1500        4000  -0              0            
+      1600        4000  -0              0            
+      1700        4000  -0              0            
+      1800        4000  -0              0            
+      1900        4000  -0              0            
+      2000        4000  -0              0            
+Loop time of 0.744926 on 4 procs for 2000 steps with 4000 atoms
+
+Performance: 231969.322 tau/day, 2684.830 timesteps/s, 10.739 Matom-step/s
+98.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.064917   | 0.069813   | 0.074844   |   1.7 |  9.37
+Neigh   | 0.15075    | 0.15915    | 0.1692     |   1.9 | 21.36
+Comm    | 0.11223    | 0.11821    | 0.12247    |   1.1 | 15.87
+Output  | 0.00030739 | 0.00036898 | 0.00046777 |   0.0 |  0.05
+Modify  | 0.36068    | 0.36657    | 0.37031    |   0.7 | 49.21
+Other   |            | 0.03082    |            |       |  4.14
+
+Nlocal:           1000 ave        1010 max         990 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            285 ave         287 max         283 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:        1714.25 ave        1764 max        1651 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 6857
+Ave neighs/atom = 1.71425
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms    group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region          top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region          top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix             5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix           grav
+unfix           ins1
+unfix           ins2
+fix             grav all gravity 10 vector 0 -1 0
+
+variable        theta equal 2*PI*elapsed/20000.0
+run             3000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 21.6 | 21.6 | 21.6 Mbytes
+   Step        Atoms        KinEng        v_theta    
+      2000        4000   60.10546       0            
+      2100        4000   47.274123      0.031415927  
+      2200        4000   33.475582      0.062831853  
+      2300        4000   24.083669      0.09424778   
+      2400        4000   17.36351       0.12566371   
+      2500        4000   18.576501      0.15707963   
+      2600        4000   17.39          0.18849556   
+      2700        4000   15.789254      0.21991149   
+      2800        4000   14.08156       0.25132741   
+      2900        4000   11.636681      0.28274334   
+      3000        4000   8.9897685      0.31415927   
+      3100        4000   7.0703519      0.34557519   
+      3200        4000   6.0741809      0.37699112   
+      3300        4000   5.8286097      0.40840704   
+      3400        4000   6.059001       0.43982297   
+      3500        4000   6.4310861      0.4712389    
+      3600        4000   6.3957528      0.50265482   
+      3700        4000   6.4858292      0.53407075   
+      3800        4000   6.4685962      0.56548668   
+      3900        4000   6.3469676      0.5969026    
+      4000        4000   6.2808022      0.62831853   
+      4100        4000   5.957048       0.65973446   
+      4200        4000   5.5378951      0.69115038   
+      4300        4000   4.8523264      0.72256631   
+      4400        4000   4.2485239      0.75398224   
+      4500        4000   3.7587486      0.78539816   
+      4600        4000   3.327008       0.81681409   
+      4700        4000   2.9421013      0.84823002   
+      4800        4000   2.75247        0.87964594   
+      4900        4000   2.5306332      0.91106187   
+      5000        4000   2.352504       0.9424778    
+Loop time of 2.48704 on 4 procs for 3000 steps with 4000 atoms
+
+Performance: 104220.238 tau/day, 1206.253 timesteps/s, 4.825 Matom-step/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.51605    | 0.70407    | 0.86299    |  14.7 | 28.31
+Neigh   | 0.3522     | 0.42808    | 0.50041    |   8.0 | 17.21
+Comm    | 0.17318    | 0.42324    | 0.7046     |  29.0 | 17.02
+Output  | 0.00079725 | 0.0013956  | 0.002092   |   1.3 |  0.06
+Modify  | 0.68507    | 0.79676    | 0.90954    |   8.9 | 32.04
+Other   |            | 0.1335     |            |       |  5.37
+
+Nlocal:           1000 ave        1330 max         670 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:          525.5 ave         781 max         417 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:        3243.75 ave        4460 max        2012 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 12975
+Ave neighs/atom = 3.24375
+Neighbor list builds = 1299
+Dangerous builds = 129
+Total wall time: 0:00:03

examples/granular/log.15Sep22.pour.flatwall.g++.1

@@ -0,0 +1,195 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable        name string pour_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 20
+variable        boxy equal 20
+variable        boxz equal 30
+
+variable        xc1 equal 0.3*${boxx}
+variable        xc1 equal 0.3*20
+variable        xc2 equal 0.7*${boxx}
+variable        xc2 equal 0.7*20
+variable        yc equal 0.5*${boxy}
+variable        yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors      * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 20 0 ${boxz}
+region          boxreg block 0 20 0 20 0 30
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  1 by 1 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff      2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+comm_modify     vel yes
+
+region          insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 30
+region          insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 30
+
+fix             1 all nve/sphere
+fix             grav all gravity 10.0 vector 0 0 -1
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+neighbor        ${skin} bin
+neighbor        0.15 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style    custom step atoms ke
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+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 = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  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
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.27 | 15.27 | 15.27 Mbytes
+   Step        Atoms        KinEng    
+         0           0  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100         926  -0            
+       200         926  -0            
+       300         926  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       400        1498  -0            
+       500        1498  -0            
+       600        1498  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       700        2275  -0            
+       800        2275  -0            
+       900        2275  -0            
+      1000        2275  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1100        2954  -0            
+      1200        2954  -0            
+      1300        2954  -0            
+      1400        3000  -0            
+      1500        3000  -0            
+      1600        3000  -0            
+      1700        3000  -0            
+      1800        3000  -0            
+      1900        3000  -0            
+      2000        3000  -0            
+      2100        3000  -0            
+      2200        3000  -0            
+      2300        3000  -0            
+      2400        3000  -0            
+      2500        3000  -0            
+      2600        3000  -0            
+      2700        3000  -0            
+      2800        3000  -0            
+      2900        3000  -0            
+      3000        3000  -0            
+      3100        3000  -0            
+      3200        3000  -0            
+      3300        3000  -0            
+      3400        3000  -0            
+      3500        3000  -0            
+      3600        3000  -0            
+      3700        3000  -0            
+      3800        3000  -0            
+      3900        3000  -0            
+      4000        3000  -0            
+      4100        3000  -0            
+      4200        3000  -0            
+      4300        3000  -0            
+      4400        3000  -0            
+      4500        3000  -0            
+      4600        3000  -0            
+      4700        3000  -0            
+      4800        3000  -0            
+      4900        3000  -0            
+      5000        3000  -0            
+Loop time of 10.7721 on 1 procs for 5000 steps with 3000 atoms
+
+Performance: 40103.467 tau/day, 464.160 timesteps/s, 1.392 Matom-step/s
+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    | 8.1117     | 8.1117     | 8.1117     |   0.0 | 75.30
+Neigh   | 1.2885     | 1.2885     | 1.2885     |   0.0 | 11.96
+Comm    | 0.059888   | 0.059888   | 0.059888   |   0.0 |  0.56
+Output  | 0.0011158  | 0.0011158  | 0.0011158  |   0.0 |  0.01
+Modify  | 1.2436     | 1.2436     | 1.2436     |   0.0 | 11.54
+Other   |            | 0.06727    |            |       |  0.62
+
+Nlocal:           3000 ave        3000 max        3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            471 ave         471 max         471 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          16713 ave       16713 max       16713 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 16713
+Ave neighs/atom = 5.571
+Neighbor list builds = 1102
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/granular/log.15Sep22.pour.flatwall.g++.4

@@ -0,0 +1,195 @@
+LAMMPS (15 Sep 2022)
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable        name string pour_two_types
+
+atom_style      sphere
+units           lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable        boxx equal 20
+variable        boxy equal 20
+variable        boxz equal 30
+
+variable        xc1 equal 0.3*${boxx}
+variable        xc1 equal 0.3*20
+variable        xc2 equal 0.7*${boxx}
+variable        xc2 equal 0.7*20
+variable        yc equal 0.5*${boxy}
+variable        yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable        rlo equal 0.25
+variable        rhi equal 0.5
+variable        dlo equal 2.0*${rlo}
+variable        dlo equal 2.0*0.25
+variable        dhi equal 2.0*${rhi}
+variable        dhi equal 2.0*0.5
+
+variable        dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors      * * 1
+region          boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region          boxreg block 0 20 0 20 0 ${boxz}
+region          boxreg block 0 20 0 20 0 30
+create_box      2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  2 by 2 by 1 MPI processor grid
+change_box      all boundary p p f
+Changing box ...
+
+pair_style      granular
+pair_coeff      1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff      2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+comm_modify     vel yes
+
+region          insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 ${boxz}
+region          insreg1 cylinder z 6 10 5 15 30
+region          insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 ${boxz}
+region          insreg2 cylinder z 14 10 5 15 30
+
+fix             1 all nve/sphere
+fix             grav all gravity 10.0 vector 0 0 -1
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix             ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix             ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+neighbor        ${skin} bin
+neighbor        0.15 bin
+neigh_modify    delay 0 every 1 check yes
+
+fix             3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style    custom step atoms ke
+thermo_modify   lost warn
+thermo          100
+
+timestep        0.001
+
+#dump           1 all custom 100 ${name}.dump id type radius mass x y z
+
+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 = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  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
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.04 | 15.04 | 15.04 Mbytes
+   Step        Atoms        KinEng    
+         0           0  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       100         926  -0            
+       200         926  -0            
+       300         926  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       400        1498  -0            
+       500        1498  -0            
+       600        1498  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+       700        2275  -0            
+       800        2275  -0            
+       900        2275  -0            
+      1000        2275  -0            
+WARNING: Less insertions than requested (../fix_pour.cpp:681)
+      1100        2954  -0            
+      1200        2954  -0            
+      1300        2954  -0            
+      1400        3000  -0            
+      1500        3000  -0            
+      1600        3000  -0            
+      1700        3000  -0            
+      1800        3000  -0            
+      1900        3000  -0            
+      2000        3000  -0            
+      2100        3000  -0            
+      2200        3000  -0            
+      2300        3000  -0            
+      2400        3000  -0            
+      2500        3000  -0            
+      2600        3000  -0            
+      2700        3000  -0            
+      2800        3000  -0            
+      2900        3000  -0            
+      3000        3000  -0            
+      3100        3000  -0            
+      3200        3000  -0            
+      3300        3000  -0            
+      3400        3000  -0            
+      3500        3000  -0            
+      3600        3000  -0            
+      3700        3000  -0            
+      3800        3000  -0            
+      3900        3000  -0            
+      4000        3000  -0            
+      4100        3000  -0            
+      4200        3000  -0            
+      4300        3000  -0            
+      4400        3000  -0            
+      4500        3000  -0            
+      4600        3000  -0            
+      4700        3000  -0            
+      4800        3000  -0            
+      4900        3000  -0            
+      5000        3000  -0            
+Loop time of 4.06277 on 4 procs for 5000 steps with 3000 atoms
+
+Performance: 106331.276 tau/day, 1230.686 timesteps/s, 3.692 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    | 0.85426    | 1.7801     | 2.7631     |  64.4 | 43.82
+Neigh   | 0.18775    | 0.25657    | 0.3279     |  11.5 |  6.32
+Comm    | 0.23605    | 1.3334     | 2.3703     |  81.6 | 32.82
+Output  | 0.00059456 | 0.0008165  | 0.0012002  |   0.0 |  0.02
+Modify  | 0.59336    | 0.64066    | 0.6864     |   4.3 | 15.77
+Other   |            | 0.05122    |            |       |  1.26
+
+Nlocal:            750 ave        1032 max         463 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:          426.5 ave         482 max         375 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:        4164.25 ave        6310 max        1941 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 16657
+Ave neighs/atom = 5.5523333
+Neighbor list builds = 1114
+Dangerous builds = 0
+Total wall time: 0:00:04

examples/granular/log.29Oct20.pour.drum.g++.1

@@ -1,271 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# 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.
-
-variable	name string rotating_drum_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 30
-variable	boxy equal 30
-variable	boxz equal 50
-
-variable	drum_rad equal ${boxx}*0.5
-variable	drum_rad equal 30*0.5
-variable	drum_height equal 20
-
-variable	xc equal 0.5*${boxx}
-variable	xc equal 0.5*30
-variable	yc equal 0.5*${boxx}
-variable	yc equal 0.5*30
-variable	zc equal 0.5*${boxz}
-variable	zc equal 0.5*50
-
-###############################################
-# Particle-related parameters
-###############################################
-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	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.4*${rhi}
-variable skin equal 0.4*0.5
-
-#############
-processors * * 1
-region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 30 0 ${boxz}
-region		boxreg block 0 30 0 30 0 50
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
-  1 by 1 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
-
-variable	theta equal 0
-
-region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
-region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
-
-region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 20 ${boxz}
-region		insreg cylinder z 15 15 14.45 20 50
-
-fix		0 all balance 100 1.0 shift xy 5 1.1
-fix		1 all nve/sphere
-fix		grav all gravity 10 vector 0 0 -1
-fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-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
-
-neighbor	${skin} bin
-neighbor	0.2 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
-fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
-
-thermo_style	custom step atoms ke v_theta
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-#For removal later
-compute		1 all property/atom radius
-variable	zmax atom z+c_1>0.5*${drum_height}
-variable	zmax atom z+c_1>0.5*20
-group		delgroup dynamic all var zmax every 10000
-dynamic group delgroup defined
-
-run		2000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 50 50 84
-  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
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 13.03 | 13.03 | 13.03 Mbytes
-Step Atoms KinEng v_theta 
-       0        0           -0            0 
-     100     4000           -0            0 
-     200     4000           -0            0 
-     300     4000           -0            0 
-     400     4000           -0            0 
-     500     4000           -0            0 
-     600     4000           -0            0 
-     700     4000           -0            0 
-     800     4000           -0            0 
-     900     4000           -0            0 
-    1000     4000           -0            0 
-    1100     4000           -0            0 
-    1200     4000           -0            0 
-    1300     4000           -0            0 
-    1400     4000           -0            0 
-    1500     4000           -0            0 
-    1600     4000           -0            0 
-    1700     4000           -0            0 
-    1800     4000           -0            0 
-    1900     4000           -0            0 
-    2000     4000           -0            0 
-Loop time of 10.5178 on 1 procs for 2000 steps with 4000 atoms
-
-Performance: 16429.309 tau/day, 190.154 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0701     | 1.0701     | 1.0701     |   0.0 | 10.17
-Neigh   | 4.2135     | 4.2135     | 4.2135     |   0.0 | 40.06
-Comm    | 0.38276    | 0.38276    | 0.38276    |   0.0 |  3.64
-Output  | 0.0013647  | 0.0013647  | 0.0013647  |   0.0 |  0.01
-Modify  | 4.7076     | 4.7076     | 4.7076     |   0.0 | 44.76
-Other   |            | 0.1424     |            |       |  1.35
-
-Nlocal:        4000.00 ave        4000 max        4000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        171.000 ave         171 max         171 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        8093.00 ave        8093 max        8093 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 8093
-Ave neighs/atom = 2.0232500
-Neighbor list builds = 1004
-Dangerous builds = 4
-
-#Remove any particles that are above z > 0.5*drum_height
-delete_atoms	group delgroup
-Deleted 0 atoms, new total = 4000
-
-#Add top lid
-region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
-fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
-
-# 'Turn' drum by switching the direction of gravity
-unfix		grav
-unfix		ins1
-unfix		ins2
-fix		grav all gravity 10 vector 0 -1 0
-
-variable	theta equal 2*PI*elapsed/20000.0
-run		3000
-Per MPI rank memory allocation (min/avg/max) = 19.37 | 19.37 | 19.37 Mbytes
-Step Atoms KinEng v_theta 
-    2000     4000    65.647582            0 
-    2100     4000    105.60001  0.031415927 
-    2200     4000    112.27573  0.062831853 
-    2300     4000    92.758671   0.09424778 
-    2400     4000    88.925835   0.12566371 
-    2500     4000    81.369163   0.15707963 
-    2600     4000    32.046943   0.18849556 
-    2700     4000    4.1926368   0.21991149 
-    2800     4000    3.9933453   0.25132741 
-    2900     4000    4.5062193   0.28274334 
-    3000     4000    5.3409521   0.31415927 
-    3100     4000    6.0165991   0.34557519 
-    3200     4000     6.606767   0.37699112 
-    3300     4000    7.3997751   0.40840704 
-    3400     4000    8.1098807   0.43982297 
-    3500     4000    8.6552424    0.4712389 
-    3600     4000    9.8445204   0.50265482 
-    3700     4000    10.098753   0.53407075 
-    3800     4000    10.039489   0.56548668 
-    3900     4000    9.6376278    0.5969026 
-    4000     4000    9.2598836   0.62831853 
-    4100     4000    8.7116037   0.65973446 
-    4200     4000    8.1274117   0.69115038 
-    4300     4000    7.1487627   0.72256631 
-    4400     4000    6.2253778   0.75398224 
-    4500     4000    5.3061398   0.78539816 
-    4600     4000    4.4319316   0.81681409 
-    4700     4000     4.205607   0.84823002 
-    4800     4000    3.2112987   0.87964594 
-    4900     4000    2.6449777   0.91106187 
-    5000     4000    2.3475497    0.9424778 
-Loop time of 32.4926 on 1 procs for 3000 steps with 4000 atoms
-
-Performance: 7977.205 tau/day, 92.329 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 8.0124     | 8.0124     | 8.0124     |   0.0 | 24.66
-Neigh   | 10.993     | 10.993     | 10.993     |   0.0 | 33.83
-Comm    | 0.86697    | 0.86697    | 0.86697    |   0.0 |  2.67
-Output  | 0.0021827  | 0.0021827  | 0.0021827  |   0.0 |  0.01
-Modify  | 12.367     | 12.367     | 12.367     |   0.0 | 38.06
-Other   |            | 0.2515     |            |       |  0.77
-
-Nlocal:        4000.00 ave        4000 max        4000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        318.000 ave         318 max         318 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        14807.0 ave       14807 max       14807 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 14807
-Ave neighs/atom = 3.7017500
-Neighbor list builds = 2189
-Dangerous builds = 1536
-Total wall time: 0:00:43

examples/granular/log.29Oct20.pour.drum.g++.4

@@ -1,271 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# 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.
-
-variable	name string rotating_drum_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 30
-variable	boxy equal 30
-variable	boxz equal 50
-
-variable	drum_rad equal ${boxx}*0.5
-variable	drum_rad equal 30*0.5
-variable	drum_height equal 20
-
-variable	xc equal 0.5*${boxx}
-variable	xc equal 0.5*30
-variable	yc equal 0.5*${boxx}
-variable	yc equal 0.5*30
-variable	zc equal 0.5*${boxz}
-variable	zc equal 0.5*50
-
-###############################################
-# Particle-related parameters
-###############################################
-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	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*${rhi}
-variable	cyl_rad_inner equal 15-1.1*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.4*${rhi}
-variable skin equal 0.4*0.5
-
-#############
-processors * * 1
-region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
-region		boxreg block 0 30 0 30 0 ${boxz}
-region		boxreg block 0 30 0 30 0 50
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
-  2 by 2 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
-pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
-
-variable	theta equal 0
-
-region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
-region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
-
-region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
-region		insreg cylinder z 15 15 14.45 20 ${boxz}
-region		insreg cylinder z 15 15 14.45 20 50
-
-fix		0 all balance 100 1.0 shift xy 5 1.1
-fix		1 all nve/sphere
-fix		grav all gravity 10 vector 0 0 -1
-fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
-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
-
-neighbor	${skin} bin
-neighbor	0.2 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
-fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
-
-thermo_style	custom step atoms ke v_theta
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-#For removal later
-compute		1 all property/atom radius
-variable	zmax atom z+c_1>0.5*${drum_height}
-variable	zmax atom z+c_1>0.5*20
-group		delgroup dynamic all var zmax every 10000
-dynamic group delgroup defined
-
-run		2000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 50 50 84
-  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
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
-Step Atoms KinEng v_theta 
-       0        0           -0            0 
-     100     4000           -0            0 
-     200     4000           -0            0 
-     300     4000           -0            0 
-     400     4000           -0            0 
-     500     4000           -0            0 
-     600     4000           -0            0 
-     700     4000           -0            0 
-     800     4000           -0            0 
-     900     4000           -0            0 
-    1000     4000           -0            0 
-    1100     4000           -0            0 
-    1200     4000           -0            0 
-    1300     4000           -0            0 
-    1400     4000           -0            0 
-    1500     4000           -0            0 
-    1600     4000           -0            0 
-    1700     4000           -0            0 
-    1800     4000           -0            0 
-    1900     4000           -0            0 
-    2000     4000           -0            0 
-Loop time of 3.86825 on 4 procs for 2000 steps with 4000 atoms
-
-Performance: 44671.398 tau/day, 517.030 timesteps/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    | 0.26114    | 0.27918    | 0.28728    |   2.0 |  7.22
-Neigh   | 1.2044     | 1.2414     | 1.3105     |   3.7 | 32.09
-Comm    | 0.38592    | 0.47065    | 0.51052    |   7.4 | 12.17
-Output  | 0.0007236  | 0.0013456  | 0.0024846  |   1.8 |  0.03
-Modify  | 1.6217     | 1.6723     | 1.7801     |   5.0 | 43.23
-Other   |            | 0.2034     |            |       |  5.26
-
-Nlocal:        1000.00 ave        1012 max         988 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        269.250 ave         278 max         256 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-Neighs:        2060.50 ave        2156 max        1921 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 8242
-Ave neighs/atom = 2.0605000
-Neighbor list builds = 1004
-Dangerous builds = 4
-
-#Remove any particles that are above z > 0.5*drum_height
-delete_atoms	group delgroup
-Deleted 0 atoms, new total = 4000
-
-#Add top lid
-region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
-region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
-fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
-
-# 'Turn' drum by switching the direction of gravity
-unfix		grav
-unfix		ins1
-unfix		ins2
-fix		grav all gravity 10 vector 0 -1 0
-
-variable	theta equal 2*PI*elapsed/20000.0
-run		3000
-Per MPI rank memory allocation (min/avg/max) = 18.55 | 18.55 | 18.55 Mbytes
-Step Atoms KinEng v_theta 
-    2000     4000    65.819213            0 
-    2100     4000    105.02389  0.031415927 
-    2200     4000    112.02469  0.062831853 
-    2300     4000    92.271262   0.09424778 
-    2400     4000    89.369506   0.12566371 
-    2500     4000    80.910925   0.15707963 
-    2600     4000    31.620722   0.18849556 
-    2700     4000    4.3019937   0.21991149 
-    2800     4000    3.9913967   0.25132741 
-    2900     4000    4.5203726   0.28274334 
-    3000     4000     5.484886   0.31415927 
-    3100     4000    6.1085958   0.34557519 
-    3200     4000    6.7085635   0.37699112 
-    3300     4000    7.4787777   0.40840704 
-    3400     4000    8.2116413   0.43982297 
-    3500     4000    8.7979302    0.4712389 
-    3600     4000     9.871649   0.50265482 
-    3700     4000    10.012426   0.53407075 
-    3800     4000    9.9067754   0.56548668 
-    3900     4000     9.725458    0.5969026 
-    4000     4000    9.3350056   0.62831853 
-    4100     4000    8.8337295   0.65973446 
-    4200     4000    8.2712493   0.69115038 
-    4300     4000    6.9609934   0.72256631 
-    4400     4000    6.0120294   0.75398224 
-    4500     4000    5.0490036   0.78539816 
-    4600     4000    4.2796544   0.81681409 
-    4700     4000    4.1736483   0.84823002 
-    4800     4000    3.0860106   0.87964594 
-    4900     4000    2.6670909   0.91106187 
-    5000     4000    2.2901814    0.9424778 
-Loop time of 10.7627 on 4 procs for 3000 steps with 4000 atoms
-
-Performance: 24083.252 tau/day, 278.741 timesteps/s
-97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.6731     | 2.0701     | 2.3327     |  18.9 | 19.23
-Neigh   | 2.7389     | 3.1706     | 3.5146     |  15.7 | 29.46
-Comm    | 0.93507    | 1.5441     | 2.1182     |  39.1 | 14.35
-Output  | 0.0021682  | 0.0044412  | 0.006026   |   2.2 |  0.04
-Modify  | 3.0031     | 3.4223     | 3.9262     |  18.3 | 31.80
-Other   |            | 0.5511     |            |       |  5.12
-
-Nlocal:        1000.00 ave        1277 max         723 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        569.750 ave         809 max         454 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Neighs:        3690.50 ave        4937 max        2426 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 14762
-Ave neighs/atom = 3.6905000
-Neighbor list builds = 2187
-Dangerous builds = 1610
-Total wall time: 0:00:14

examples/granular/log.29Oct20.pour.flatwall.g++.1

@@ -1,188 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) on flat wall
-
-variable   	name string pour_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 20
-variable	boxy equal 20
-variable	boxz equal 30
-
-variable	xc1 equal 0.3*${boxx}
-variable	xc1 equal 0.3*20
-variable	xc2 equal 0.7*${boxx}
-variable	xc2 equal 0.7*20
-variable	yc equal 0.5*${boxy}
-variable	yc equal 0.5*20
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.3*${rhi}
-variable skin equal 0.3*0.5
-
-#############
-processors	* * 1
-region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 30
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
-  1 by 1 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
-pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
-
-comm_modify 	vel yes
-
-region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 30
-region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 30
-
-fix		1 all nve/sphere
-fix		grav all gravity 10.0 vector 0 0 -1
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-
-neighbor	${skin} bin
-neighbor	0.15 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
-
-thermo_style	custom step atoms ke
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-run		5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.15
-  ghost atom cutoff = 1.15
-  binsize = 0.575, bins = 35 35 53
-  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
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
-Step Atoms KinEng 
-       0        0           -0 
-     100      926           -0 
-     200      926           -0 
-     300      926           -0 
-     400     1498           -0 
-     500     1498           -0 
-     600     1498           -0 
-     700     2275           -0 
-     800     2275           -0 
-     900     2275           -0 
-    1000     2275           -0 
-    1100     2954           -0 
-    1200     2954           -0 
-    1300     2954           -0 
-    1400     3000           -0 
-    1500     3000           -0 
-    1600     3000           -0 
-    1700     3000           -0 
-    1800     3000           -0 
-    1900     3000           -0 
-    2000     3000           -0 
-    2100     3000           -0 
-    2200     3000           -0 
-    2300     3000           -0 
-    2400     3000           -0 
-    2500     3000           -0 
-    2600     3000           -0 
-    2700     3000           -0 
-    2800     3000           -0 
-    2900     3000           -0 
-    3000     3000           -0 
-    3100     3000           -0 
-    3200     3000           -0 
-    3300     3000           -0 
-    3400     3000           -0 
-    3500     3000           -0 
-    3600     3000           -0 
-    3700     3000           -0 
-    3800     3000           -0 
-    3900     3000           -0 
-    4000     3000           -0 
-    4100     3000           -0 
-    4200     3000           -0 
-    4300     3000           -0 
-    4400     3000           -0 
-    4500     3000           -0 
-    4600     3000           -0 
-    4700     3000           -0 
-    4800     3000           -0 
-    4900     3000           -0 
-    5000     3000           -0 
-Loop time of 24.3889 on 1 procs for 5000 steps with 3000 atoms
-
-Performance: 17713.003 tau/day, 205.012 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 14.362     | 14.362     | 14.362     |   0.0 | 58.89
-Neigh   | 3.3483     | 3.3483     | 3.3483     |   0.0 | 13.73
-Comm    | 0.42893    | 0.42893    | 0.42893    |   0.0 |  1.76
-Output  | 0.0025065  | 0.0025065  | 0.0025065  |   0.0 |  0.01
-Modify  | 6.059      | 6.059      | 6.059      |   0.0 | 24.84
-Other   |            | 0.1876     |            |       |  0.77
-
-Nlocal:        3000.00 ave        3000 max        3000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        462.000 ave         462 max         462 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        17694.0 ave       17694 max       17694 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 17694
-Ave neighs/atom = 5.8980000
-Neighbor list builds = 1133
-Dangerous builds = 0
-Total wall time: 0:00:24

examples/granular/log.29Oct20.pour.flatwall.g++.4

@@ -1,188 +0,0 @@
-LAMMPS (29 Oct 2020)
-  using 1 OpenMP thread(s) per MPI task
-# pour two types of particles (cohesive and non-cohesive) on flat wall
-
-variable   	name string pour_two_types
-
-atom_style	sphere
-units		lj
-
-###############################################
-# Geometry-related parameters
-###############################################
-
-variable	boxx equal 20
-variable	boxy equal 20
-variable	boxz equal 30
-
-variable	xc1 equal 0.3*${boxx}
-variable	xc1 equal 0.3*20
-variable	xc2 equal 0.7*${boxx}
-variable	xc2 equal 0.7*20
-variable	yc equal 0.5*${boxy}
-variable	yc equal 0.5*20
-
-###############################################
-# Particle-related parameters
-###############################################
-variable	rlo equal 0.25
-variable	rhi equal 0.5
-variable	dlo equal 2.0*${rlo}
-variable	dlo equal 2.0*0.25
-variable	dhi equal 2.0*${rhi}
-variable	dhi equal 2.0*0.5
-
-variable	dens equal 1.0
-
-variable skin equal 0.3*${rhi}
-variable skin equal 0.3*0.5
-
-#############
-processors	* * 1
-region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 ${boxz}
-region 		boxreg block 0 20 0 20 0 30
-create_box	2 boxreg
-Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
-  2 by 2 by 1 MPI processor grid
-change_box	all boundary p p f
-Changing box ...
-
-pair_style	granular
-pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
-pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
-
-comm_modify 	vel yes
-
-region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 ${boxz}
-region		insreg1 cylinder z 6 10 5 15 30
-region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 ${boxz}
-region		insreg2 cylinder z 14 10 5 15 30
-
-fix		1 all nve/sphere
-fix		grav all gravity 10.0 vector 0 0 -1
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
-fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
-fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
-Particle insertion: 562 every 346 steps, 1500 by step 693
-
-neighbor	${skin} bin
-neighbor	0.15 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
-
-thermo_style	custom step atoms ke
-thermo_modify	lost warn
-thermo		100
-
-timestep	0.001
-
-#dump		1 all custom 100 ${name}.dump id type radius mass x y z
-
-run		5000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.15
-  ghost atom cutoff = 1.15
-  binsize = 0.575, bins = 35 35 53
-  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
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
-Step Atoms KinEng 
-       0        0           -0 
-     100      926           -0 
-     200      926           -0 
-     300      926           -0 
-     400     1498           -0 
-     500     1498           -0 
-     600     1498           -0 
-     700     2275           -0 
-     800     2275           -0 
-     900     2275           -0 
-    1000     2275           -0 
-    1100     2954           -0 
-    1200     2954           -0 
-    1300     2954           -0 
-    1400     3000           -0 
-    1500     3000           -0 
-    1600     3000           -0 
-    1700     3000           -0 
-    1800     3000           -0 
-    1900     3000           -0 
-    2000     3000           -0 
-    2100     3000           -0 
-    2200     3000           -0 
-    2300     3000           -0 
-    2400     3000           -0 
-    2500     3000           -0 
-    2600     3000           -0 
-    2700     3000           -0 
-    2800     3000           -0 
-    2900     3000           -0 
-    3000     3000           -0 
-    3100     3000           -0 
-    3200     3000           -0 
-    3300     3000           -0 
-    3400     3000           -0 
-    3500     3000           -0 
-    3600     3000           -0 
-    3700     3000           -0 
-    3800     3000           -0 
-    3900     3000           -0 
-    4000     3000           -0 
-    4100     3000           -0 
-    4200     3000           -0 
-    4300     3000           -0 
-    4400     3000           -0 
-    4500     3000           -0 
-    4600     3000           -0 
-    4700     3000           -0 
-    4800     3000           -0 
-    4900     3000           -0 
-    5000     3000           -0 
-Loop time of 12.1982 on 4 procs for 5000 steps with 3000 atoms
-
-Performance: 35414.923 tau/day, 409.895 timesteps/s
-97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.7141     | 3.8131     | 6.2143     | 107.3 | 31.26
-Neigh   | 0.77648    | 0.96585    | 1.1892     |  18.3 |  7.92
-Comm    | 0.7427     | 3.5566     | 5.9731     | 128.4 | 29.16
-Output  | 0.0067544  | 0.0086352  | 0.011408   |   1.8 |  0.07
-Modify  | 3.3476     | 3.5826     | 3.8235     |  11.5 | 29.37
-Other   |            | 0.2715     |            |       |  2.23
-
-Nlocal:        750.000 ave        1033 max         463 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:        435.000 ave         492 max         378 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:        4434.50 ave        7028 max        1967 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 17738
-Ave neighs/atom = 5.9126667
-Neighbor list builds = 1139
-Dangerous builds = 0
-Total wall time: 0:00:12

examples/mscg/log.16Mar23.g++.1

@@ -0,0 +1,105 @@
+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
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+Reading data file ...
+  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1000 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.007 seconds
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
+   Step    
+         0 
+       250 
+       500 
+       750 
+      1000 
+      1250 
+      1500 
+      1750 
+      2000 
+      2250 
+      2500 
+      2750 
+      3000 
+      3250 
+      3500 
+      3750 
+      4000 
+      4250 
+      4500 
+Loop time of 0.245891 on 1 procs for 19 steps with 1000 atoms
+
+print "TEST_1a mscg range finder"
+TEST_1a mscg range finder
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
+   Step    
+         0 
+       250 
+       500 
+       750 
+      1000 
+      1250 
+      1500 
+      1750 
+      2000 
+      2250 
+      2500 
+      2750 
+      3000 
+      3250 
+      3500 
+      3750 
+      4000 
+      4250 
+      4500 
+Loop time of 0.433986 on 1 procs for 19 steps with 1000 atoms
+
+print "TEST_1b mscg force matching"
+TEST_1b mscg force matching
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:00

examples/mscg/log.31Mar17.g++.1

@@ -1,145 +0,0 @@
-LAMMPS (13 Apr 2017)
-units real
-atom_style full
-pair_style zero 10.0
-
-read_data data.meoh
-  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-pair_coeff * *
-
-thermo 1
-thermo_style custom step
-
-# Test 1a: range finder functionality
-fix 1 all mscg 1 range on
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair zero, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 0.581537 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 2.823 ns/day, 8.502 hours/ns, 32.672 timesteps/s
-99.2% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.5815     |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1a mscg range finder"
-TEST_1a mscg range finder
-unfix 1
-
-# Test 1b: force matching functionality
-fix 1 all mscg 1
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 0.841917 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 1.950 ns/day, 12.309 hours/ns, 22.568 timesteps/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          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.8419     |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1b mscg force matching"
-TEST_1b mscg force matching
-
-print TEST_DONE
-TEST_DONE
-Total wall time: 0:00:01

examples/mscg/output_16Mar23/1_1.dat

@@ -0,0 +1,71 @@
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examples/mscg/output_16Mar23/1_1.table

@@ -0,0 +1,104 @@
+# Header information on force file
+
+1_1
+N 99 R 0.200000 10.000000
+
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+2 0.300000 119.349776 77.864922
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+99 10.000000 0.000000 -0.009931

examples/mscg/output_16Mar23/b-spline.out

@@ -0,0 +1,2 @@
+n: 1 1 6 11 3.000000000000000e+00 1.000000000000000e+01
+9.109454054135307e+00 6.178334150703818e+00 -6.242976259059743e+00 4.778144787445235e+00 -1.082885612852992e+00 4.521835893850554e-01 -6.477047196208028e-01 2.947887062333265e-01 -4.195609079009661e-02 1.111775827831465e-02 -8.823466147380592e-02 -1.696076806027540e-02 3.192205281984208e-02 3.656991607866288e-03 -9.931306149957592e-03 

examples/mscg/output_16Mar23/sol_info.out

@@ -0,0 +1,17 @@
+fm_matrix_rows:3000; fm_matrix_columns:15;
+Singular vector:
+2.307693e+00
+1.998418e+00
+1.400114e+00
+1.183608e+00
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examples/mscg/output_16Mar23/x.out

@@ -0,0 +1,2 @@
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examples/mscg/output_9Jan17/1_1.dat

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examples/mscg/output_9Jan17/1_1.table

@@ -1,82 +0,0 @@
-# Header information on force file
-
-1_1
-N 77 R 2.500000 10.100000
-
-1 2.500000 69.428523 567.097082
-2 2.600000 29.053372 240.405928
-3 2.700000 12.454545 91.570608
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-5 2.900000 3.637808 16.198681
-6 3.000000 2.308070 10.396072
-7 3.100000 1.446757 6.830188
-8 3.200000 0.912149 3.861971
-9 3.300000 0.636753 1.645949
-10 3.400000 0.542478 0.239543
-11 3.500000 0.551885 -0.427676
-12 3.600000 0.598929 -0.513202
-13 3.700000 0.635629 -0.220802
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-16 4.000000 0.501378 1.034070
-17 4.100000 0.389375 1.205998
-18 4.200000 0.268600 1.209501
-19 4.300000 0.154310 1.076305
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examples/mscg/output_9Jan17/b-spline.out

@@ -1,2 +0,0 @@
-n: 1 1 6 12 2.400000000000002e+00 1.010000000000000e+01
-1.200460787805587e+03 2.169623423326193e+01 2.388396964379328e+01 -1.197754948555067e+01 6.472482422420378e+00 -1.483711824891365e+00 7.768139601662113e-01 -7.869494711740244e-01 4.830820182054661e-01 -1.892989444995645e-01 1.021275453070386e-01 -1.637649039972671e-01 5.570978712841167e-02 7.637188693695119e-03 -4.109175461195019e-03 -5.352186189455146e-02 

examples/mscg/output_9Jan17/sol_info.out

@@ -1,18 +0,0 @@
-fm_matrix_rows:3000; fm_matrix_columns:16;
-Singular vector:
-2.442317e+00
-2.105009e+00
-1.433251e+00
-1.184602e+00
-9.739627e-01
-6.944898e-01
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-1.446682e-02
-4.167763e-05

examples/mscg/output_9Jan17/x.out

@@ -1 +0,0 @@
-<EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD>@47h<<3C>5@<40><><EFBFBD><EFBFBD>K<EFBFBD>7@<40>R<EFBFBD>]<5D><>'<27><><EFBFBD><EFBFBD>n<EFBFBD><6E>@݌I<DD8C>H<EFBFBD><48><EFBFBD><19>?<3F><><EFBFBD><EFBFBD>?r<>I<EFBFBD><49>.<2E><><11>^<5E><><EFBFBD><EFBFBD>?W<57><7F><EFBFBD>:ȿ(O<1D>%<25>?<3F>Ns<4E>?<3F>Ŀ<EFBFBD>:<3A>C<EFBFBD><43><EFBFBD>?<3F><><EFBFBD>:,H?<3F>}<7D>c<EFBFBD><63>p<EFBFBD><70><EFBFBD><EFBFBD><EFBFBD>7g<37><67>

examples/pour/log.16Mar23.pour.2d.g++.1

@@ -0,0 +1,125 @@
+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 2d granular particles into container
+
+dimension	2
+atom_style	sphere
+boundary	f fm p
+newton		off
+comm_modify	vel yes
+
+region		reg block 0 100 0 50 -0.5 0.5 units box
+create_box	1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+  1 by 1 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix             1 all nve/sphere
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
+fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
+
+region          slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix             ins all pour 1000 1 4767548 vol 0.4 10 	        diam range 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix             3 all enforce2d
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo		1000
+thermo_modify	lost ignore norm no
+compute_modify	thermo_temp dynamic/dof yes
+
+#dump		id all atom 250 dump.pour
+
+#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
+#dump_modify	2 pad 5
+
+#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
+#dump_modify	3 pad 5
+
+run		25000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 167 84 2
+  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/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.805 | 5.805 | 5.805 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              5000         
+      1000         224   202.80417      0              5000         
+      2000         224   373.00249      0              5000         
+      3000         224   599.26757      0              5000         
+      4000         448   1078.4787      0              5000         
+      5000         448   1589.4845      0              5000         
+      6000         448   1743.8281      26.918824      5000         
+WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
+      7000         669   1818.5075      88.370238      5000         
+      8000         669   1850.1368      105.77613      5000         
+      9000         669   1757.9791      107.52328      5000         
+WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
+     10000         886   1792.8816      79.515458      5000         
+     11000         886   1639.0751      64.104708      5000         
+     12000         886   1541.1208      55.91813       5000         
+     13000        1000   1462.8753      69.093182      5000         
+     14000        1000   1277.8754      48.097953      5000         
+     15000        1000   1144.6235      50.637004      5000         
+     16000        1000   847.34312      43.242219      5000         
+     17000        1000   574.34264      41.336666      5000         
+     18000        1000   383.60272      32.744393      5000         
+     19000        1000   174.44969      31.691706      5000         
+     20000        1000   44.566368      14.781893      5000         
+     21000        1000   22.655785      9.8501131      5000         
+     22000        1000   17.403069      6.4074514      5000         
+     23000        1000   13.892292      4.8987582      5000         
+     24000        1000   11.699592      4.0659436      5000         
+     25000        1000   9.6606627      3.6642658      5000         
+Loop time of 2.84114 on 1 procs for 25000 steps with 1000 atoms
+
+Performance: 760257.044 tau/day, 8799.271 timesteps/s, 8.799 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    | 1.092      | 1.092      | 1.092      |   0.0 | 38.44
+Neigh   | 0.30793    | 0.30793    | 0.30793    |   0.0 | 10.84
+Comm    | 0.012168   | 0.012168   | 0.012168   |   0.0 |  0.43
+Output  | 0.00076223 | 0.00076223 | 0.00076223 |   0.0 |  0.03
+Modify  | 1.3179     | 1.3179     | 1.3179     |   0.0 | 46.38
+Other   |            | 0.1104     |            |       |  3.89
+
+Nlocal:           1000 ave        1000 max        1000 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:           2344 ave        2344 max        2344 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2344
+Ave neighs/atom = 2.344
+Neighbor list builds = 2097
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/pour/log.16Mar23.pour.2d.g++.4

@@ -0,0 +1,125 @@
+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 2d granular particles into container
+
+dimension	2
+atom_style	sphere
+boundary	f fm p
+newton		off
+comm_modify	vel yes
+
+region		reg block 0 100 0 50 -0.5 0.5 units box
+create_box	1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+  4 by 1 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix             1 all nve/sphere
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
+fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
+
+region          slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
+fix             ins all pour 1000 1 4767548 vol 0.4 10 	        diam range 0.5 1.0 region slab
+Particle insertion: 224 every 3000 steps, 1000 by step 12001
+
+fix             3 all enforce2d
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo		1000
+thermo_modify	lost ignore norm no
+compute_modify	thermo_temp dynamic/dof yes
+
+#dump		id all atom 250 dump.pour
+
+#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
+#dump_modify	2 pad 5
+
+#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
+#dump_modify	3 pad 5
+
+run		25000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 167 84 2
+  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/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              5000         
+      1000         224   202.80417      0              5000         
+      2000         224   373.00249      0              5000         
+      3000         224   599.26757      0              5000         
+      4000         448   1078.4787      0              5000         
+      5000         448   1589.4845      0              5000         
+      6000         448   1743.8281      26.918824      5000         
+WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
+      7000         669   1818.5075      88.370238      5000         
+      8000         669   1850.1368      105.77613      5000         
+      9000         669   1757.9791      107.52328      5000         
+WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
+     10000         886   1792.8816      79.515458      5000         
+     11000         886   1639.0751      64.104716      5000         
+     12000         886   1541.1046      55.902437      5000         
+     13000        1000   1461.0291      68.011357      5000         
+     14000        1000   1286.1144      48.551003      5000         
+     15000        1000   1155.6137      55.503871      5000         
+     16000        1000   833.49034      46.163926      5000         
+     17000        1000   581.69308      43.140124      5000         
+     18000        1000   369.375        37.675729      5000         
+     19000        1000   188.74424      31.66369       5000         
+     20000        1000   48.73107       23.067611      5000         
+     21000        1000   27.652985      14.176945      5000         
+     22000        1000   22.545416      9.6960211      5000         
+     23000        1000   17.575825      6.6345699      5000         
+     24000        1000   12.464163      4.9073459      5000         
+     25000        1000   9.9507487      3.1967219      5000         
+Loop time of 0.793403 on 4 procs for 25000 steps with 1000 atoms
+
+Performance: 2722450.224 tau/day, 31509.841 timesteps/s, 31.510 Matom-step/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.2392     | 0.24458    | 0.25441    |   1.2 | 30.83
+Neigh   | 0.075663   | 0.07738    | 0.078869   |   0.4 |  9.75
+Comm    | 0.037752   | 0.045698   | 0.049012   |   2.2 |  5.76
+Output  | 0.00063359 | 0.0006788  | 0.00078796 |   0.0 |  0.09
+Modify  | 0.30883    | 0.3111     | 0.31377    |   0.3 | 39.21
+Other   |            | 0.114      |            |       | 14.36
+
+Nlocal:            250 ave         254 max         244 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+Nghost:          19.75 ave          28 max          11 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:            600 ave         624 max         569 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 2400
+Ave neighs/atom = 2.4
+Neighbor list builds = 2138
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/pour/log.16Mar23.pour.2d.molecule.g++.1

@@ -0,0 +1,148 @@
+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 2d granular particles into container
+
+dimension	2
+atom_style	sphere
+atom_modify     map array
+boundary	f fm p
+newton		off
+comm_modify	vel yes cutoff 2.5
+
+fix             prop all property/atom mol ghost yes
+
+region		reg block 0 100 0 50 -0.5 0.5 units box
+create_box	1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+  1 by 1 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
+fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
+
+molecule        object molecule.vshape
+Read molecule template object:
+  1 molecules
+  0 fragments
+  5 atoms with max type 1
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+fix             3 all rigid/small molecule mol object
+  create bodies CPU = 0.000 seconds
+  0 rigid bodies with 0 atoms
+  2.236068 = max distance from body owner to body atom
+
+# ensure region size + molecule size does not overlap wall
+
+region          slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
+fix             ins all pour 500 0 4767548 vol 0.8 10 	        region slab mol object rigid 3
+Particle insertion: 26 every 3000 steps, 500 by step 57001
+
+fix             4 all enforce2d
+
+compute		1 all erotate/sphere
+compute         Tsphere all temp/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	lost ignore norm no temp Tsphere
+compute_modify	Tsphere dynamic/dof yes
+
+thermo		1000
+
+#dump		id all atom 100 tmp.dump
+
+#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
+#variable	mol2 atom mol%10
+#dump		2 all image 250 image.*.jpg v_mol2 type #		zoom 1.6 adiam 1.5
+#dump_modify	2 pad 5 amap 0 10 sa 1 10 ${colors}
+
+#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
+#variable	mol3 atom mol%10
+#dump		3 all movie 250 movie.mpg v_mol3 type #		zoom 1.6 adiam 1.5
+#dump_modify	3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+run	        25000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Gravity may not be correctly applied to rigid bodies if they consist of overlapped particles (src/RIGID/fix_rigid_small.cpp:554)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 2.5
+  binsize = 0.6, bins = 167 84 2
+  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/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.811 | 5.811 | 5.811 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              5000         
+      1000         130   248.65568      0.002050506    5000         
+      2000         130   452.01354      0.0020557556   5000         
+      3000         130   720.36849      0.0021462148   5000         
+      4000         260   1281.7126      0.0021462148   5000         
+      5000         260   1875.9602      0.0021462148   5000         
+      6000         260   1742.7747      2.0692779      5000         
+      7000         390   1860.2142      1.7515066      5000         
+      8000         390   1853.6219      2.3354959      5000         
+      9000         390   1749.6466      5.1516327      5000         
+     10000         520   1860.4314      4.2186838      5000         
+     11000         520   1636.9411      4.006706       5000         
+     12000         520   1454.1835      4.3341069      5000         
+     13000         650   1881.6358      3.9606372      5000         
+     14000         650   1648.6494      3.8239413      5000         
+     15000         650   1463.0973      2.9363979      5000         
+     16000         780   1571.0119      3.9061213      5000         
+     17000         780   1472.941       2.0289533      5000         
+     18000         780   1370.5265      3.1038747      5000         
+     19000         910   1433.6728      2.7600498      5000         
+     20000         910   1375.3634      2.964893       5000         
+     21000         910   1184.8059      2.5050961      5000         
+     22000        1040   1312.0948      1.844008       5000         
+     23000        1040   1181.4208      1.7766375      5000         
+     24000        1040   1263.1226      2.1430511      5000         
+     25000        1170   1152.9064      2.4175531      5000         
+Loop time of 3.37143 on 1 procs for 25000 steps with 1170 atoms
+
+Performance: 640677.536 tau/day, 7415.249 timesteps/s, 8.676 Matom-step/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.91106    | 0.91106    | 0.91106    |   0.0 | 27.02
+Neigh   | 0.19015    | 0.19015    | 0.19015    |   0.0 |  5.64
+Comm    | 0.016916   | 0.016916   | 0.016916   |   0.0 |  0.50
+Output  | 0.0011065  | 0.0011065  | 0.0011065  |   0.0 |  0.03
+Modify  | 2.1372     | 2.1372     | 2.1372     |   0.0 | 63.39
+Other   |            | 0.115      |            |       |  3.41
+
+Nlocal:           1170 ave        1170 max        1170 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:           1685 ave        1685 max        1685 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1685
+Ave neighs/atom = 1.4401709
+Neighbor list builds = 1707
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/pour/log.16Mar23.pour.2d.molecule.g++.4

@@ -0,0 +1,148 @@
+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 2d granular particles into container
+
+dimension	2
+atom_style	sphere
+atom_modify     map array
+boundary	f fm p
+newton		off
+comm_modify	vel yes cutoff 2.5
+
+fix             prop all property/atom mol ghost yes
+
+region		reg block 0 100 0 50 -0.5 0.5 units box
+create_box	1 reg
+Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
+  4 by 1 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
+
+pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
+fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
+
+molecule        object molecule.vshape
+Read molecule template object:
+  1 molecules
+  0 fragments
+  5 atoms with max type 1
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+fix             3 all rigid/small molecule mol object
+  create bodies CPU = 0.000 seconds
+  0 rigid bodies with 0 atoms
+  2.236068 = max distance from body owner to body atom
+
+# ensure region size + molecule size does not overlap wall
+
+region          slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
+fix             ins all pour 500 0 4767548 vol 0.8 10 	        region slab mol object rigid 3
+Particle insertion: 26 every 3000 steps, 500 by step 57001
+
+fix             4 all enforce2d
+
+compute		1 all erotate/sphere
+compute         Tsphere all temp/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo_modify	lost ignore norm no temp Tsphere
+compute_modify	Tsphere dynamic/dof yes
+
+thermo		1000
+
+#dump		id all atom 100 tmp.dump
+
+#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
+#variable	mol2 atom mol%10
+#dump		2 all image 250 image.*.jpg v_mol2 type #		zoom 1.6 adiam 1.5
+#dump_modify	2 pad 5 amap 0 10 sa 1 10 ${colors}
+
+#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
+#variable	mol3 atom mol%10
+#dump		3 all movie 250 movie.mpg v_mol3 type #		zoom 1.6 adiam 1.5
+#dump_modify	3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+run	        25000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Gravity may not be correctly applied to rigid bodies if they consist of overlapped particles (src/RIGID/fix_rigid_small.cpp:554)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 2.5
+  binsize = 0.6, bins = 167 84 2
+  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/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              5000         
+      1000         130   248.65568      0.002050506    5000         
+      2000         130   452.01354      0.0020557556   5000         
+      3000         130   720.36849      0.0021462148   5000         
+      4000         260   1281.7126      0.0021462148   5000         
+      5000         260   1875.9602      0.0021462148   5000         
+      6000         260   1742.7747      2.0692779      5000         
+      7000         390   1860.2142      1.7515066      5000         
+      8000         390   1853.6219      2.3354959      5000         
+      9000         390   1749.6466      5.1516327      5000         
+     10000         520   1860.4314      4.2186838      5000         
+     11000         520   1636.9411      4.006706       5000         
+     12000         520   1454.1835      4.3341069      5000         
+     13000         650   1881.6358      3.9606372      5000         
+     14000         650   1648.6494      3.8239413      5000         
+     15000         650   1463.0973      2.9363979      5000         
+     16000         780   1571.0119      3.9061213      5000         
+     17000         780   1472.941       2.0289532      5000         
+     18000         780   1370.5265      3.1038747      5000         
+     19000         910   1433.6728      2.7600454      5000         
+     20000         910   1375.3629      2.9649297      5000         
+     21000         910   1184.8017      2.5049255      5000         
+     22000        1040   1312.0653      1.8441521      5000         
+     23000        1040   1181.5473      1.7693597      5000         
+     24000        1040   1263.4442      2.1476891      5000         
+     25000        1170   1152.2404      2.4292153      5000         
+Loop time of 1.59966 on 4 procs for 25000 steps with 1170 atoms
+
+Performance: 1350285.365 tau/day, 15628.303 timesteps/s, 18.285 Matom-step/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.23769    | 0.30075    | 0.35002    |   7.5 | 18.80
+Neigh   | 0.048877   | 0.062647   | 0.073072   |   3.7 |  3.92
+Comm    | 0.075225   | 0.087826   | 0.096819   |   2.9 |  5.49
+Output  | 0.0010015  | 0.0011427  | 0.0015053  |   0.6 |  0.07
+Modify  | 0.97758    | 0.99506    | 1.0071     |   1.1 | 62.20
+Other   |            | 0.1522     |            |       |  9.52
+
+Nlocal:          292.5 ave         314 max         274 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:           44.5 ave          67 max          23 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:            430 ave         452 max         393 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+
+Total # of neighbors = 1720
+Ave neighs/atom = 1.4700855
+Neighbor list builds = 1707
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/pour/log.16Mar23.pour.g++.1

@@ -0,0 +1,178 @@
+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 granular particles into chute container, then induce flow
+
+atom_style	sphere
+boundary	p p fm
+newton		off
+comm_modify	vel yes
+
+region		reg block -10 10 -10 10 -0.5 16 units box
+create_box	1 reg
+Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
+  1 by 1 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style      gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix		1 all nve/sphere
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 		zplane 0.0 2000.0
+
+region		slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
+fix		ins all pour 3000 1 300719 vol 0.13 50 region slab
+Particle insertion: 402 every 3162 steps, 3000 by step 22135
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo		1000
+thermo_modify	lost ignore norm no
+compute_modify	thermo_temp dynamic/dof yes
+
+#dump		id all atom 1000 dump.pour
+
+#dump		2 all image 1000 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 1000 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	3 pad 5
+
+run		25000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 34 34 28
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.956 | 5.956 | 5.956 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              6600         
+      1000         402   753.1301       0              6600         
+      2000         402   1389.6785      0              6600         
+      3000         402   1439.3007      16.360577      6600         
+      4000         804   1694.9311      52.966189      6600         
+      5000         804   1564.7533      67.202593      6600         
+      6000         804   1303.6937      65.31424       6600         
+      7000        1206   1590.3342      63.948699      6600         
+      8000        1206   1489.2483      54.736993      6600         
+      9000        1206   1234.442       56.141183      6600         
+     10000        1608   1314.3588      49.189129      6600         
+     11000        1608   1238.0609      42.558653      6600         
+     12000        1608   1143.6455      41.554747      6600         
+     13000        2010   1229.989       49.661038      6600         
+     14000        2010   1176.3015      40.982761      6600         
+     15000        2010   1011.4718      45.872673      6600         
+     16000        2412   1128.8326      47.405058      6600         
+     17000        2412   1035.4314      40.22595       6600         
+     18000        2412   873.87039      40.07875       6600         
+     19000        2814   967.91799      41.49685       6600         
+     20000        2814   928.0341       39.924344      6600         
+     21000        2814   820.35467      37.621246      6600         
+     22000        2814   549.00702      41.541324      6600         
+     23000        3000   441.94025      41.467527      6600         
+     24000        3000   339.91044      25.849093      6600         
+     25000        3000   243.91083      20.921917      6600         
+Loop time of 8.07068 on 1 procs for 25000 steps with 3000 atoms
+
+Performance: 267635.587 tau/day, 3097.634 timesteps/s, 9.293 Matom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.6682     | 4.6682     | 4.6682     |   0.0 | 57.84
+Neigh   | 1.0497     | 1.0497     | 1.0497     |   0.0 | 13.01
+Comm    | 0.16028    | 0.16028    | 0.16028    |   0.0 |  1.99
+Output  | 0.00076244 | 0.00076244 | 0.00076244 |   0.0 |  0.01
+Modify  | 2.0196     | 2.0196     | 2.0196     |   0.0 | 25.02
+Other   |            | 0.172      |            |       |  2.13
+
+Nlocal:           3000 ave        3000 max        3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            667 ave         667 max         667 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13503 ave       13503 max       13503 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13503
+Ave neighs/atom = 4.501
+Neighbor list builds = 1150
+Dangerous builds = 0
+
+unfix		ins
+fix		2 all gravity 1.0 chute 26.0
+run		25000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.64 | 10.64 | 10.64 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+     25000        3000   243.91083      20.921917      6600         
+     26000        3000   111.73212      19.181089      6600         
+     27000        3000   175.53659      12.143401      6600         
+     28000        3000   315.95861      12.721047      6600         
+     29000        3000   516.24386      15.103525      6600         
+     30000        3000   779.3423       19.057186      6600         
+     31000        3000   1118.6219      21.320808      6600         
+     32000        3000   1512.8878      25.012099      6600         
+     33000        3000   1969.247       30.402739      6600         
+     34000        3000   2499.318       37.297539      6600         
+     35000        3000   3074.9401      45.925996      6600         
+     36000        3000   3768.2108      39.734162      6600         
+     37000        3000   4400.6971      44.337674      6600         
+     38000        3000   5178.4457      63.168989      6600         
+     39000        3000   6028.928       56.570416      6600         
+     40000        3000   6947.424       67.360376      6600         
+     41000        3000   7896.0016      69.368604      6600         
+     42000        3000   8977.9347      66.242546      6600         
+     43000        3000   10026.618      55.776273      6600         
+     44000        3000   11106.873      69.943396      6600         
+     45000        3000   12264.363      79.440158      6600         
+     46000        3000   13562.635      67.026549      6600         
+     47000        3000   14796.806      70.121289      6600         
+     48000        3000   16254.182      70.690438      6600         
+     49000        3000   17711.386      63.668043      6600         
+     50000        3000   19144.269      66.708659      6600         
+Loop time of 17.582 on 1 procs for 25000 steps with 3000 atoms
+
+Performance: 122853.050 tau/day, 1421.910 timesteps/s, 4.266 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    | 11.641     | 11.641     | 11.641     |   0.0 | 66.21
+Neigh   | 1.7715     | 1.7715     | 1.7715     |   0.0 | 10.08
+Comm    | 0.38219    | 0.38219    | 0.38219    |   0.0 |  2.17
+Output  | 0.0010728  | 0.0010728  | 0.0010728  |   0.0 |  0.01
+Modify  | 3.4549     | 3.4549     | 3.4549     |   0.0 | 19.65
+Other   |            | 0.3309     |            |       |  1.88
+
+Nlocal:           3000 ave        3000 max        3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            748 ave         748 max         748 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          14117 ave       14117 max       14117 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14117
+Ave neighs/atom = 4.7056667
+Neighbor list builds = 848
+Dangerous builds = 0
+Total wall time: 0:00:25

examples/pour/log.16Mar23.pour.g++.4

@@ -0,0 +1,178 @@
+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 granular particles into chute container, then induce flow
+
+atom_style	sphere
+boundary	p p fm
+newton		off
+comm_modify	vel yes
+
+region		reg block -10 10 -10 10 -0.5 16 units box
+create_box	1 reg
+Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
+  2 by 2 by 1 MPI processor grid
+
+neighbor	0.2 bin
+neigh_modify	delay 0
+
+# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
+# are used in this example file to produce a quick simulation and movie.
+# More appropriate values for realistic simulations would be
+# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
+
+pair_style      gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
+pair_coeff	* *
+
+timestep	0.001
+
+fix		1 all nve/sphere
+fix		2 all gravity 1.0 spherical 0.0 -180.0
+fix		zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 		zplane 0.0 2000.0
+
+region		slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
+fix		ins all pour 3000 1 300719 vol 0.13 50 region slab
+Particle insertion: 402 every 3162 steps, 3000 by step 22135
+
+compute		1 all erotate/sphere
+thermo_style	custom step atoms ke c_1 vol
+thermo		1000
+thermo_modify	lost ignore norm no
+compute_modify	thermo_temp dynamic/dof yes
+
+#dump		id all atom 1000 dump.pour
+
+#dump		2 all image 1000 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 1000 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
+#dump_modify	3 pad 5
+
+run		25000
+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 = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 34 34 28
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton off, size, history
+      pair build: half/size/bin/newtoff
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.831 | 5.831 | 5.831 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+         0           0  -0              0              6600         
+      1000         402   753.1301       0              6600         
+      2000         402   1389.6785      0              6600         
+      3000         402   1439.3007      16.360577      6600         
+      4000         804   1694.9311      52.966189      6600         
+      5000         804   1564.7533      67.202593      6600         
+      6000         804   1303.6937      65.31424       6600         
+      7000        1206   1590.3342      63.948699      6600         
+      8000        1206   1489.2483      54.736993      6600         
+      9000        1206   1234.442       56.141183      6600         
+     10000        1608   1314.3588      49.189127      6600         
+     11000        1608   1237.9823      42.555046      6600         
+     12000        1608   1142.8729      41.96142       6600         
+     13000        2010   1230.1948      49.194135      6600         
+     14000        2010   1178.1648      39.43872       6600         
+     15000        2010   1031.6441      46.416609      6600         
+     16000        2412   1109.7641      45.866965      6600         
+     17000        2412   1047.232       38.618366      6600         
+     18000        2412   888.02373      41.307438      6600         
+     19000        2814   965.06339      40.889834      6600         
+     20000        2814   922.71203      40.04001       6600         
+     21000        2814   815.9575       38.366756      6600         
+     22000        2814   570.89153      37.83039       6600         
+     23000        3000   428.71007      37.62527       6600         
+     24000        3000   341.87262      24.030639      6600         
+     25000        3000   243.78921      22.003596      6600         
+Loop time of 2.70972 on 4 procs for 25000 steps with 3000 atoms
+
+Performance: 797131.262 tau/day, 9226.056 timesteps/s, 27.678 Matom-step/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2559     | 1.2759     | 1.2886     |   1.2 | 47.09
+Neigh   | 0.29364    | 0.29822    | 0.30487    |   0.8 | 11.01
+Comm    | 0.24161    | 0.25182    | 0.26235    |   1.5 |  9.29
+Output  | 0.00076819 | 0.00084565 | 0.00098501 |   0.0 |  0.03
+Modify  | 0.59267    | 0.61574    | 0.63388    |   2.3 | 22.72
+Other   |            | 0.2672     |            |       |  9.86
+
+Nlocal:            750 ave         759 max         734 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost:         381.75 ave         392 max         367 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs:        3569.75 ave        3651 max        3448 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 14279
+Ave neighs/atom = 4.7596667
+Neighbor list builds = 1151
+Dangerous builds = 0
+
+unfix		ins
+fix		2 all gravity 1.0 chute 26.0
+run		25000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 10.43 | 10.43 | 10.43 Mbytes
+   Step        Atoms        KinEng          c_1           Volume    
+     25000        3000   243.78921      22.003596      6600         
+     26000        3000   119.4338       18.414134      6600         
+     27000        3000   172.50337      12.019175      6600         
+     28000        3000   316.78411      12.871972      6600         
+     29000        3000   524.47221      16.004598      6600         
+     30000        3000   812.57656      20.096736      6600         
+     31000        3000   1181.7814      28.226314      6600         
+     32000        3000   1612.855       28.279192      6600         
+     33000        3000   2075.6364      29.358829      6600         
+     34000        3000   2634.5344      36.312508      6600         
+     35000        3000   3213.2814      43.992962      6600         
+     36000        3000   3900.499       38.674908      6600         
+     37000        3000   4594.329       46.025242      6600         
+     38000        3000   5367.8353      46.404081      6600         
+     39000        3000   6180.9788      56.484589      6600         
+     40000        3000   7111.5267      51.165038      6600         
+     41000        3000   7998.6331      65.039037      6600         
+     42000        3000   9037.3716      69.653749      6600         
+     43000        3000   10148.985      65.082635      6600         
+     44000        3000   11242.901      62.787818      6600         
+     45000        3000   12445.247      64.68269       6600         
+     46000        3000   13773.582      59.313484      6600         
+     47000        3000   15000.566      54.417728      6600         
+     48000        3000   16312.814      60.23943       6600         
+     49000        3000   17730.721      60.028021      6600         
+     50000        3000   19221.273      62.659312      6600         
+Loop time of 5.52345 on 4 procs for 25000 steps with 3000 atoms
+
+Performance: 391059.670 tau/day, 4526.154 timesteps/s, 13.578 Matom-step/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.1235     | 3.1506     | 3.1758     |   1.1 | 57.04
+Neigh   | 0.47171    | 0.47561    | 0.48174    |   0.5 |  8.61
+Comm    | 0.39363    | 0.39957    | 0.4049     |   0.6 |  7.23
+Output  | 0.0010759  | 0.0011654  | 0.0012802  |   0.2 |  0.02
+Modify  | 0.93409    | 0.95091    | 0.96521    |   1.2 | 17.22
+Other   |            | 0.5456     |            |       |  9.88
+
+Nlocal:            750 ave         759 max         744 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:         404.75 ave         411 max         402 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Neighs:        3694.75 ave        3722 max        3672 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 14779
+Ave neighs/atom = 4.9263333
+Neighbor list builds = 856
+Dangerous builds = 0
+Total wall time: 0:00:08

examples/pour/log.27Nov18.pour.2d.g++.1

@@ -1,121 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour 2d granular particles into container
-
-dimension	2
-atom_style	sphere
-boundary	f fm p
-newton		off
-comm_modify	vel yes
-
-region		reg block 0 100 0 50 -0.5 0.5 units box
-create_box	1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
-  1 by 1 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
-
-pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix             1 all nve/sphere
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
-fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
-
-region          slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
-fix             ins all pour 1000 1 4767548 vol 0.4 10 	        diam range 0.5 1.0 region slab
-Particle insertion: 224 every 3000 steps, 1000 by step 12001
-
-fix             3 all enforce2d
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo		1000
-thermo_modify	lost ignore norm no
-compute_modify	thermo_temp dynamic/dof yes
-
-#dump		id all atom 250 dump.pour
-
-#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
-#dump_modify	2 pad 5
-
-#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
-#dump_modify	3 pad 5
-
-run		25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 167 84 2
-  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/bin/newtoff
-      stencil: half/bin/2d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         5000 
-    1000      224    201.77464            0         5000 
-    2000      224    372.42868            0         5000 
-    3000      224    599.60221            0         5000 
-    4000      448    1084.3752            0         5000 
-    5000      448    1592.4543            0         5000 
-    6000      448    1763.3153    37.274939         5000 
-    7000      672     1805.206    89.331853         5000 
-    8000      672    1778.0015    111.58381         5000 
-    9000      672    1592.6805    97.550311         5000 
-   10000      896     1631.962    76.905078         5000 
-   11000      896    1590.1527    68.644552         5000 
-   12000      896    1564.4707    60.119562         5000 
-   13000     1000     1490.072    56.982972         5000 
-   14000     1000    1266.4669    57.579371         5000 
-   15000     1000    1034.1055    46.079374         5000 
-   16000     1000    748.70283    43.933154         5000 
-   17000     1000    462.65166    37.522016         5000 
-   18000     1000    327.40481    29.450285         5000 
-   19000     1000    223.24319    31.981144         5000 
-   20000     1000    54.792042    23.449101         5000 
-   21000     1000    25.805484    16.352528         5000 
-   22000     1000    20.617765    11.756965         5000 
-   23000     1000    16.115382    7.9435503         5000 
-   24000     1000    11.971003    5.9411126         5000 
-   25000     1000    10.404117    4.3811155         5000 
-Loop time of 2.72875 on 1 procs for 25000 steps with 1000 atoms
-
-Performance: 791570.958 tau/day, 9161.701 timesteps/s
-98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.95597    | 0.95597    | 0.95597    |   0.0 | 35.03
-Neigh   | 0.38475    | 0.38475    | 0.38475    |   0.0 | 14.10
-Comm    | 0.010862   | 0.010862   | 0.010862   |   0.0 |  0.40
-Output  | 0.00054383 | 0.00054383 | 0.00054383 |   0.0 |  0.02
-Modify  | 1.2364     | 1.2364     | 1.2364     |   0.0 | 45.31
-Other   |            | 0.1402     |            |       |  5.14
-
-Nlocal:    1000 ave 1000 max 1000 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:    2374 ave 2374 max 2374 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2374
-Ave neighs/atom = 2.374
-Neighbor list builds = 2089
-Dangerous builds = 0
-Total wall time: 0:00:02

examples/pour/log.27Nov18.pour.2d.g++.4

@@ -1,121 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour 2d granular particles into container
-
-dimension	2
-atom_style	sphere
-boundary	f fm p
-newton		off
-comm_modify	vel yes
-
-region		reg block 0 100 0 50 -0.5 0.5 units box
-create_box	1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
-  4 by 1 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
-
-pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix             1 all nve/sphere
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
-fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
-
-region          slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
-fix             ins all pour 1000 1 4767548 vol 0.4 10 	        diam range 0.5 1.0 region slab
-Particle insertion: 224 every 3000 steps, 1000 by step 12001
-
-fix             3 all enforce2d
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo		1000
-thermo_modify	lost ignore norm no
-compute_modify	thermo_temp dynamic/dof yes
-
-#dump		id all atom 250 dump.pour
-
-#dump		2 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
-#dump_modify	2 pad 5
-
-#dump		3 all movie 500 movie.mpg type type #		zoom 1.6 adiam 1.5
-#dump_modify	3 pad 5
-
-run		25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 167 84 2
-  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/bin/newtoff
-      stencil: half/bin/2d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         5000 
-    1000      224    201.77464            0         5000 
-    2000      224    372.42868            0         5000 
-    3000      224    599.60221            0         5000 
-    4000      448    1084.3752            0         5000 
-    5000      448    1592.4543            0         5000 
-    6000      448    1763.3153    37.274939         5000 
-    7000      672     1805.206    89.331853         5000 
-    8000      672    1778.0015    111.58381         5000 
-    9000      672    1592.6805    97.550311         5000 
-   10000      896    1630.8521    79.742572         5000 
-   11000      896    1593.1588    67.633788         5000 
-   12000      896    1562.2084    65.097236         5000 
-   13000     1000    1504.1203    63.468934         5000 
-   14000     1000    1266.5724    55.837334         5000 
-   15000     1000    1041.8665    48.938774         5000 
-   16000     1000    766.27305    43.846151         5000 
-   17000     1000    466.30103    43.206188         5000 
-   18000     1000    320.50154     26.84775         5000 
-   19000     1000    207.91453    29.183522         5000 
-   20000     1000    52.447982     19.30378         5000 
-   21000     1000    22.027641    10.395933         5000 
-   22000     1000    15.395099    6.7003289         5000 
-   23000     1000     11.97674    5.2548063         5000 
-   24000     1000    7.8974699    3.7396899         5000 
-   25000     1000    6.1288038    2.2056805         5000 
-Loop time of 0.901039 on 4 procs for 25000 steps with 1000 atoms
-
-Performance: 2397232.992 tau/day, 27745.752 timesteps/s
-96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.21557    | 0.22754    | 0.23651    |   1.9 | 25.25
-Neigh   | 0.098304   | 0.10178    | 0.10595    |   1.0 | 11.30
-Comm    | 0.051792   | 0.066485   | 0.079589   |   3.8 |  7.38
-Output  | 0.00052619 | 0.00061941 | 0.00082016 |   0.0 |  0.07
-Modify  | 0.31782    | 0.32767    | 0.33815    |   1.5 | 36.37
-Other   |            | 0.1769     |            |       | 19.64
-
-Nlocal:    250 ave 267 max 232 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Nghost:    18 ave 23 max 14 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs:    606 ave 664 max 559 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-
-Total # of neighbors = 2424
-Ave neighs/atom = 2.424
-Neighbor list builds = 2060
-Dangerous builds = 0
-Total wall time: 0:00:00

examples/pour/log.27Nov18.pour.2d.molecule.g++.1

@@ -1,142 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour 2d granular particles into container
-
-dimension	2
-atom_style	sphere
-atom_modify     map array
-boundary	f fm p
-newton		off
-comm_modify	vel yes cutoff 2.5
-
-fix             prop all property/atom mol ghost yes
-
-region		reg block 0 100 0 50 -0.5 0.5 units box
-create_box	1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
-  1 by 1 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
-
-pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
-fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
-
-molecule        object molecule.vshape
-Read molecule object:
-  5 atoms with max type 1
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-fix             3 all rigid/small molecule mol object
-0 rigid bodies with 0 atoms
-  2.23607 = max distance from body owner to body atom
-
-# ensure region size + molecule size does not overlap wall
-
-region          slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
-fix             ins all pour 500 0 4767548 vol 0.8 10 	        region slab mol object rigid 3
-Particle insertion: 26 every 3000 steps, 500 by step 57001
-
-fix             4 all enforce2d
-
-compute		1 all erotate/sphere
-compute         Tsphere all temp/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	lost ignore norm no temp Tsphere
-compute_modify	Tsphere dynamic/dof yes
-
-thermo		1000
-
-#dump		id all atom 100 tmp.dump
-
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#variable	mol2 atom mol%10
-#dump		2 all image 250 image.*.jpg v_mol2 type #		zoom 1.6 adiam 1.5
-#dump_modify	2 pad 5 amap 0 10 sa 1 10 ${colors}
-
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#variable	mol3 atom mol%10
-#dump		3 all movie 250 movie.mpg v_mol3 type #		zoom 1.6 adiam 1.5
-#dump_modify	3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-run	        25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 2.5
-  binsize = 0.6, bins = 167 84 2
-  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/bin/newtoff
-      stencil: half/bin/2d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.81 | 5.81 | 5.81 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         5000 
-    1000      130    259.24123 2.3772821e-30         5000 
-    2000      130    465.39775 9.5010246e-30         5000 
-    3000      130    736.55426 2.1365791e-29         5000 
-    4000      260     1274.295 6.045774e-05         5000 
-    5000      260    1855.4991 0.0021687846         5000 
-    6000      260     1743.415    1.9678991         5000 
-    7000      390    1675.8228    2.0085353         5000 
-    8000      390    1845.2936     2.678293         5000 
-    9000      390    1747.0301    2.5461774         5000 
-   10000      520    2204.3744    1.3847146         5000 
-   11000      520    1872.5943    6.5018283         5000 
-   12000      520    1448.8705    3.2789997         5000 
-   13000      650    1687.7845    2.4723994         5000 
-   14000      650    1534.5832    1.7381523         5000 
-   15000      650    1517.5812    2.4425352         5000 
-   16000      780    1681.4276    3.5245463         5000 
-   17000      780    1660.4845    3.5652485         5000 
-   18000      780    1400.1788    4.1717202         5000 
-   19000      910    1525.4386    3.2537276         5000 
-   20000      910    1326.4257    3.5226044         5000 
-   21000      910    1125.4321    3.1564949         5000 
-   22000     1040    1262.0253    1.6097601         5000 
-   23000     1040       1042.7    3.1078701         5000 
-   24000     1040    1167.4717    1.4954047         5000 
-   25000     1170    1214.9087    2.4525535         5000 
-Loop time of 3.36515 on 1 procs for 25000 steps with 1170 atoms
-
-Performance: 641872.369 tau/day, 7429.078 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.73922    | 0.73922    | 0.73922    |   0.0 | 21.97
-Neigh   | 0.22808    | 0.22808    | 0.22808    |   0.0 |  6.78
-Comm    | 0.013331   | 0.013331   | 0.013331   |   0.0 |  0.40
-Output  | 0.00082207 | 0.00082207 | 0.00082207 |   0.0 |  0.02
-Modify  | 2.2694     | 2.2694     | 2.2694     |   0.0 | 67.44
-Other   |            | 0.1143     |            |       |  3.40
-
-Nlocal:    1170 ave 1170 max 1170 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:    1699 ave 1699 max 1699 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1699
-Ave neighs/atom = 1.45214
-Neighbor list builds = 1715
-Dangerous builds = 0
-Total wall time: 0:00:03

examples/pour/log.27Nov18.pour.2d.molecule.g++.4

@@ -1,142 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour 2d granular particles into container
-
-dimension	2
-atom_style	sphere
-atom_modify     map array
-boundary	f fm p
-newton		off
-comm_modify	vel yes cutoff 2.5
-
-fix             prop all property/atom mol ghost yes
-
-region		reg block 0 100 0 50 -0.5 0.5 units box
-create_box	1 reg
-Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
-  4 by 1 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
-
-pair_style      gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		xplane 0 100
-fix		ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 		yplane 0 NULL
-
-molecule        object molecule.vshape
-Read molecule object:
-  5 atoms with max type 1
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-fix             3 all rigid/small molecule mol object
-0 rigid bodies with 0 atoms
-  2.23607 = max distance from body owner to body atom
-
-# ensure region size + molecule size does not overlap wall
-
-region          slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
-fix             ins all pour 500 0 4767548 vol 0.8 10 	        region slab mol object rigid 3
-Particle insertion: 26 every 3000 steps, 500 by step 57001
-
-fix             4 all enforce2d
-
-compute		1 all erotate/sphere
-compute         Tsphere all temp/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	lost ignore norm no temp Tsphere
-compute_modify	Tsphere dynamic/dof yes
-
-thermo		1000
-
-#dump		id all atom 100 tmp.dump
-
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#variable	mol2 atom mol%10
-#dump		2 all image 250 image.*.jpg v_mol2 type #		zoom 1.6 adiam 1.5
-#dump_modify	2 pad 5 amap 0 10 sa 1 10 ${colors}
-
-#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
-#variable	mol3 atom mol%10
-#dump		3 all movie 250 movie.mpg v_mol3 type #		zoom 1.6 adiam 1.5
-#dump_modify	3 pad 5 amap 0 10 sa 1 10 ${colors}
-
-run	        25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 2.5
-  binsize = 0.6, bins = 167 84 2
-  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/bin/newtoff
-      stencil: half/bin/2d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         5000 
-    1000      130    259.24123 2.3773387e-30         5000 
-    2000      130    465.39775 9.5010816e-30         5000 
-    3000      130    736.55426 2.1365846e-29         5000 
-    4000      260     1274.295 6.045774e-05         5000 
-    5000      260    1855.4991 0.0021687846         5000 
-    6000      260     1743.415    1.9678991         5000 
-    7000      390    1675.8228    2.0085353         5000 
-    8000      390    1845.2936     2.678293         5000 
-    9000      390    1747.0301    2.5461774         5000 
-   10000      520    2204.3744    1.3847146         5000 
-   11000      520    1872.5943    6.5018283         5000 
-   12000      520    1448.8705    3.2789997         5000 
-   13000      650    1687.7845    2.4723994         5000 
-   14000      650    1534.5832    1.7381523         5000 
-   15000      650    1517.5812    2.4425352         5000 
-   16000      780    1680.8761    3.5506853         5000 
-   17000      780    1661.6046    3.6673972         5000 
-   18000      780    1391.3201    4.1075002         5000 
-   19000      910    1526.6687     3.410537         5000 
-   20000      910    1387.6908    2.7370047         5000 
-   21000      910    1056.6723    2.5690119         5000 
-   22000     1040    1226.7461    1.2299974         5000 
-   23000     1040    1106.7165    3.1057108         5000 
-   24000     1040    1161.9203    2.0994962         5000 
-   25000     1170    1187.5093    2.9596172         5000 
-Loop time of 1.4211 on 4 procs for 25000 steps with 1170 atoms
-
-Performance: 1519946.444 tau/day, 17591.973 timesteps/s
-94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.19053    | 0.21869    | 0.23582    |   3.7 | 15.39
-Neigh   | 0.06394    | 0.066575   | 0.070017   |   0.9 |  4.68
-Comm    | 0.055579   | 0.070079   | 0.080658   |   3.4 |  4.93
-Output  | 0.0012593  | 0.0031545  | 0.0088205  |   5.8 |  0.22
-Modify  | 0.89034    | 0.9006     | 0.91315    |   0.9 | 63.37
-Other   |            | 0.162      |            |       | 11.40
-
-Nlocal:    292.5 ave 296 max 285 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Nghost:    44 ave 60 max 21 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Neighs:    433.25 ave 449 max 418 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 1733
-Ave neighs/atom = 1.4812
-Neighbor list builds = 1708
-Dangerous builds = 0
-Total wall time: 0:00:01

examples/pour/log.27Nov18.pour.g++.1

@@ -1,175 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour granular particles into chute container, then induce flow
-
-atom_style	sphere
-boundary	p p fm
-newton		off
-comm_modify	vel yes
-
-region		reg block -10 10 -10 10 -0.5 16 units box
-create_box	1 reg
-Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
-  1 by 1 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
-
-pair_style      gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix		1 all nve/sphere
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 		zplane 0.0 2000.0
-
-region		slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
-fix		ins all pour 3000 1 300719 vol 0.13 50 region slab
-Particle insertion: 402 every 3162 steps, 3000 by step 22135
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo		1000
-thermo_modify	lost ignore norm no
-compute_modify	thermo_temp dynamic/dof yes
-
-#dump		id all atom 1000 dump.pour
-
-#dump		2 all image 1000 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
-#dump_modify	2 pad 5
-
-#dump		3 all movie 1000 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
-#dump_modify	3 pad 5
-
-run		25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 34 34 28
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         6600 
-    1000      402    768.04606            0         6600 
-    2000      402    1407.1714            0         6600 
-    3000      402     1373.819     15.59952         6600 
-    4000      804    1737.1399    39.311164         6600 
-    5000      804    1571.3184    67.501382         6600 
-    6000      804    1318.6439    77.636174         6600 
-    7000     1206    1522.1986    68.863683         6600 
-    8000     1206    1387.2223    64.067846         6600 
-    9000     1206    1265.9044    51.726525         6600 
-   10000     1608    1460.3212    48.844763         6600 
-   11000     1608    1310.2001    53.532609         6600 
-   12000     1608    1134.4592    48.567743         6600 
-   13000     2010    1182.5037    45.620614         6600 
-   14000     2010    1192.4303    39.066935         6600 
-   15000     2010    967.05968    42.363789         6600 
-   16000     2412    1119.8304    39.217157         6600 
-   17000     2412    1063.7921     45.71714         6600 
-   18000     2412    855.28326    42.745948         6600 
-   19000     2814     970.7019    40.155896         6600 
-   20000     2814    923.94347    34.590568         6600 
-   21000     2814    793.75092    36.707509         6600 
-   22000     2814     543.4546    37.669131         6600 
-   23000     3000    446.47658    39.719019         6600 
-   24000     3000    331.57201    24.034747         6600 
-   25000     3000    239.90493    18.457205         6600 
-Loop time of 8.66761 on 1 procs for 25000 steps with 3000 atoms
-
-Performance: 249203.592 tau/day, 2884.301 timesteps/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    | 4.5311     | 4.5311     | 4.5311     |   0.0 | 52.28
-Neigh   | 1.4556     | 1.4556     | 1.4556     |   0.0 | 16.79
-Comm    | 0.2322     | 0.2322     | 0.2322     |   0.0 |  2.68
-Output  | 0.00084257 | 0.00084257 | 0.00084257 |   0.0 |  0.01
-Modify  | 2.1642     | 2.1642     | 2.1642     |   0.0 | 24.97
-Other   |            | 0.2837     |            |       |  3.27
-
-Nlocal:    3000 ave 3000 max 3000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    658 ave 658 max 658 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    13479 ave 13479 max 13479 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 13479
-Ave neighs/atom = 4.493
-Neighbor list builds = 1149
-Dangerous builds = 0
-
-unfix		ins
-fix		2 all gravity 1.0 chute 26.0
-run		25000
-Per MPI rank memory allocation (min/avg/max) = 13.24 | 13.24 | 13.24 Mbytes
-Step Atoms KinEng c_1 Volume 
-   25000     3000    239.90493    18.457205         6600 
-   26000     3000    86.453151    19.990229         6600 
-   27000     3000    104.03763    12.243926         6600 
-   28000     3000    187.74939    11.703132         6600 
-   29000     3000    316.59921    14.610301         6600 
-   30000     3000    520.76149     18.82089         6600 
-   31000     3000    821.71283    25.266473         6600 
-   32000     3000    1153.8578    30.714985         6600 
-   33000     3000    1520.1476    38.247011         6600 
-   34000     3000    2006.3144    44.480026         6600 
-   35000     3000    2556.4751    55.768118         6600 
-   36000     3000    3160.9914    63.728696         6600 
-   37000     3000    3877.5537    71.484742         6600 
-   38000     3000    4675.4987     79.37485         6600 
-   39000     3000    5479.8489    94.281786         6600 
-   40000     3000    6350.6439    106.39353         6600 
-   41000     3000    7245.0837    113.40306         6600 
-   42000     3000    8227.1726    129.62268         6600 
-   43000     3000    9422.0189    144.63991         6600 
-   44000     3000    10616.036    149.84326         6600 
-   45000     3000    11908.182    169.96204         6600 
-   46000     3000    13257.313    184.73533         6600 
-   47000     3000      14765.4    201.20237         6600 
-   48000     3000    16184.643    202.00907         6600 
-   49000     3000    17573.204    215.30429         6600 
-   50000     3000    19117.749    232.28939         6600 
-Loop time of 16.4345 on 1 procs for 25000 steps with 3000 atoms
-
-Performance: 131430.508 tau/day, 1521.186 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 9.893      | 9.893      | 9.893      |   0.0 | 60.20
-Neigh   | 2.1448     | 2.1448     | 2.1448     |   0.0 | 13.05
-Comm    | 0.47991    | 0.47991    | 0.47991    |   0.0 |  2.92
-Output  | 0.0011523  | 0.0011523  | 0.0011523  |   0.0 |  0.01
-Modify  | 3.4635     | 3.4635     | 3.4635     |   0.0 | 21.07
-Other   |            | 0.4522     |            |       |  2.75
-
-Nlocal:    3000 ave 3000 max 3000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    742 ave 742 max 742 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    13997 ave 13997 max 13997 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 13997
-Ave neighs/atom = 4.66567
-Neighbor list builds = 836
-Dangerous builds = 0
-Total wall time: 0:00:25

examples/pour/log.27Nov18.pour.g++.4

@@ -1,175 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Pour granular particles into chute container, then induce flow
-
-atom_style	sphere
-boundary	p p fm
-newton		off
-comm_modify	vel yes
-
-region		reg block -10 10 -10 10 -0.5 16 units box
-create_box	1 reg
-Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
-  2 by 2 by 1 MPI processor grid
-
-neighbor	0.2 bin
-neigh_modify	delay 0
-
-# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
-# are used in this example file to produce a quick simulation and movie.
-# More appropriate values for realistic simulations would be
-# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
-
-pair_style      gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
-
-timestep	0.001
-
-fix		1 all nve/sphere
-fix		2 all gravity 1.0 spherical 0.0 -180.0
-fix		zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 		zplane 0.0 2000.0
-
-region		slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
-fix		ins all pour 3000 1 300719 vol 0.13 50 region slab
-Particle insertion: 402 every 3162 steps, 3000 by step 22135
-
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo		1000
-thermo_modify	lost ignore norm no
-compute_modify	thermo_temp dynamic/dof yes
-
-#dump		id all atom 1000 dump.pour
-
-#dump		2 all image 1000 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
-#dump_modify	2 pad 5
-
-#dump		3 all movie 1000 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
-#dump_modify	3 pad 5
-
-run		25000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.2
-  ghost atom cutoff = 1.2
-  binsize = 0.6, bins = 34 34 28
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair gran/hooke/history, perpetual
-      attributes: half, newton off, size, history
-      pair build: half/size/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.83 | 5.83 | 5.83 Mbytes
-Step Atoms KinEng c_1 Volume 
-       0        0           -0            0         6600 
-    1000      402    768.04606            0         6600 
-    2000      402    1407.1714            0         6600 
-    3000      402     1373.819     15.59952         6600 
-    4000      804    1737.1399    39.311164         6600 
-    5000      804    1571.3184    67.501382         6600 
-    6000      804    1318.6439    77.636174         6600 
-    7000     1206    1521.8348    69.010381         6600 
-    8000     1206    1391.0761    64.407583         6600 
-    9000     1206      1264.98     50.32567         6600 
-   10000     1608    1462.7175    49.903609         6600 
-   11000     1608    1317.5878    52.401196         6600 
-   12000     1608    1120.9416    46.067058         6600 
-   13000     2010    1200.1517    49.662302         6600 
-   14000     2010    1180.2805    38.850379         6600 
-   15000     2010    970.23519    39.121533         6600 
-   16000     2412    1101.3888    44.051087         6600 
-   17000     2412    1054.4967    43.489619         6600 
-   18000     2412    850.25959    42.296696         6600 
-   19000     2814    959.68841    42.757546         6600 
-   20000     2814    933.72206    42.668586         6600 
-   21000     2814     779.2842    42.116934         6600 
-   22000     2814    537.68477    35.113909         6600 
-   23000     3000    456.26221    36.394458         6600 
-   24000     3000    334.38331    26.256087         6600 
-   25000     3000     233.7217    18.768345         6600 
-Loop time of 2.79912 on 4 procs for 25000 steps with 3000 atoms
-
-Performance: 771671.423 tau/day, 8931.382 timesteps/s
-97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0916     | 1.1431     | 1.1982     |   4.0 | 40.84
-Neigh   | 0.37439    | 0.39186    | 0.41149    |   2.6 | 14.00
-Comm    | 0.32241    | 0.32795    | 0.33831    |   1.1 | 11.72
-Output  | 0.00068283 | 0.0029467  | 0.0094671  |   6.9 |  0.11
-Modify  | 0.5813     | 0.5952     | 0.60947    |   1.5 | 21.26
-Other   |            | 0.3381     |            |       | 12.08
-
-Nlocal:    750 ave 765 max 730 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Nghost:    390.75 ave 393 max 385 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Neighs:    3548 ave 3643 max 3454 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 14192
-Ave neighs/atom = 4.73067
-Neighbor list builds = 1152
-Dangerous builds = 0
-
-unfix		ins
-fix		2 all gravity 1.0 chute 26.0
-run		25000
-Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.39 | 13.06 Mbytes
-Step Atoms KinEng c_1 Volume 
-   25000     3000     233.7217    18.768345         6600 
-   26000     3000     80.58756    21.114703         6600 
-   27000     3000    112.90794    11.760837         6600 
-   28000     3000    211.68857    11.667711         6600 
-   29000     3000    368.27114    15.483397         6600 
-   30000     3000    611.33941    21.023859         6600 
-   31000     3000    902.04662    29.663904         6600 
-   32000     3000    1188.6213    31.996848         6600 
-   33000     3000    1626.3144    38.244424         6600 
-   34000     3000    2068.1939    45.793779         6600 
-   35000     3000    2654.4292    55.900641         6600 
-   36000     3000    3212.0662    64.492942         6600 
-   37000     3000    3942.9079    73.557353         6600 
-   38000     3000    4710.2169     84.24051         6600 
-   39000     3000     5513.597    93.737814         6600 
-   40000     3000     6367.338    112.43633         6600 
-   41000     3000    7417.7889    130.70338         6600 
-   42000     3000    8428.2678    124.66302         6600 
-   43000     3000    9498.0121    136.37107         6600 
-   44000     3000    10680.269    149.21074         6600 
-   45000     3000     11852.03    154.67802         6600 
-   46000     3000    12896.699    167.10324         6600 
-   47000     3000    14218.465    196.70386         6600 
-   48000     3000    15555.796    204.40316         6600 
-   49000     3000    16694.338    208.98934         6600 
-   50000     3000    17936.665    192.19442         6600 
-Loop time of 5.65089 on 4 procs for 25000 steps with 3000 atoms
-
-Performance: 382240.368 tau/day, 4424.078 timesteps/s
-94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5656     | 2.5853     | 2.6068     |   0.9 | 45.75
-Neigh   | 0.57736    | 0.59939    | 0.61824    |   1.9 | 10.61
-Comm    | 0.58146    | 0.63908    | 0.70461    |   5.5 | 11.31
-Output  | 0.00081015 | 0.002184   | 0.0061922  |   5.0 |  0.04
-Modify  | 0.91975    | 0.93371    | 0.95875    |   1.5 | 16.52
-Other   |            | 0.8912     |            |       | 15.77
-
-Nlocal:    750 ave 758 max 741 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost:    404 ave 417 max 395 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Neighs:    3603.75 ave 3695 max 3528 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 14415
-Ave neighs/atom = 4.805
-Neighbor list builds = 827
-Dangerous builds = 0
-Total wall time: 0:00:08

lib/plumed/Install.py

@@ -17,17 +17,17 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.8.1"
+version = "2.8.2"
 mode = "static"
 
 # help message
 
 HELP = """
 Syntax from src dir: make lib-plumed args="-b"
-                 or: make lib-plumed args="-b -v 2.4.3"
+                 or: make lib-plumed args="-b -v 2.8.2"
                  or: make lib-plumed args="-p /usr/local/plumed2 -m shared"
 
-Syntax from lib dir: python Install.py -b -v 2.4.3
+Syntax from lib dir: python Install.py -b -v 2.8.2
                  or: python Install.py -b
                  or: python Install.py -p /usr/local/plumed2 -m shared
 
@@ -37,30 +37,14 @@ make lib-plumed args="-b"   # download/build in lib/plumed/plumed2
 make lib-plumed args="-p $HOME/plumed2 -m shared" # use existing Plumed2 installation in $HOME/plumed2
 """
 
-# known checksums for different PLUMED versions. used to validate the download.
+# known checksums for different PLUMED versions. used to validate downloads.
 checksums = { \
-        '2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
-        '2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
         '2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \
-        '2.5.0' : '6224cd089493661e19ceacccd35cf911', \
-        '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
-        '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
-        '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
-        '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
         '2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \
-        '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
-        '2.6.1' : '89a9a450fc6025299fe16af235957163', \
-        '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \
-        '2.6.5' : 'b67356f027e5c2747823b0422c3b0ec2', \
         '2.6.6' : '6b470dcdce04c221ea42d8500b03c49b', \
-        '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \
+        '2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \
-        '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \
-        '2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \
-        '2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \
-        '2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \
-        '2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \
-        '2.8.0' : '489b23daba70da78cf0506cbc31689c6', \
         '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
+        '2.8.2' : '599092b6a0aa6fff992612537ad98994', \
         }
 
 # parse and process arguments

python/install.py

@@ -59,10 +59,14 @@ olddir = os.path.abspath('.')
 os.chdir(os.path.dirname(args.package))
 
 # remove any wheel files left over from previous calls
-print("Purging existing wheels...")
+if os.path.isdir(os.path.join(olddir,"build")):
-for wheel in glob.glob('lammps-*.whl'):
+  print("Cleaning old build directory")
-  print("deleting " + wheel)
+  shutil.rmtree(os.path.join(olddir,"build"))
-  os.remove(wheel)
+
+#print("Purging existing wheels...")
+#for wheel in glob.glob('lammps-*.whl'):
+#  print("deleting " + wheel)
+#  os.remove(wheel)
 
 # copy shared object to the current folder so that
 # it will show up in the installation at the expected location

python/lammps/core.py

@@ -814,7 +814,8 @@ class lammps(object):
 
     # set length of vector for items that are not a scalar
     vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
-                 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3 }
+                 'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
+                 'special_lj':4, 'special_coul':4 }
     if name in vec_dict:
       veclen = vec_dict[name]
     elif name == 'respa_dt':

src/.gitignore

@@ -462,8 +462,6 @@
 /atom_vec_full.h
 /atom_vec_full_hars.cpp
 /atom_vec_full_hars.h
-/atom_vec_granular.cpp
-/atom_vec_granular.h
 /atom_vec_molecular.cpp
 /atom_vec_molecular.h
 /atom_vec_oxdna.cpp
@@ -492,6 +490,8 @@
 /bond_gromos.h
 /bond_harmonic.cpp
 /bond_harmonic.h
+/bond_harmonic_restrain.cpp
+/bond_harmonic_restrain.h
 /bond_harmonic_shift.cpp
 /bond_harmonic_shift.h
 /bond_harmonic_shift_cut.cpp
@@ -534,6 +534,10 @@
 /compute_damage_atom.h
 /compute_dilatation_atom.cpp
 /compute_dilatation_atom.h
+/compute_dipole_tip4p.cpp
+/compute_dipole_tip4p.h
+/compute_dipole_tip4p_chunk.cpp
+/compute_dipole_tip4p_chunk.h
 /compute_dpd.cpp
 /compute_dpd.h
 /compute_dpd_atom.cpp
@@ -752,6 +756,8 @@
 /fix_damping_cundall.h
 /fix_dpd_energy.cpp
 /fix_dpd_energy.h
+/fix_efield_tip4p.cpp
+/fix_efield_tip4p.h
 /fix_electron_stopping.cpp
 /fix_electron_stopping.h
 /fix_electron_stopping_fit.cpp
@@ -1565,6 +1571,8 @@
 /fix_srp.h
 /fix_srp_react.cpp
 /fix_srp_react.h
+/fix_heat_flow.cpp
+/fix_heat_flow.h
 /fix_tfmc.cpp
 /fix_tfmc.h
 /fix_ttm.cpp
@@ -1573,6 +1581,22 @@
 /fix_ttm_grid.h
 /fix_ttm_mod.cpp
 /fix_ttm_mod.h
+/granular_model.cpp
+/granular_model.h
+/gran_sub_mod_normal.cpp
+/gran_sub_mod_normal.h
+/gran_sub_mod_damping.cpp
+/gran_sub_mod_damping.h
+/gran_sub_mod_tangential.cpp
+/gran_sub_mod_tangential.h
+/gran_sub_mod_twisting.cpp
+/gran_sub_mod_twisting.h
+/gran_sub_mod_rolling.cpp
+/gran_sub_mod_rolling.h
+/gran_sub_mod_heat.cpp
+/gran_sub_mod_heat.h
+/gran_sub_mod.cpp
+/gran_sub_mod.h
 /pair_born_coul_long_cs.cpp
 /pair_born_coul_long_cs.h
 /pair_born_coul_dsf_cs.cpp

src/AMOEBA/amoeba_induce.cpp

@@ -19,7 +19,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "my_page.h"

src/AMOEBA/amoeba_utils.cpp

@@ -17,7 +17,7 @@
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/improper_amoeba.cpp

@@ -36,6 +36,10 @@ using namespace MathConst;
 ImproperAmoeba::ImproperAmoeba(LAMMPS *lmp) : Improper(lmp)
 {
   writedata = 1;
+
+  // the second atom in the quadruplet is the atom of symmetry
+
+  symmatoms[1] = 1;
 }
 
 /* ---------------------------------------------------------------------- */

src/AMOEBA/pair_amoeba.cpp

@@ -20,7 +20,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "math_special.h"
@@ -861,8 +861,8 @@ void PairAmoeba::init_style()
   Fix *myfix;
   if (first_flag) {
     id_pole = utils::strdup("AMOEBA_pole");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM 13 0 0 1",id_pole,group->names[0]));
-    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
+    fixpole = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // creation of per-atom storage
@@ -873,14 +873,14 @@ void PairAmoeba::init_style()
 
   if (first_flag && use_pred) {
     id_udalt = utils::strdup("AMOEBA_udalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
                                         id_udalt, group->names[0], maxualt));
-    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
 
     id_upalt = utils::strdup("AMOEBA_upalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
                                         id_upalt, group->names[0], maxualt));
-    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // create pages for storing pairwise data:
@@ -995,21 +995,21 @@ void PairAmoeba::init_style()
   if (id_pole) {
     myfix = modify->get_fix_by_id(id_pole);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_pole);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_pole);
-    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
+    fixpole = dynamic_cast<FixStoreAtom *>(myfix);
 
   }
 
   if (id_udalt) {
     myfix = modify->get_fix_by_id(id_udalt);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_udalt);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_udalt);
-    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
 
     myfix = modify->get_fix_by_id(id_upalt);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_upalt);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_upalt);
-    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // assign hydrogen neighbors (redID) to each owned atom

src/AMOEBA/pair_amoeba.h

@@ -166,9 +166,9 @@ class PairAmoeba : public Pair {
   int *amgroup;    // AMOEBA polarization group, 1 to Ngroup
 
   char *id_pole, *id_udalt, *id_upalt;
-  class FixStorePeratom *fixpole;     // stores pole = multipole components
+  class FixStoreAtom *fixpole;     // stores pole = multipole components
-  class FixStorePeratom *fixudalt;    // stores udalt = induced dipole history
+  class FixStoreAtom *fixudalt;    // stores udalt = induced dipole history
-  class FixStorePeratom *fixupalt;    // stores upalt = induced dipole history
+  class FixStoreAtom *fixupalt;    // stores upalt = induced dipole history
 
   // static per-type properties defined in force-field file
 

src/CLASS2/improper_class2.cpp

@@ -39,6 +39,10 @@ using namespace MathConst;
 ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
 {
   writedata = 1;
+
+  // the second atom in the quadruplet is the atom of symmetry
+
+  symmatoms[1] = 1;
 }
 
 /* ---------------------------------------------------------------------- */

src/COLVARS/ndx_group.cpp

@@ -81,6 +81,8 @@ void Ndx2Group::command(int narg, char **arg)
   if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
   if (atom->tag_enable == 0)
     error->all(FLERR,"Must have atom IDs for ndx2group command");
+  if (atom->map_style == Atom::MAP_NONE)
+    error->all(FLERR,"Must have an atom map for ndx2group command");
   if (comm->me == 0) {
     fp = fopen(arg[0], "r");
     if (fp == nullptr)
@@ -153,11 +155,12 @@ void Ndx2Group::command(int narg, char **arg)
           MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
 
           // read tags for atoms in group and broadcast
-          std::vector<tagint> tags = read_section(fp,name);
+          std::vector<tagint> tags = read_section(fp,next);
           num = tags.size();
           MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
           MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
           create(name,tags);
+          name = next;
         }
       } else {
         MPI_Bcast(&len,1,MPI_INT,0,world);

src/CORESHELL/compute_temp_cs.cpp

@@ -24,7 +24,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "memory.h"
@@ -67,8 +67,8 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
   // id = compute-ID + COMPUTE_STORE, fix group = compute group
 
   id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-    modify->add_fix(fmt::format("{} {} STORE/PERATOM 0 1", id_fix, group->names[igroup])));
+    modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 0", id_fix, group->names[igroup])));
 
   // set fix store values = 0 for now
   // fill them in via setup() once Comm::borders() has been called

src/CORESHELL/compute_temp_cs.h

@@ -54,7 +54,7 @@ class ComputeTempCS : public Compute {
   double **vint;
 
   char *id_fix;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
 
   void dof_compute();
   void vcm_pairs();

src/EXTRA-COMPUTE/compute_dipole_tip4p.cpp

@@ -0,0 +1,220 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_dipole_tip4p.h"
+
+#include "angle.h"
+#include "atom.h"
+#include "bond.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "pair.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+enum { MASSCENTER, GEOMCENTER };
+
+/* ---------------------------------------------------------------------- */
+
+ComputeDipoleTIP4P::ComputeDipoleTIP4P(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
+{
+  if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute dipole/tip4p command");
+
+  scalar_flag = 1;
+  vector_flag = 1;
+  size_vector = 3;
+  extscalar = 0;
+  extvector = 0;
+
+  vector = new double[size_vector];
+  vector[0] = vector[1] = vector[2] = 0.0;
+  usecenter = MASSCENTER;
+
+  if (narg == 4) {
+    if (utils::strmatch(arg[3], "^geom"))
+      usecenter = GEOMCENTER;
+    else if (strcmp(arg[3], "mass") == 0)
+      usecenter = MASSCENTER;
+    else
+      error->all(FLERR, "Illegal compute dipole/tip4p command");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeDipoleTIP4P::~ComputeDipoleTIP4P()
+{
+  delete[] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeDipoleTIP4P::init()
+{
+  if (!force->pair) error->all(FLERR, "Pair style must be defined for compute dipole/ti4p");
+
+  int itmp;
+  double *p_qdist = (double *) force->pair->extract("qdist", itmp);
+  int *p_typeO = (int *) force->pair->extract("typeO", itmp);
+  int *p_typeH = (int *) force->pair->extract("typeH", itmp);
+  int *p_typeA = (int *) force->pair->extract("typeA", itmp);
+  int *p_typeB = (int *) force->pair->extract("typeB", itmp);
+  if (!p_qdist || !p_typeO || !p_typeH || !p_typeA || !p_typeB)
+    error->all(FLERR, "Pair style is incompatible with compute dipole/tip4p");
+  typeO = *p_typeO;
+  typeH = *p_typeH;
+  int typeA = *p_typeA;
+  int typeB = *p_typeB;
+
+  if (!force->angle || !force->bond || !force->angle->setflag || !force->bond->setflag)
+    error->all(FLERR, "Bond and angle potentials must be defined for compute dipole/tip4p");
+  if ((typeA < 1) || (typeA > atom->nangletypes) || (force->angle->setflag[typeA] == 0))
+    error->all(FLERR, "Bad TIP4P angle type for compute dipole/tip4p");
+  if ((typeB < 1) || (typeB > atom->nbondtypes) || (force->bond->setflag[typeB] == 0))
+    error->all(FLERR, "Bad TIP4P bond type for compute dipole/tip4p");
+  double theta = force->angle->equilibrium_angle(typeA);
+  double blen = force->bond->equilibrium_distance(typeB);
+  alpha = *p_qdist / (cos(0.5 * theta) * blen);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeDipoleTIP4P::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  const auto x = atom->x;
+  const auto mask = atom->mask;
+  const auto type = atom->type;
+  const auto image = atom->image;
+  const auto mass = atom->mass;
+  const auto rmass = atom->rmass;
+  const auto q = atom->q;
+  const auto mu = atom->mu;
+  const auto nlocal = atom->nlocal;
+
+  double dipole[3] = {0.0, 0.0, 0.0};
+  double comproc[3] = {0.0, 0.0, 0.0};
+  double com[3] = {0.0, 0.0, 0.0};
+  double masstotal = 0.0;
+  double chrgtotal = 0.0;
+  double massproc = 0.0;
+  double chrgproc = 0.0;
+  double unwrap[3], xM[3];
+  double *xi;
+
+  for (int i = 0; i < nlocal; ++i) {
+    if (mask[i] & groupbit) {
+      double massone = 1.0;    // for usecenter == GEOMCENTER
+      if (usecenter == MASSCENTER) {
+        if (rmass)
+          massone = rmass[i];
+        else
+          massone = mass[type[i]];
+      }
+      massproc += massone;
+      if (atom->q_flag) chrgproc += q[i];
+      domain->unmap(x[i], image[i], unwrap);
+      comproc[0] += unwrap[0] * massone;
+      comproc[1] += unwrap[1] * massone;
+      comproc[2] += unwrap[2] * massone;
+    }
+  }
+  MPI_Allreduce(&massproc, &masstotal, 1, MPI_DOUBLE, MPI_SUM, world);
+  MPI_Allreduce(&chrgproc, &chrgtotal, 1, MPI_DOUBLE, MPI_SUM, world);
+  MPI_Allreduce(comproc, com, 3, MPI_DOUBLE, MPI_SUM, world);
+
+  if (masstotal > 0.0) {
+    com[0] /= masstotal;
+    com[1] /= masstotal;
+    com[2] /= masstotal;
+  }
+
+  // compute dipole moment
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      if (type[i] == typeO) {
+        find_M(i, xM);
+        xi = xM;
+      } else {
+        xi = x[i];
+      }
+      domain->unmap(xi, image[i], unwrap);
+      if (atom->q_flag) {
+        dipole[0] += q[i] * unwrap[0];
+        dipole[1] += q[i] * unwrap[1];
+        dipole[2] += q[i] * unwrap[2];
+      }
+      if (atom->mu_flag) {
+        dipole[0] += mu[i][0];
+        dipole[1] += mu[i][1];
+        dipole[2] += mu[i][2];
+      }
+    }
+  }
+
+  MPI_Allreduce(dipole, vector, 3, MPI_DOUBLE, MPI_SUM, world);
+
+  // correct for position dependence with a net charged group
+  vector[0] -= chrgtotal * com[0];
+  vector[1] -= chrgtotal * com[1];
+  vector[2] -= chrgtotal * com[2];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeDipoleTIP4P::compute_scalar()
+{
+  if (invoked_vector != update->ntimestep) compute_vector();
+
+  invoked_scalar = update->ntimestep;
+  scalar = sqrt(vector[0] * vector[0] + vector[1] * vector[1] + vector[2] * vector[2]);
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeDipoleTIP4P::find_M(int i, double *xM)
+{
+  double **x = atom->x;
+
+  int iH1 = atom->map(atom->tag[i] + 1);
+  int iH2 = atom->map(atom->tag[i] + 2);
+
+  if ((iH1 == -1) || (iH2 == -1)) error->one(FLERR, "TIP4P hydrogen is missing");
+  if ((atom->type[iH1] != typeH) || (atom->type[iH2] != typeH))
+    error->one(FLERR, "TIP4P hydrogen has incorrect atom type");
+
+  // set iH1,iH2 to index of closest image to O
+
+  iH1 = domain->closest_image(i, iH1);
+  iH2 = domain->closest_image(i, iH2);
+
+  double delx1 = x[iH1][0] - x[i][0];
+  double dely1 = x[iH1][1] - x[i][1];
+  double delz1 = x[iH1][2] - x[i][2];
+
+  double delx2 = x[iH2][0] - x[i][0];
+  double dely2 = x[iH2][1] - x[i][1];
+  double delz2 = x[iH2][2] - x[i][2];
+
+  xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
+  xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
+  xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
+}

src/EXTRA-COMPUTE/compute_dipole_tip4p.h

@@ -0,0 +1,46 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+// clang-format off
+ComputeStyle(dipole/tip4p,ComputeDipoleTIP4P);
+// clang-format on
+#else
+
+#ifndef LMP_COMPUTE_DIPOLE_TIP4P_H
+#define LMP_COMPUTE_DIPOLE_TIP4P_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeDipoleTIP4P : public Compute {
+ public:
+  ComputeDipoleTIP4P(class LAMMPS *, int, char **);
+  ~ComputeDipoleTIP4P() override;
+  void init() override;
+  void compute_vector() override;
+  double compute_scalar() override;
+
+ private:
+  int usecenter;
+
+  int typeO, typeH;
+  double alpha;
+  void find_M(int i, double *xM);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif