From 21293f1c08a3217e8ce29a95e5d4db7de0562152 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 13 Mar 2023 12:10:14 -0400 Subject: [PATCH 01/21] update links and hashes for new plumed2 releases --- cmake/Modules/Packages/PLUMED.cmake | 4 ++-- lib/plumed/Install.py | 8 +++++--- tools/singularity/almalinux9.def | 2 +- tools/singularity/centos7.def | 2 +- tools/singularity/centos8.def | 2 +- tools/singularity/fedora35_mingw.def | 2 +- tools/singularity/fedora36_mingw.def | 2 +- tools/singularity/rocky8.def | 2 +- tools/singularity/ubuntu18.04.def | 2 +- tools/singularity/ubuntu18.04_amd_rocm.def | 2 +- tools/singularity/ubuntu18.04_gpu.def | 2 +- tools/singularity/ubuntu18.04_intel_opencl.def | 2 +- tools/singularity/ubuntu18.04_nvidia.def | 2 +- tools/singularity/ubuntu20.04.def | 2 +- tools/singularity/ubuntu20.04_amd_rocm.def | 2 +- tools/singularity/ubuntu20.04_gpu.def | 2 +- tools/singularity/ubuntu20.04_intel_opencl.def | 2 +- tools/singularity/ubuntu20.04_nvidia.def | 2 +- tools/singularity/ubuntu20.04_oneapi.def | 2 +- tools/singularity/ubuntu22.04.def | 2 +- 20 files changed, 25 insertions(+), 23 deletions(-) diff --git a/cmake/Modules/Packages/PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake index f231d148bd..9a4a9556ee 100644 --- a/cmake/Modules/Packages/PLUMED.cmake +++ b/cmake/Modules/Packages/PLUMED.cmake @@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED) set(PLUMED_BUILD_BYPRODUCTS "/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_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of 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 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball") mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index bb6f27fddb..21e8ac51ff 100644 --- a/lib/plumed/Install.py +++ b/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 @@ -59,8 +59,10 @@ checksums = { \ '2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \ '2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \ '2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \ + '2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \ '2.8.0' : '489b23daba70da78cf0506cbc31689c6', \ '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \ + '2.8.2' : '599092b6a0aa6fff992612537ad98994', \ } # parse and process arguments diff --git a/tools/singularity/almalinux9.def b/tools/singularity/almalinux9.def index e16ebbbdb5..eacaf3b565 100644 --- a/tools/singularity/almalinux9.def +++ b/tools/singularity/almalinux9.def @@ -44,7 +44,7 @@ From: library/almalinux:9 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/centos7.def b/tools/singularity/centos7.def index c0fe278e94..fcdb2ff204 100644 --- a/tools/singularity/centos7.def +++ b/tools/singularity/centos7.def @@ -37,7 +37,7 @@ From: library/centos:7 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/centos8.def b/tools/singularity/centos8.def index 7cb0c51a9e..97f818f9eb 100644 --- a/tools/singularity/centos8.def +++ b/tools/singularity/centos8.def @@ -42,7 +42,7 @@ From: centos:8 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/fedora35_mingw.def b/tools/singularity/fedora35_mingw.def index 2661c77db4..693512bb97 100644 --- a/tools/singularity/fedora35_mingw.def +++ b/tools/singularity/fedora35_mingw.def @@ -49,7 +49,7 @@ From: fedora:35 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/fedora36_mingw.def b/tools/singularity/fedora36_mingw.def index 873b646e84..09c3a71d94 100644 --- a/tools/singularity/fedora36_mingw.def +++ b/tools/singularity/fedora36_mingw.def @@ -49,7 +49,7 @@ From: fedora:36 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/rocky8.def b/tools/singularity/rocky8.def index 0882bfd72b..bd076b5f6c 100644 --- a/tools/singularity/rocky8.def +++ b/tools/singularity/rocky8.def @@ -43,7 +43,7 @@ From: rockylinux/rockylinux:8 # manually install Plumed mkdir plumed cd plumed - version=2.8.1 + version=2.8.2 curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz tar -xzf plumed.tar.gz cd plumed-${version} diff --git a/tools/singularity/ubuntu18.04.def b/tools/singularity/ubuntu18.04.def index 02351d9ecb..142ef7ffd4 100644 --- a/tools/singularity/ubuntu18.04.def +++ b/tools/singularity/ubuntu18.04.def @@ -107,7 +107,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_amd_rocm.def b/tools/singularity/ubuntu18.04_amd_rocm.def index 38eaa6e322..4b9c53f00b 100644 --- a/tools/singularity/ubuntu18.04_amd_rocm.def +++ b/tools/singularity/ubuntu18.04_amd_rocm.def @@ -136,7 +136,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_gpu.def b/tools/singularity/ubuntu18.04_gpu.def index 0bfccf915b..7fa4e8ae4d 100644 --- a/tools/singularity/ubuntu18.04_gpu.def +++ b/tools/singularity/ubuntu18.04_gpu.def @@ -175,7 +175,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_intel_opencl.def b/tools/singularity/ubuntu18.04_intel_opencl.def index 2d562771bb..d6c9c65690 100644 --- a/tools/singularity/ubuntu18.04_intel_opencl.def +++ b/tools/singularity/ubuntu18.04_intel_opencl.def @@ -108,7 +108,7 @@ From: ubuntu:18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu18.04_nvidia.def b/tools/singularity/ubuntu18.04_nvidia.def index 2a3a34b1b2..91b0465a6d 100644 --- a/tools/singularity/ubuntu18.04_nvidia.def +++ b/tools/singularity/ubuntu18.04_nvidia.def @@ -107,7 +107,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu18.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04.def b/tools/singularity/ubuntu20.04.def index 2a2a1dd660..d62b4c9f86 100644 --- a/tools/singularity/ubuntu20.04.def +++ b/tools/singularity/ubuntu20.04.def @@ -103,7 +103,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_amd_rocm.def b/tools/singularity/ubuntu20.04_amd_rocm.def index f947de9ee9..753f215469 100644 --- a/tools/singularity/ubuntu20.04_amd_rocm.def +++ b/tools/singularity/ubuntu20.04_amd_rocm.def @@ -123,7 +123,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_gpu.def b/tools/singularity/ubuntu20.04_gpu.def index 05da01ccac..115ca6eee5 100644 --- a/tools/singularity/ubuntu20.04_gpu.def +++ b/tools/singularity/ubuntu20.04_gpu.def @@ -161,7 +161,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_intel_opencl.def b/tools/singularity/ubuntu20.04_intel_opencl.def index cc547fef29..c8680a16c7 100644 --- a/tools/singularity/ubuntu20.04_intel_opencl.def +++ b/tools/singularity/ubuntu20.04_intel_opencl.def @@ -101,7 +101,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_nvidia.def b/tools/singularity/ubuntu20.04_nvidia.def index 8ec334ad8b..3affc30b8b 100644 --- a/tools/singularity/ubuntu20.04_nvidia.def +++ b/tools/singularity/ubuntu20.04_nvidia.def @@ -103,7 +103,7 @@ From: nvidia/cuda:11.6.2-devel-ubuntu20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu20.04_oneapi.def b/tools/singularity/ubuntu20.04_oneapi.def index 25c913f392..70d69c7d80 100644 --- a/tools/singularity/ubuntu20.04_oneapi.def +++ b/tools/singularity/ubuntu20.04_oneapi.def @@ -140,7 +140,7 @@ From: ubuntu:20.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed diff --git a/tools/singularity/ubuntu22.04.def b/tools/singularity/ubuntu22.04.def index 8a4f262f75..ef43347982 100644 --- a/tools/singularity/ubuntu22.04.def +++ b/tools/singularity/ubuntu22.04.def @@ -103,7 +103,7 @@ From: ubuntu:22.04 # Plumed ########################################################################### - export PLUMED_PKG_VERSION=2.8.1 + export PLUMED_PKG_VERSION=2.8.2 mkdir plumed cd plumed From 03454aeefb8920662c76ffab77f154ee1889b154 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 13 Mar 2023 23:07:11 -0400 Subject: [PATCH 02/21] compile GPU library with thread support when BUILD_OMP is enabled --- cmake/Modules/Packages/GPU.cmake | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 90645d699b..a0578394f1 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -176,6 +176,10 @@ if(GPU_API STREQUAL "CUDA") target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) 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) @@ -251,12 +255,18 @@ elseif(GPU_API STREQUAL "OPENCL") else() target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT) 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) 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}) @@ -407,6 +417,10 @@ elseif(GPU_API STREQUAL "HIP") target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT) endif() target_link_libraries(gpu PRIVATE hip::host) + if(BUILD_OMP) + find_package(OpenMP COMPONENTS CXX REQUIRED) + target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX) + endif() if(HIP_USE_DEVICE_SORT) if(HIP_PLATFORM STREQUAL "amd") From 14180774b7e94caa3b0a9fdef4e60adc0b1d2ae7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 14 Mar 2023 07:00:34 -0400 Subject: [PATCH 03/21] mention OpenMP support in the GPU library --- doc/src/Build_extras.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 4dd8c10b3f..e6366075ff 100644 --- a/doc/src/Build_extras.rst +++ b/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 From 88c8781396db1ec05f967648102fb4647fdebcd0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 14 Mar 2023 10:17:20 -0400 Subject: [PATCH 04/21] silence compiler warnings --- src/pair_lj_cut_coul_cut.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 5438e82377..e62e08ea4b 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -465,7 +465,7 @@ void PairLJCutCoulCut::born_matrix(int i, int j, int itype, int jtype, double rs double factor_coul, double factor_lj, double &dupair, double &du2pair) { - double rinv, r2inv, r3inv, r6inv, du, du2; + double rinv, r2inv, r3inv, r6inv; double du_lj, du2_lj, du_coul, du2_coul; double *q = atom->q; From fa9062a87e74523048b561321c8f3859e774fd30 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 15 Mar 2023 18:39:32 -0400 Subject: [PATCH 05/21] make Force::special_lj and Force::special_coul accessible through the library interface --- python/lammps/core.py | 3 ++- src/library.cpp | 12 +++++++++++ .../c-library/test_library_properties.cpp | 21 +++++++++++++++++++ unittest/python/python-commands.py | 6 ++++++ 4 files changed, 41 insertions(+), 1 deletion(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index e4f8d807b6..80961186f3 100644 --- a/python/lammps/core.py +++ b/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': diff --git a/src/library.cpp b/src/library.cpp index 9f817a1199..cc4e748f57 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1232,6 +1232,8 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name) if (strcmp(name,"nghost") == 0) return LAMMPS_INT; if (strcmp(name,"nmax") == 0) return LAMMPS_INT; if (strcmp(name,"ntypes") == 0) return LAMMPS_INT; + if (strcmp(name,"special_lj") == 0) return LAMMPS_DOUBLE; + if (strcmp(name,"special_coul") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"q_flag") == 0) return LAMMPS_INT; @@ -1470,6 +1472,14 @@ report the "native" data type. The following tables are provided: - int - 1 - maximum of nlocal+nghost across all MPI ranks (for per-atom data array size). + * - special_lj + - double + - 4 + - special :doc:`pair weighting factors ` for LJ interactions (first element is always 1.0) + * - special_coul + - double + - 4 + - special :doc:`pair weighting factors ` for Coulomb interactions (first element is always 1.0) * - q_flag - int - 1 @@ -1625,6 +1635,8 @@ void *lammps_extract_global(void *handle, const char *name) if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal; if (strcmp(name,"nghost") == 0) return (void *) &lmp->atom->nghost; if (strcmp(name,"nmax") == 0) return (void *) &lmp->atom->nmax; + if (strcmp(name,"special_lj") == 0) return (void *) lmp->force->special_lj; + if (strcmp(name,"special_coul") == 0) return (void *) lmp->force->special_coul; if (strcmp(name,"q_flag") == 0) return (void *) &lmp->atom->q_flag; diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp index bb0f6e2894..d6dd55f75e 100644 --- a/unittest/c-library/test_library_properties.cpp +++ b/unittest/c-library/test_library_properties.cpp @@ -297,6 +297,7 @@ TEST_F(LibraryProperties, global) std::string input = path_join(INPUT_DIR, "in.fourmol"); if (!verbose) ::testing::internal::CaptureStdout(); + lammps_command(lmp, "special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0"); lammps_file(lmp, input.c_str()); lammps_command(lmp, "run 2 post no"); if (!verbose) ::testing::internal::GetCapturedStdout(); @@ -321,6 +322,26 @@ TEST_F(LibraryProperties, global) EXPECT_EQ(lammps_extract_global_datatype(lmp, "dt"), LAMMPS_DOUBLE); double *d_ptr = (double *)lammps_extract_global(lmp, "dt"); EXPECT_DOUBLE_EQ((*d_ptr), 0.1); + + EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_lj"), LAMMPS_DOUBLE); + EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_coul"), LAMMPS_DOUBLE); + double *special_lj = (double *)lammps_extract_global(lmp, "special_lj"); + double *special_coul= (double *)lammps_extract_global(lmp, "special_coul"); + EXPECT_DOUBLE_EQ(special_lj[0], 1.0); + EXPECT_DOUBLE_EQ(special_lj[1], 0.0); + EXPECT_DOUBLE_EQ(special_lj[2], 0.5); + EXPECT_DOUBLE_EQ(special_lj[3], 0.8); + EXPECT_DOUBLE_EQ(special_coul[0], 1.0); + EXPECT_DOUBLE_EQ(special_coul[1], 0.1); + EXPECT_DOUBLE_EQ(special_coul[2], 0.5); + EXPECT_DOUBLE_EQ(special_coul[3], 1.0); + lammps_command(lmp, "special_bonds lj/coul 1.0 1.0 1.0"); + EXPECT_DOUBLE_EQ(special_lj[1], 1.0); + EXPECT_DOUBLE_EQ(special_lj[2], 1.0); + EXPECT_DOUBLE_EQ(special_lj[3], 1.0); + EXPECT_DOUBLE_EQ(special_coul[1], 1.0); + EXPECT_DOUBLE_EQ(special_coul[2], 1.0); + EXPECT_DOUBLE_EQ(special_coul[3], 1.0); }; TEST_F(LibraryProperties, neighlist) diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 13be27f067..33b19ba4f0 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -536,6 +536,7 @@ create_atoms 1 single & def test_extract_global(self): self.lmp.command("region box block -1 1 -2 2 -3 3") self.lmp.command("create_box 1 box") + self.lmp.command("special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0") self.assertEqual(self.lmp.extract_global("units"), "lj") self.assertEqual(self.lmp.extract_global("ntimestep"), 0) self.assertEqual(self.lmp.extract_global("dt"), 0.005) @@ -552,10 +553,15 @@ create_atoms 1 single & self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0]) self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1]) self.assertEqual(self.lmp.extract_global("triclinic"), 0) + self.assertEqual(self.lmp.extract_global("special_lj"), [1.0, 0.0, 0.5, 0.8]) + self.assertEqual(self.lmp.extract_global("special_coul"), [1.0, 0.1, 0.5, 1.0]) self.assertEqual(self.lmp.extract_global("sublo_lambda"), None) self.assertEqual(self.lmp.extract_global("subhi_lambda"), None) self.assertEqual(self.lmp.extract_global("respa_levels"), None) self.assertEqual(self.lmp.extract_global("respa_dt"), None) + self.lmp.command("special_bonds lj/coul 0.0 1.0 1.0") + self.assertEqual(self.lmp.extract_global("special_lj"), [1.0, 0.0, 1.0, 1.0]) + self.assertEqual(self.lmp.extract_global("special_coul"), [1.0, 0.0, 1.0, 1.0]) # set and initialize r-RESPA self.lmp.command("run_style respa 3 5 2 pair 2 kspace 3") From 0e3dc6fefa09314da70a487cb03303973004e883 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 08:01:26 -0400 Subject: [PATCH 06/21] Download the latest MSCG snapshot to address bug in library. --- cmake/Modules/Packages/MSCG.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake index e4260e059e..2b8e8eda06 100644 --- a/cmake/Modules/Packages/MSCG.cmake +++ b/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_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of 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 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball") mark_as_advanced(MSCG_URL) mark_as_advanced(MSCG_MD5) From 5c5e7b7e48afd28c62d07655d547b4e12eaab982 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 08:39:23 -0400 Subject: [PATCH 07/21] update fix mscg example --- examples/mscg/log.16Mar23.g++.1 | 105 +++++++++++++ examples/mscg/log.31Mar17.g++.1 | 145 ------------------ examples/mscg/output_16Mar23/1_1.dat | 71 +++++++++ examples/mscg/output_16Mar23/1_1.table | 104 +++++++++++++ examples/mscg/output_16Mar23/b-spline.out | 2 + .../{output_9Jan17 => output_16Mar23}/rmin.in | 0 .../rmin_b.in | 0 examples/mscg/output_16Mar23/sol_info.out | 17 ++ examples/mscg/output_16Mar23/x.out | 2 + examples/mscg/output_9Jan17/1_1.dat | 77 ---------- examples/mscg/output_9Jan17/1_1.table | 82 ---------- examples/mscg/output_9Jan17/b-spline.out | 2 - examples/mscg/output_9Jan17/sol_info.out | 18 --- examples/mscg/output_9Jan17/x.out | 1 - 14 files changed, 301 insertions(+), 325 deletions(-) create mode 100644 examples/mscg/log.16Mar23.g++.1 delete mode 100644 examples/mscg/log.31Mar17.g++.1 create mode 100644 examples/mscg/output_16Mar23/1_1.dat create mode 100644 examples/mscg/output_16Mar23/1_1.table create mode 100644 examples/mscg/output_16Mar23/b-spline.out rename examples/mscg/{output_9Jan17 => output_16Mar23}/rmin.in (100%) rename examples/mscg/{output_9Jan17 => output_16Mar23}/rmin_b.in (100%) create mode 100644 examples/mscg/output_16Mar23/sol_info.out create mode 100644 examples/mscg/output_16Mar23/x.out delete mode 100644 examples/mscg/output_9Jan17/1_1.dat delete mode 100644 examples/mscg/output_9Jan17/1_1.table delete mode 100644 examples/mscg/output_9Jan17/b-spline.out delete mode 100644 examples/mscg/output_9Jan17/sol_info.out delete mode 100644 examples/mscg/output_9Jan17/x.out diff --git a/examples/mscg/log.16Mar23.g++.1 b/examples/mscg/log.16Mar23.g++.1 new file mode 100644 index 0000000000..8c99fd3e15 --- /dev/null +++ b/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 diff --git a/examples/mscg/log.31Mar17.g++.1 b/examples/mscg/log.31Mar17.g++.1 deleted file mode 100644 index c67bc483db..0000000000 --- a/examples/mscg/log.31Mar17.g++.1 +++ /dev/null @@ -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 diff --git a/examples/mscg/output_16Mar23/1_1.dat b/examples/mscg/output_16Mar23/1_1.dat new file mode 100644 index 0000000000..d73cd05fe6 --- /dev/null +++ b/examples/mscg/output_16Mar23/1_1.dat @@ -0,0 +1,71 @@ +3.000000 9.109433117503674e+00 +3.100000 6.562933520937051e+00 +3.200000 3.803570347770783e+00 +3.300000 1.524835163098694e+00 +3.400000 3.680752991750511e-02 +3.500000 -6.369395346711866e-01 +3.600000 -6.624341032589213e-01 +3.700000 -2.983998819283989e-01 +3.800000 1.996942072449469e-01 +3.900000 6.507540486137935e-01 +4.000000 9.561503221901252e-01 +4.100000 1.082978861799261e+00 +4.200000 1.046366050930359e+00 +4.300000 8.917742185869113e-01 +4.400000 6.773070351372578e-01 +4.500000 4.561974686292022e-01 +4.600000 2.640422255436971e-01 +4.700000 1.180848207166380e-01 +4.800000 2.124502216672507e-02 +4.900000 -3.366915456585443e-02 +5.000000 -5.974945208074427e-02 +5.100000 -7.177537677873873e-02 +5.200000 -8.204929079011507e-02 +5.300000 -9.745573177789707e-02 +5.400000 -1.196283642109915e-01 +5.500000 -1.463411396781238e-01 +5.600000 -1.729465415853768e-01 +5.700000 -1.938138298537278e-01 +5.800000 -2.037672856165882e-01 +5.900000 -1.995060297815394e-01 +6.000000 -1.805447650094144e-01 +6.100000 -1.489384048916932e-01 +6.200000 -1.085276302304308e-01 +6.300000 -6.416601955090541e-02 +6.400000 -2.094717961426480e-02 +6.500000 1.656812406982645e-02 +6.600000 4.511482523443927e-02 +6.700000 6.322611594801032e-02 +6.800000 7.107524696431811e-02 +6.900000 7.005702917383723e-02 +7.000000 6.235932355899154e-02 +7.100000 5.053453114940768e-02 +7.200000 3.707108297716843e-02 +7.300000 2.397003518601587e-02 +7.400000 1.245439896007831e-02 +7.500000 3.015413982707119e-03 +7.600000 -4.408442264121739e-03 +7.700000 -1.024733994435217e-02 +7.800000 -1.511598231239246e-02 +7.900000 -1.962949115765983e-02 +8.000000 -2.422153184874873e-02 +8.100000 -2.902066868449916e-02 +8.200000 -3.387453677654857e-02 +8.300000 -3.843224513464188e-02 +8.400000 -4.222901944115068e-02 +8.500000 -4.477084482559266e-02 +8.600000 -4.561910863915099e-02 +8.700000 -4.447439067652353e-02 +8.800000 -4.123808661911404e-02 +8.900000 -3.601776131390161e-02 +9.000000 -2.911033476210515e-02 +9.100000 -2.098441550402311e-02 +9.200000 -1.226263400387303e-02 +9.300000 -3.703976034631109e-03 +9.400000 3.815231963949414e-03 +9.500000 9.355387087425532e-03 +9.600000 1.205664749783030e-02 +9.700000 1.131702059340882e-02 +9.800000 6.971799313021964e-03 +9.900000 -5.270015594498346e-04 +10.000000 -9.931209090702869e-03 diff --git a/examples/mscg/output_16Mar23/1_1.table b/examples/mscg/output_16Mar23/1_1.table new file mode 100644 index 0000000000..148d909ad3 --- /dev/null +++ b/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 + +1 0.200000 127.263594 80.411422 +2 0.300000 119.349776 77.864922 +3 0.400000 111.690609 75.318423 +4 0.500000 104.286092 72.771923 +5 0.600000 97.136225 70.225423 +6 0.700000 90.241007 67.678924 +7 0.800000 83.600440 65.132424 +8 0.900000 77.214522 62.585925 +9 1.000000 71.083255 60.039425 +10 1.100000 65.206637 57.492925 +11 1.200000 59.584670 54.946426 +12 1.300000 54.217352 52.399926 +13 1.400000 49.104684 49.853427 +14 1.500000 44.246667 47.306927 +15 1.600000 39.643299 44.760427 +16 1.700000 35.294581 42.213928 +17 1.800000 31.200513 39.667428 +18 1.900000 27.361096 37.120929 +19 2.000000 23.776328 34.574429 +20 2.100000 20.446210 32.027929 +21 2.200000 17.370742 29.481430 +22 2.300000 14.549924 26.934930 +23 2.400000 11.983756 24.388431 +24 2.500000 9.672238 21.841931 +25 2.600000 7.615370 19.295432 +26 2.700000 5.813151 16.748932 +27 2.800000 4.265583 14.202432 +28 2.900000 2.972665 11.655933 +29 3.000000 1.934397 9.109433 +30 3.100000 1.150778 6.562934 +31 3.200000 0.632453 3.803570 +32 3.300000 0.366033 1.524835 +33 3.400000 0.287951 0.036808 +34 3.500000 0.317957 -0.636940 +35 3.600000 0.382926 -0.662434 +36 3.700000 0.430968 -0.298400 +37 3.800000 0.435903 0.199694 +38 3.900000 0.393381 0.650754 +39 4.000000 0.313035 0.956150 +40 4.100000 0.211079 1.082979 +41 4.200000 0.104612 1.046366 +42 4.300000 0.007705 0.891774 +43 4.400000 -0.070749 0.677307 +44 4.500000 -0.127425 0.456197 +45 4.600000 -0.163437 0.264042 +46 4.700000 -0.182543 0.118085 +47 4.800000 -0.189509 0.021245 +48 4.900000 -0.188888 -0.033669 +49 5.000000 -0.184217 -0.059749 +50 5.100000 -0.177641 -0.071775 +51 5.200000 -0.169950 -0.082049 +52 5.300000 -0.160975 -0.097456 +53 5.400000 -0.150120 -0.119628 +54 5.500000 -0.136822 -0.146341 +55 5.600000 -0.120858 -0.172947 +56 5.700000 -0.102520 -0.193814 +57 5.800000 -0.082640 -0.203767 +58 5.900000 -0.062477 -0.199506 +59 6.000000 -0.043474 -0.180545 +60 6.100000 -0.027000 -0.148938 +61 6.200000 -0.014127 -0.108528 +62 6.300000 -0.005492 -0.064166 +63 6.400000 -0.001236 -0.020947 +64 6.500000 -0.001018 0.016568 +65 6.600000 -0.004102 0.045115 +66 6.700000 -0.009519 0.063226 +67 6.800000 -0.016234 0.071075 +68 6.900000 -0.023290 0.070057 +69 7.000000 -0.029911 0.062359 +70 7.100000 -0.035556 0.050535 +71 7.200000 -0.039936 0.037071 +72 7.300000 -0.042988 0.023970 +73 7.400000 -0.044809 0.012454 +74 7.500000 -0.045583 0.003015 +75 7.600000 -0.045513 -0.004408 +76 7.700000 -0.044781 -0.010247 +77 7.800000 -0.043512 -0.015116 +78 7.900000 -0.041775 -0.019629 +79 8.000000 -0.039583 -0.024222 +80 8.100000 -0.036920 -0.029021 +81 8.200000 -0.033776 -0.033875 +82 8.300000 -0.030160 -0.038432 +83 8.400000 -0.026127 -0.042229 +84 8.500000 -0.021777 -0.044771 +85 8.600000 -0.017258 -0.045619 +86 8.700000 -0.012753 -0.044474 +87 8.800000 -0.008467 -0.041238 +88 8.900000 -0.004605 -0.036018 +89 9.000000 -0.001348 -0.029110 +90 9.100000 0.001156 -0.020984 +91 9.200000 0.002819 -0.012263 +92 9.300000 0.003617 -0.003704 +93 9.400000 0.003612 0.003815 +94 9.500000 0.002953 0.009355 +95 9.600000 0.001882 0.012057 +96 9.700000 0.000714 0.011317 +97 9.800000 -0.000201 0.006972 +98 9.900000 -0.000523 -0.000527 +99 10.000000 0.000000 -0.009931 diff --git a/examples/mscg/output_16Mar23/b-spline.out b/examples/mscg/output_16Mar23/b-spline.out new file mode 100644 index 0000000000..8571ede9b7 --- /dev/null +++ b/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 diff --git a/examples/mscg/output_9Jan17/rmin.in b/examples/mscg/output_16Mar23/rmin.in similarity index 100% rename from examples/mscg/output_9Jan17/rmin.in rename to examples/mscg/output_16Mar23/rmin.in diff --git a/examples/mscg/output_9Jan17/rmin_b.in b/examples/mscg/output_16Mar23/rmin_b.in similarity index 100% rename from examples/mscg/output_9Jan17/rmin_b.in rename to examples/mscg/output_16Mar23/rmin_b.in diff --git a/examples/mscg/output_16Mar23/sol_info.out b/examples/mscg/output_16Mar23/sol_info.out new file mode 100644 index 0000000000..eb4460f9ce --- /dev/null +++ b/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 +9.718949e-01 +7.471241e-01 +5.277965e-01 +5.084369e-01 +3.510398e-01 +2.997000e-01 +2.142454e-01 +1.201800e-01 +7.143923e-02 +3.077326e-02 +1.835581e-02 diff --git a/examples/mscg/output_16Mar23/x.out b/examples/mscg/output_16Mar23/x.out new file mode 100644 index 0000000000..d9ae514466 --- /dev/null +++ b/examples/mscg/output_16Mar23/x.out @@ -0,0 +1,2 @@ +ٝ\ +8"@!D:@vH@H3HSԖ p??俀% s?:yD{zAĆ?#Tgl#)^YX?KpkDm? XV \ No newline at end of file diff --git a/examples/mscg/output_9Jan17/1_1.dat b/examples/mscg/output_9Jan17/1_1.dat deleted file mode 100644 index fcfbe0d7c8..0000000000 --- a/examples/mscg/output_9Jan17/1_1.dat +++ /dev/null @@ -1,77 +0,0 @@ -2.500000 5.670970817963099e+02 -2.600000 2.404059283529051e+02 -2.700000 9.157060823529977e+01 -2.800000 3.428273061369140e+01 -2.900000 1.619868149395266e+01 -3.000000 1.039607214301755e+01 -3.100000 6.830187514267188e+00 -3.200000 3.861970842349535e+00 -3.300000 1.645948643278161e+00 -3.400000 2.395428971623918e-01 -3.500000 -4.276763637833773e-01 -3.600000 -5.132022977965877e-01 -3.700000 -2.208024961234051e-01 -3.800000 2.402697744243800e-01 -3.900000 6.956064296165573e-01 -4.000000 1.034070044257954e+00 -4.100000 1.205997975111669e+00 -4.200000 1.209501102128581e+00 -4.300000 1.076304670380924e+00 -4.400000 8.575891319958883e-01 -4.500000 6.098309880892070e-01 -4.600000 3.807992942746473e-01 -4.700000 1.995994191469442e-01 -4.800000 7.699059877424269e-02 -4.900000 9.750744163981299e-03 -5.000000 -1.480308769532222e-02 -5.100000 -1.429422279228416e-02 -5.200000 -6.765899050869768e-03 -5.300000 -6.214398421078919e-03 -5.400000 -1.951586041390797e-02 -5.500000 -4.689090237947263e-02 -5.600000 -8.376292122940529e-02 -5.700000 -1.226699982917263e-01 -5.800000 -1.551768041657136e-01 -5.900000 -1.737865035767736e-01 -6.000000 -1.738272491408507e-01 -6.100000 -1.546779867768825e-01 -6.200000 -1.193171291488982e-01 -6.300000 -7.321054075616322e-02 -6.400000 -2.317411193286228e-02 -6.500000 2.376366715221714e-02 -6.600000 6.149913249600215e-02 -6.700000 8.597538938112201e-02 -6.800000 9.590170060736655e-02 -6.900000 9.245100462148878e-02 -7.000000 7.855487875847664e-02 -7.100000 5.818301960249692e-02 -7.200000 3.562272334783877e-02 -7.300000 1.475836615985744e-02 -7.400000 -1.639617536128255e-03 -7.500000 -1.237881063914745e-02 -7.600000 -1.768202571195587e-02 -7.700000 -1.877757119362295e-02 -7.800000 -1.748001968416543e-02 -7.900000 -1.577097622918088e-02 -8.000000 -1.537984660448136e-02 -8.100000 -1.737044400054951e-02 -8.200000 -2.187939410237979e-02 -8.300000 -2.823987455760605e-02 -8.400000 -3.525715284001425e-02 -8.500000 -4.148996251287761e-02 -8.600000 -4.553187949229211e-02 -8.700000 -4.629269831051163e-02 -8.800000 -4.327548798226762e-02 -8.900000 -3.674131754868225e-02 -9.000000 -2.758883541814894e-02 -9.100000 -1.712151838480657e-02 -9.200000 -6.810600249997737e-03 -9.300000 1.941999556272785e-03 -9.400000 8.040747353879739e-03 -9.500000 1.092691524686838e-02 -9.600000 1.063606620723048e-02 -9.700000 7.416550438142138e-03 -9.800000 1.175066786686231e-03 -9.900000 -9.084427187675534e-03 -10.000000 -2.582180514463068e-02 -10.100000 -5.352186189454393e-02 diff --git a/examples/mscg/output_9Jan17/1_1.table b/examples/mscg/output_9Jan17/1_1.table deleted file mode 100644 index 9d78fabc77..0000000000 --- a/examples/mscg/output_9Jan17/1_1.table +++ /dev/null @@ -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 -4 2.800000 6.161878 34.282731 -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 -14 3.800000 0.634656 0.240270 -15 3.900000 0.587862 0.695606 -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 -20 4.400000 0.057615 0.857589 -21 4.500000 -0.015756 0.609831 -22 4.600000 -0.065288 0.380799 -23 4.700000 -0.094307 0.199599 -24 4.800000 -0.108137 0.076991 -25 4.900000 -0.112474 0.009751 -26 5.000000 -0.112221 -0.014803 -27 5.100000 -0.110767 -0.014294 -28 5.200000 -0.109714 -0.006766 -29 5.300000 -0.109065 -0.006214 -30 5.400000 -0.107778 -0.019516 -31 5.500000 -0.104458 -0.046891 -32 5.600000 -0.097925 -0.083763 -33 5.700000 -0.087603 -0.122670 -34 5.800000 -0.073711 -0.155177 -35 5.900000 -0.057263 -0.173787 -36 6.000000 -0.039882 -0.173827 -37 6.100000 -0.023457 -0.154678 -38 6.200000 -0.009757 -0.119317 -39 6.300000 -0.000131 -0.073211 -40 6.400000 0.004688 -0.023174 -41 6.500000 0.004659 0.023764 -42 6.600000 0.000396 0.061499 -43 6.700000 -0.006978 0.085975 -44 6.800000 -0.016072 0.095902 -45 6.900000 -0.025489 0.092451 -46 7.000000 -0.034040 0.078555 -47 7.100000 -0.040877 0.058183 -48 7.200000 -0.045567 0.035623 -49 7.300000 -0.048086 0.014758 -50 7.400000 -0.048742 -0.001640 -51 7.500000 -0.048041 -0.012379 -52 7.600000 -0.046538 -0.017682 -53 7.700000 -0.044715 -0.018778 -54 7.800000 -0.042902 -0.017480 -55 7.900000 -0.041239 -0.015771 -56 8.000000 -0.039682 -0.015380 -57 8.100000 -0.038044 -0.017370 -58 8.200000 -0.036082 -0.021879 -59 8.300000 -0.033576 -0.028240 -60 8.400000 -0.030401 -0.035257 -61 8.500000 -0.026564 -0.041490 -62 8.600000 -0.022213 -0.045532 -63 8.700000 -0.017621 -0.046293 -64 8.800000 -0.013143 -0.043275 -65 8.900000 -0.009142 -0.036741 -66 9.000000 -0.005926 -0.027589 -67 9.100000 -0.003690 -0.017122 -68 9.200000 -0.002494 -0.006811 -69 9.300000 -0.002250 0.001942 -70 9.400000 -0.002749 0.008041 -71 9.500000 -0.003698 0.010927 -72 9.600000 -0.004776 0.010636 -73 9.700000 -0.005678 0.007417 -74 9.800000 -0.006108 0.001175 -75 9.900000 -0.005712 -0.009084 -76 10.000000 -0.003967 -0.025822 -77 10.100000 0.000000 -0.053522 diff --git a/examples/mscg/output_9Jan17/b-spline.out b/examples/mscg/output_9Jan17/b-spline.out deleted file mode 100644 index c1dcd731ca..0000000000 --- a/examples/mscg/output_9Jan17/b-spline.out +++ /dev/null @@ -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 diff --git a/examples/mscg/output_9Jan17/sol_info.out b/examples/mscg/output_9Jan17/sol_info.out deleted file mode 100644 index 5f02270f51..0000000000 --- a/examples/mscg/output_9Jan17/sol_info.out +++ /dev/null @@ -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 -5.376709e-01 -4.616070e-01 -3.257062e-01 -2.683729e-01 -1.530153e-01 -9.336288e-02 -5.042150e-02 -2.126912e-02 -1.446682e-02 -4.167763e-05 diff --git a/examples/mscg/output_9Jan17/x.out b/examples/mscg/output_9Jan17/x.out deleted file mode 100644 index 124cf8bf41..0000000000 --- a/examples/mscg/output_9Jan17/x.out +++ /dev/null @@ -1 +0,0 @@ --@47h<5@K7@R]'n@݌IH??rI.^?W:ȿ(O%?Ns?Ŀ:C?:,H?}cp7g \ No newline at end of file From f63befc80f33819fc2ce4395e2c1d2a658396867 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 10:29:00 -0400 Subject: [PATCH 08/21] consolidate replicated commands to single location --- cmake/Modules/Packages/GPU.cmake | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index a0578394f1..034c4b3a9f 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -176,12 +176,6 @@ if(GPU_API STREQUAL "CUDA") target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) 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) add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp) target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR) @@ -255,12 +249,6 @@ elseif(GPU_API STREQUAL "OPENCL") else() target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT) 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) add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp) target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL) @@ -417,10 +405,6 @@ elseif(GPU_API STREQUAL "HIP") target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT) endif() target_link_libraries(gpu PRIVATE hip::host) - if(BUILD_OMP) - find_package(OpenMP COMPONENTS CXX REQUIRED) - target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX) - endif() if(HIP_USE_DEVICE_SORT) if(HIP_PLATFORM STREQUAL "amd") @@ -489,10 +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) From d71a78449a0b66b6fa1252aea2ea73e273a15426 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 12:29:51 -0400 Subject: [PATCH 09/21] fix two bugs in the ndx2group command --- src/COLVARS/ndx_group.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp index 4f8a682a2a..1d24db3900 100644 --- a/src/COLVARS/ndx_group.cpp +++ b/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 tags = read_section(fp,name); + std::vector 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); From feb1b9e029a170a7fe4b7f7edb1b95fd1ad5e0aa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 12:55:30 -0400 Subject: [PATCH 10/21] fix whitespace --- src/improper.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/improper.h b/src/improper.h index fbe86dfcd1..22a5d09926 100644 --- a/src/improper.h +++ b/src/improper.h @@ -36,11 +36,11 @@ class Improper : protected Pointers { // CENTROID_SAME = same as two-body stress // CENTROID_AVAIL = different and implemented // CENTROID_NOTAVAIL = different, not yet implemented - + int symmatoms[4]; // symmetry atom(s) of improper style // value of 0: interchangable atoms // value of 1: central atom - // values >1: additional atoms of symmetry + // values >1: additional atoms of symmetry // KOKKOS host/device flag and data masks From 4a66389bf1110e5687631121877d867a9e458dd7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 16:29:42 -0400 Subject: [PATCH 11/21] purge build folder from within install.py script --- cmake/CMakeLists.txt | 3 +-- python/install.py | 4 ++++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 5a30cd5aa5..14961209c8 100644 --- a/cmake/CMakeLists.txt +++ b/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 - COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps + install-python ${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() diff --git a/python/install.py b/python/install.py index 591e8525dc..561e93caa9 100644 --- a/python/install.py +++ b/python/install.py @@ -59,6 +59,10 @@ olddir = os.path.abspath('.') os.chdir(os.path.dirname(args.package)) # remove any wheel files left over from previous calls +if os.path.isdir(os.path.join(olddir,"build")): + print("Cleaning old build directory") + shutil.rmtree(os.path.join(olddir,"build")) + print("Purging existing wheels...") for wheel in glob.glob('lammps-*.whl'): print("deleting " + wheel) From d3a23817f14e5b83741332f983df3c792495f894 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 17:25:11 -0400 Subject: [PATCH 12/21] disable purging old wheel files --- python/install.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/python/install.py b/python/install.py index 561e93caa9..6c27ebd0bd 100644 --- a/python/install.py +++ b/python/install.py @@ -63,10 +63,10 @@ if os.path.isdir(os.path.join(olddir,"build")): print("Cleaning old build directory") shutil.rmtree(os.path.join(olddir,"build")) -print("Purging existing wheels...") -for wheel in glob.glob('lammps-*.whl'): - print("deleting " + wheel) - 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 From bf944488436c48fc6c7e8d256665bed1cd7f798d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 18:32:54 -0400 Subject: [PATCH 13/21] simplify and avoid segfault without pair style --- src/EXTRA-FIX/fix_efield_tip4p.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/EXTRA-FIX/fix_efield_tip4p.cpp b/src/EXTRA-FIX/fix_efield_tip4p.cpp index a204fe6f7d..3d6a2f66b7 100644 --- a/src/EXTRA-FIX/fix_efield_tip4p.cpp +++ b/src/EXTRA-FIX/fix_efield_tip4p.cpp @@ -46,6 +46,7 @@ void FixEfieldTIP4P::init() if (atom->tag_enable == 0) error->all(FLERR, "Fix efield/tip4p requires atom IDs"); if (!atom->q_flag) error->all(FLERR, "Fix efield/tip4p requires atom attribute q"); + if (!force->pair) error->all(FLERR, "A TIP4P pair style must be defined fix efield/tip4p"); int itmp; double *p_qdist = (double *) force->pair->extract("qdist", itmp); @@ -60,13 +61,12 @@ void FixEfieldTIP4P::init() int typeA = *p_typeA; int typeB = *p_typeB; - if (force->angle == nullptr || force->bond == nullptr || force->angle->setflag == nullptr || - force->bond->setflag == nullptr) - error->all(FLERR, "Bond and angle potentials must be defined for compute {}", style); + if (!force->angle || !force->bond || !force->angle->setflag || !force->bond->setflag) + error->all(FLERR, "Bond and angle potentials must be defined for fix efield/tip4p"); if ((typeA < 1) || (typeA > atom->nangletypes) || (force->angle->setflag[typeA] == 0)) - error->all(FLERR, "Bad TIP4P angle type for compute {}", style); + error->all(FLERR, "Bad TIP4P angle type for fix efield/tip4p"); if ((typeB < 1) || (typeB > atom->nbondtypes) || (force->bond->setflag[typeB] == 0)) - error->all(FLERR, "Bad TIP4P bond type for PPPM/TIP4P"); + error->all(FLERR, "Bad TIP4P bond type for fix efield/tip4p"); // determine alpha parameter From ea20c934ea5f10d06d09035093c178e14cbb2796 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 18:33:23 -0400 Subject: [PATCH 14/21] print warning when using fix efield with a TIP4P pair style --- src/fix_efield.cpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp index 3046f21ef3..d1765ed536 100644 --- a/src/fix_efield.cpp +++ b/src/fix_efield.cpp @@ -26,6 +26,7 @@ #include "input.h" #include "memory.h" #include "modify.h" +#include "pair.h" #include "region.h" #include "respa.h" #include "update.h" @@ -145,6 +146,13 @@ void FixEfield::init() if (atom->mu_flag && atom->torque_flag) muflag = 1; if (!qflag && !muflag) error->all(FLERR, "Fix {} requires atom attribute q or mu", style); + // warn if TIP4P pair style is used with plain fix efield + if ((strcmp(style, "efield") == 0) && (comm->me == 0)) { + int itmp; + if (force->pair && force->pair->extract("qdist", itmp)) + error->warning(FLERR, "Fix efield produces incorrect forces when applied to TIP4P atoms"); + } + // check variables if (xstr) { From 08153b7b4dbe4c0b430c89da68ea796f5c1d670c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 21:01:32 -0400 Subject: [PATCH 15/21] trim list of known plumed source packages. --- lib/plumed/Install.py | 20 +------------------- 1 file changed, 1 insertion(+), 19 deletions(-) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index 21e8ac51ff..9c42da4089 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -37,30 +37,12 @@ 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', \ - '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \ - '2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \ - '2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \ - '2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \ - '2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \ '2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \ - '2.8.0' : '489b23daba70da78cf0506cbc31689c6', \ '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \ '2.8.2' : '599092b6a0aa6fff992612537ad98994', \ } From e7b7d5804e46faee3f192806d788eec970013335 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 21:23:02 -0400 Subject: [PATCH 16/21] Update URL for EPEL --- doc/src/Install_linux.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index 91e7529879..53f4965e08 100644 --- a/doc/src/Install_linux.rst +++ b/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 `_ +in the `Extra Packages for Enterprise Linux (EPEL) repository `_ 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. From c9b383d3f0ca367f02d2996f8b712900066afafb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 22:18:35 -0400 Subject: [PATCH 17/21] grammar --- src/GRANULAR/fix_pour.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 477fc4720b..f92bca5073 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -678,7 +678,7 @@ void FixPour::pre_exchange() int ninserted_atoms = nnear - nprevious; int ninserted_mols = ninserted_atoms / natom; ninserted += ninserted_mols; - if (ninserted_mols < nnew && me == 0) error->warning(FLERR, "Less insertions than requested"); + if (ninserted_mols < nnew && me == 0) error->warning(FLERR, "Fewer insertions than requested"); // reset global natoms,nbonds,etc // increment maxtag_all and maxmol_all if necessary From 073f21c0d9eb653020716d488df5d4f5d86ef281 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 22:35:25 -0400 Subject: [PATCH 18/21] spelling --- doc/src/Modify_gran_sub_mod.rst | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/src/Modify_gran_sub_mod.rst b/doc/src/Modify_gran_sub_mod.rst index fe8b0da275..e1d559e6bf 100644 --- a/doc/src/Modify_gran_sub_mod.rst +++ b/doc/src/Modify_gran_sub_mod.rst @@ -20,16 +20,16 @@ parent GranSubMod class, several types of sub-model classes are derived: * 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 +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 onlyneeds 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). +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 From a232915e716126f317dcd332e9fcc1b8448214bd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 22:37:58 -0400 Subject: [PATCH 19/21] update example logs for changed granular pair style --- .../log.15Sep22.granregion.box.g++.1 | 493 -------------- .../log.15Sep22.granregion.box.g++.4 | 493 -------------- .../log.15Sep22.granregion.funnel.g++.1 | 633 ----------------- .../log.15Sep22.granregion.funnel.g++.4 | 633 ----------------- .../log.15Sep22.granregion.mixer.g++.1 | 632 ----------------- .../log.15Sep22.granregion.mixer.g++.4 | 632 ----------------- .../log.16Mar23.granregion.box.g++.1 | 484 +++++++++++++ .../log.16Mar23.granregion.box.g++.4 | 484 +++++++++++++ .../log.16Mar23.granregion.funnel.g++.1 | 635 ++++++++++++++++++ .../log.16Mar23.granregion.funnel.g++.4 | 635 ++++++++++++++++++ .../log.16Mar23.granregion.mixer.g++.1 | 634 +++++++++++++++++ .../log.16Mar23.granregion.mixer.g++.4 | 634 +++++++++++++++++ examples/pour/log.16Mar23.pour.2d.g++.1 | 125 ++++ examples/pour/log.16Mar23.pour.2d.g++.4 | 125 ++++ .../pour/log.16Mar23.pour.2d.molecule.g++.1 | 148 ++++ .../pour/log.16Mar23.pour.2d.molecule.g++.4 | 148 ++++ examples/pour/log.16Mar23.pour.g++.1 | 178 +++++ examples/pour/log.16Mar23.pour.g++.4 | 178 +++++ examples/pour/log.27Nov18.pour.2d.g++.1 | 121 ---- examples/pour/log.27Nov18.pour.2d.g++.4 | 121 ---- .../pour/log.27Nov18.pour.2d.molecule.g++.1 | 142 ---- .../pour/log.27Nov18.pour.2d.molecule.g++.4 | 142 ---- examples/pour/log.27Nov18.pour.g++.1 | 175 ----- examples/pour/log.27Nov18.pour.g++.4 | 175 ----- 24 files changed, 4408 insertions(+), 4392 deletions(-) delete mode 100644 examples/granregion/log.15Sep22.granregion.box.g++.1 delete mode 100644 examples/granregion/log.15Sep22.granregion.box.g++.4 delete mode 100644 examples/granregion/log.15Sep22.granregion.funnel.g++.1 delete mode 100644 examples/granregion/log.15Sep22.granregion.funnel.g++.4 delete mode 100644 examples/granregion/log.15Sep22.granregion.mixer.g++.1 delete mode 100644 examples/granregion/log.15Sep22.granregion.mixer.g++.4 create mode 100644 examples/granregion/log.16Mar23.granregion.box.g++.1 create mode 100644 examples/granregion/log.16Mar23.granregion.box.g++.4 create mode 100644 examples/granregion/log.16Mar23.granregion.funnel.g++.1 create mode 100644 examples/granregion/log.16Mar23.granregion.funnel.g++.4 create mode 100644 examples/granregion/log.16Mar23.granregion.mixer.g++.1 create mode 100644 examples/granregion/log.16Mar23.granregion.mixer.g++.4 create mode 100644 examples/pour/log.16Mar23.pour.2d.g++.1 create mode 100644 examples/pour/log.16Mar23.pour.2d.g++.4 create mode 100644 examples/pour/log.16Mar23.pour.2d.molecule.g++.1 create mode 100644 examples/pour/log.16Mar23.pour.2d.molecule.g++.4 create mode 100644 examples/pour/log.16Mar23.pour.g++.1 create mode 100644 examples/pour/log.16Mar23.pour.g++.4 delete mode 100644 examples/pour/log.27Nov18.pour.2d.g++.1 delete mode 100644 examples/pour/log.27Nov18.pour.2d.g++.4 delete mode 100644 examples/pour/log.27Nov18.pour.2d.molecule.g++.1 delete mode 100644 examples/pour/log.27Nov18.pour.2d.molecule.g++.4 delete mode 100644 examples/pour/log.27Nov18.pour.g++.1 delete mode 100644 examples/pour/log.27Nov18.pour.g++.4 diff --git a/examples/granregion/log.15Sep22.granregion.box.g++.1 b/examples/granregion/log.15Sep22.granregion.box.g++.1 deleted file mode 100644 index 0df89d49ee..0000000000 --- a/examples/granregion/log.15Sep22.granregion.box.g++.1 +++ /dev/null @@ -1,493 +0,0 @@ -LAMMPS (15 Sep 2022) -# 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: Less insertions than requested (../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: Less insertions than requested (../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: Less insertions than requested (../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 0.078687 on 1 procs for 5000 steps with 100 atoms - -Performance: 27450544.413 tau/day, 63542.927 timesteps/s, 6.354 Matom-step/s -80.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0084151 | 0.0084151 | 0.0084151 | 0.0 | 10.69 -Neigh | 0.012728 | 0.012728 | 0.012728 | 0.0 | 16.18 -Comm | 0.0056143 | 0.0056143 | 0.0056143 | 0.0 | 7.14 -Output | 0.00051411 | 0.00051411 | 0.00051411 | 0.0 | 0.65 -Modify | 0.041412 | 0.041412 | 0.041412 | 0.0 | 52.63 -Other | | 0.01 | | | 12.71 - -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 -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) = 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 0.59595162 0.018005316 - 6600 100 1.2039397 1.2039397 0.60567524 0.021604669 - 6700 100 1.2269911 1.2269911 0.61770224 0.018907995 - 6800 100 1.2447035 1.2447035 0.6257652 0.02053766 - 6900 100 1.2625323 1.2625323 0.63486698 0.020106134 - 7000 100 1.2617127 1.2617127 0.63318163 0.019670429 - 7100 100 1.260715 1.260715 0.63311254 0.019810631 - 7200 100 1.2790404 1.2790404 0.64079001 0.020218903 - 7300 100 1.2760228 1.2760228 0.6395331 0.021749906 - 7400 100 1.2799658 1.2799658 0.64139084 0.020472922 - 7500 100 1.2846473 1.2846473 0.64343085 0.020610025 - 7600 100 1.2883965 1.2883965 0.64491873 0.02074884 - 7700 100 1.2926891 1.2926891 0.64684545 0.020599654 - 7800 100 1.3032201 1.3032201 0.65119455 0.02183405 - 7900 100 1.3025628 1.3025628 0.65068661 0.021248589 - 8000 100 1.3052302 1.3052302 0.65208602 0.021399549 - 8100 100 1.3069867 1.3069867 0.65304849 0.021254794 - 8200 100 1.3092024 1.3092024 0.6543837 0.021220909 - 8300 100 1.3101468 1.3101468 0.65519741 0.021328361 - 8400 100 1.3116005 1.3116005 0.65545253 0.021493555 - 8500 100 1.3153616 1.3153616 0.65731542 0.021433279 - 8600 100 1.3164556 1.3164556 0.65791227 0.021531213 - 8700 100 1.3187245 1.3187245 0.65915974 0.02170181 - 8800 100 1.3215981 1.3215981 0.66036644 0.022358849 - 8900 100 1.3206845 1.3206845 0.65984651 0.021901337 - 9000 100 1.3213046 1.3213046 0.66020378 0.021876353 - 9100 100 1.3225084 1.3225084 0.66088847 0.021811098 - 9200 100 1.3240309 1.3240309 0.66180646 0.021768929 - 9300 100 1.325458 1.325458 0.66280401 0.02165852 - 9400 100 1.3322968 1.3322968 0.66615126 0.022139018 - 9500 100 1.3416035 1.3416035 0.67030794 0.022243129 - 9600 100 1.3353326 1.3353326 0.66692811 0.022622122 - 9700 100 1.336265 1.336265 0.66727395 0.022171165 - 9800 100 1.3344531 1.3344531 0.66634538 0.022025131 - 9900 100 1.3337098 1.3337098 0.66601721 0.022111706 - 10000 100 1.3335539 1.3335539 0.66597627 0.022133817 -Loop time of 0.235008 on 1 procs for 5000 steps with 100 atoms - -Performance: 9191156.994 tau/day, 21275.826 timesteps/s, 2.128 Matom-step/s -94.1% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.029846 | 0.029846 | 0.029846 | 0.0 | 12.70 -Neigh | 0.030211 | 0.030211 | 0.030211 | 0.0 | 12.86 -Comm | 0.005731 | 0.005731 | 0.005731 | 0.0 | 2.44 -Output | 0.00051873 | 0.00051873 | 0.00051873 | 0.0 | 0.22 -Modify | 0.1583 | 0.1583 | 0.1583 | 0.0 | 67.36 -Other | | 0.01041 | | | 4.43 - -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 1.3335539 1.3335539 0.66597627 0.022207076 - 10100 100 0.29976134 0.29976134 0.1752962 0.0091355801 - 10200 100 0.1548002 0.1548002 0.1005356 0.0062509071 - 10300 100 0.082468613 0.082468613 0.066729575 0.0017315098 - 10400 100 0.06731284 0.06731284 0.056685383 0.0011965765 - 10500 100 0.050167538 0.050167538 0.042388389 0.0010830279 - 10600 100 0.041091371 0.041091371 0.034743534 0.00092984522 - 10700 100 0.033199041 0.033199041 0.027954031 0.0018451338 - 10800 100 0.027880411 0.027880411 0.024437224 0.0013039536 - 10900 100 0.024634597 0.024634597 0.021815184 0.00030935286 - 11000 100 0.020741105 0.020741105 0.018754221 0.0006306901 - 11100 100 0.017210914 0.017210914 0.015842306 0.00075930229 - 11200 100 0.01254319 0.01254319 0.012145795 0.00047388541 - 11300 100 0.010032468 0.010032468 0.0095918697 0.0014677116 - 11400 100 0.0081538458 0.0081538458 0.0080985914 0.00032485316 - 11500 100 0.0072918155 0.0072918155 0.0070156789 0.00023642827 - 11600 100 0.0070136586 0.0070136586 0.0067263114 7.8490444e-05 - 11700 100 0.0061722946 0.0061722946 0.0058832419 0.00013450793 - 11800 100 0.0052444487 0.0052444487 0.0049294304 8.6973121e-05 - 11900 100 0.0048212279 0.0048212279 0.0045261412 0.00010458031 - 12000 100 0.0046782797 0.0046782797 0.0044011937 0.00018881094 - 12100 100 0.0042066617 0.0042066617 0.0040330976 0.00015507521 - 12200 100 0.0038529032 0.0038529032 0.003664712 1.1476621e-05 - 12300 100 0.0033203238 0.0033203238 0.0032404054 0.00027622191 - 12400 100 0.003113731 0.003113731 0.0030491123 3.8532421e-05 - 12500 100 0.0029925149 0.0029925149 0.0029415075 4.2673261e-05 - 12600 100 0.0028383323 0.0028383323 0.0027902992 9.328552e-05 - 12700 100 0.0026386104 0.0026386104 0.0026095714 7.7740986e-05 - 12800 100 0.0023509873 0.0023509873 0.0023518594 3.1944764e-05 - 12900 100 0.0022296104 0.0022296104 0.0022030693 4.5393502e-05 - 13000 100 0.0021991358 0.0021991358 0.0021560478 0.0001221212 - 13100 100 0.0021011001 0.0021011001 0.0020752855 2.4605107e-05 - 13200 100 0.002004495 0.002004495 0.0020040212 2.4805625e-05 - 13300 100 0.0018394135 0.0018394135 0.0018288384 6.2227066e-05 - 13400 100 0.0016314086 0.0016314086 0.0016058102 0.00010372886 - 13500 100 0.0015042857 0.0015042857 0.0014660263 0.00020805178 - 13600 100 0.0013584764 0.0013584764 0.0013177418 5.1603333e-05 - 13700 100 0.0012407449 0.0012407449 0.0011902637 8.87401e-05 - 13800 100 0.0011673364 0.0011673364 0.0011324247 2.3668551e-05 - 13900 100 0.0011429204 0.0011429204 0.0011072347 1.414364e-05 - 14000 100 0.001087543 0.001087543 0.0010616439 3.0874865e-05 - 14100 100 0.00098839393 0.00098839393 0.00096445684 6.5331515e-05 - 14200 100 0.00095139076 0.00095139076 0.00093658993 2.5649208e-05 - 14300 100 0.00089532494 0.00089532494 0.00082626435 2.6200482e-05 - 14400 100 0.00077973015 0.00077973015 0.00070733785 2.29298e-05 - 14500 100 0.00068559117 0.00068559117 0.00062297009 8.4841907e-06 - 14600 100 0.00059199698 0.00059199698 0.00052453148 1.2737231e-05 - 14700 100 0.00055052378 0.00055052378 0.00048459372 1.3028328e-05 - 14800 100 0.00049397913 0.00049397913 0.00044094284 6.1129918e-06 - 14900 100 0.00048082746 0.00048082746 0.00043128724 3.7301936e-06 - 15000 100 0.00046847825 0.00046847825 0.00041484245 5.7974184e-06 -Loop time of 0.0802044 on 1 procs for 5000 steps with 100 atoms - -Performance: 26931180.398 tau/day, 62340.695 timesteps/s, 6.234 Matom-step/s -82.1% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0080809 | 0.0080809 | 0.0080809 | 0.0 | 10.08 -Neigh | 0.0048815 | 0.0048815 | 0.0048815 | 0.0 | 6.09 -Comm | 0.0055605 | 0.0055605 | 0.0055605 | 0.0 | 6.93 -Output | 0.00050386 | 0.00050386 | 0.00050386 | 0.0 | 0.63 -Modify | 0.051104 | 0.051104 | 0.051104 | 0.0 | 63.72 -Other | | 0.01007 | | | 12.56 - -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 = 100 -Dangerous builds = 0 - -region container delete -variable theta equal (step-15000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes - Step Atoms Temp c_1 c_2 Press - 15000 100 0.00046847825 0.00046847825 0.00041484245 5.7974184e-06 - 15100 100 0.96677694 0.96677694 0.64420785 0.01431184 - 15200 100 1.0659255 1.0659255 0.69293741 0.013240486 - 15300 100 1.1647631 1.1647631 0.75191941 0.014622673 - 15400 100 1.3411593 1.3411593 0.85696383 0.02561549 - 15500 100 1.6033758 1.6033758 0.99094919 0.026221789 - 15600 100 1.7889645 1.7889645 1.075315 0.024116301 - 15700 100 1.8077023 1.8077023 1.0842652 0.031781756 - 15800 100 2.0252655 2.0252655 1.1517407 0.037201818 - 15900 100 2.1479427 2.1479427 1.2061238 0.027668435 - 16000 100 2.1788838 2.1788838 1.2205599 0.029114273 - 16100 100 2.3257431 2.3257431 1.2921157 0.035663063 - 16200 100 2.3885449 2.3885449 1.3282237 0.032255517 - 16300 100 2.3670966 2.3670966 1.3091694 0.029579008 - 16400 100 2.5097781 2.5097781 1.3712036 0.034579196 - 16500 100 2.6440883 2.6440883 1.4440043 0.03347813 - 16600 100 2.7230084 2.7230084 1.481565 0.036660339 - 16700 100 2.8246108 2.8246108 1.5298387 0.035623641 - 16800 100 3.0338694 3.0338694 1.6333504 0.038818594 - 16900 100 3.1219584 3.1219584 1.6790766 0.043444123 - 17000 100 3.4103817 3.4103817 1.8222668 0.044524654 - 17100 100 3.3869069 3.3869069 1.8170743 0.050670801 - 17200 100 3.4220314 3.4220314 1.8312364 0.045956123 - 17300 100 3.396894 3.396894 1.8158291 0.050420297 - 17400 100 3.4508224 3.4508224 1.8429996 0.049923733 - 17500 100 3.5039601 3.5039601 1.8822352 0.051047713 - 17600 100 3.3743905 3.3743905 1.8380347 0.047922214 - 17700 100 3.3729709 3.3729709 1.8224123 0.04758126 - 17800 100 3.3237798 3.3237798 1.7962316 0.045427975 - 17900 100 3.2441052 3.2441052 1.7782748 0.044651231 - 18000 100 3.1169205 3.1169205 1.704639 0.047440495 - 18100 100 3.1704608 3.1704608 1.7326375 0.045656546 - 18200 100 3.1113438 3.1113438 1.7002232 0.041619255 - 18300 100 3.2506111 3.2506111 1.7693075 0.048028527 - 18400 100 3.3840681 3.3840681 1.8370672 0.04443243 - 18500 100 3.4822823 3.4822823 1.9125273 0.043687118 - 18600 100 3.5214372 3.5214372 1.9364829 0.049798605 - 18700 100 3.5439229 3.5439229 1.9441301 0.046240266 - 18800 100 3.6046761 3.6046761 1.9791448 0.054369382 - 18900 100 3.8598403 3.8598403 2.0999449 0.049863074 - 19000 100 3.8606461 3.8606461 2.0885493 0.050269245 - 19100 100 4.076627 4.076627 2.2025766 0.058050893 - 19200 100 3.8280814 3.8280814 2.0749884 0.05730905 - 19300 100 3.8211633 3.8211633 2.0759453 0.05145071 - 19400 100 3.7726284 3.7726284 2.0466555 0.053566404 - 19500 100 3.7468403 3.7468403 2.03218 0.048422025 - 19600 100 3.6408955 3.6408955 1.9873843 0.046565134 - 19700 100 3.6454187 3.6454187 2.0042204 0.049299897 - 19800 100 3.5165071 3.5165071 1.937379 0.046319859 - 19900 100 3.4670702 3.4670702 1.9140316 0.045650114 - 20000 100 3.6114294 3.6114294 1.9798674 0.05431148 -Loop time of 0.203164 on 1 procs for 5000 steps with 100 atoms - -Performance: 10631806.993 tau/day, 24610.664 timesteps/s, 2.461 Matom-step/s -92.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.01242 | 0.01242 | 0.01242 | 0.0 | 6.11 -Neigh | 0.044478 | 0.044478 | 0.044478 | 0.0 | 21.89 -Comm | 0.0057766 | 0.0057766 | 0.0057766 | 0.0 | 2.84 -Output | 0.00051702 | 0.00051702 | 0.00051702 | 0.0 | 0.25 -Modify | 0.12923 | 0.12923 | 0.12923 | 0.0 | 63.61 -Other | | 0.01074 | | | 5.29 - -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: 142 ave 142 max 142 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 142 -Ave neighs/atom = 1.42 -Neighbor list builds = 909 -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 3.6114294 3.6114294 1.9798674 0.053887263 - 20100 100 1.0907336 1.0907336 0.69799767 0.013925984 - 20200 100 0.92304387 0.92304387 0.59520318 0.012377709 - 20300 100 0.84004201 0.84004201 0.55081472 0.012108246 - 20400 100 0.89491209 0.89491209 0.56269969 0.01221427 - 20500 100 0.92011482 0.92011482 0.56971815 0.011353588 - 20600 100 0.95722998 0.95722998 0.58038747 0.01185569 - 20700 100 0.92635786 0.92635786 0.55373959 0.011953734 - 20800 100 0.93088162 0.93088162 0.55094813 0.012887472 - 20900 100 0.97288373 0.97288373 0.56309599 0.013731021 - 21000 100 0.63378762 0.63378762 0.3779177 0.010114787 - 21100 100 0.34618473 0.34618473 0.21652381 0.0070717708 - 21200 100 0.18660008 0.18660008 0.1302051 0.006504227 - 21300 100 0.13917709 0.13917709 0.09667499 0.0032593765 - 21400 100 0.11627047 0.11627047 0.080272858 0.0028891045 - 21500 100 0.086269781 0.086269781 0.064184981 0.0019374959 - 21600 100 0.08052393 0.08052393 0.059561101 0.001214522 - 21700 100 0.036026032 0.036026032 0.030243348 0.001199233 - 21800 100 0.02392645 0.02392645 0.022284244 0.00060060634 - 21900 100 0.016991266 0.016991266 0.017366625 0.00065672411 - 22000 100 0.016974877 0.016974877 0.016399245 0.0005903103 - 22100 100 0.015491818 0.015491818 0.014806105 0.00051181051 - 22200 100 0.011908698 0.011908698 0.011206673 0.00099478656 - 22300 100 0.010002714 0.010002714 0.0093749794 0.00028214624 - 22400 100 0.0081652616 0.0081652616 0.0079594664 0.00026841276 - 22500 100 0.0067602843 0.0067602843 0.0067498831 0.00019472612 - 22600 100 0.0061024058 0.0061024058 0.0062958451 0.00016615781 - 22700 100 0.005331422 0.005331422 0.0056152366 0.00021543475 - 22800 100 0.0040796708 0.0040796708 0.004140932 0.00024397062 - 22900 100 0.0042042089 0.0042042089 0.0040406804 0.00015880055 - 23000 100 0.0056083872 0.0056083872 0.0046056699 0.00029203396 - 23100 100 0.0035006398 0.0035006398 0.003343101 0.00010571574 - 23200 100 0.0032402473 0.0032402473 0.003122476 0.00012784403 - 23300 100 0.0030100724 0.0030100724 0.0029649423 8.5613724e-05 - 23400 100 0.002746305 0.002746305 0.0027519317 9.6521844e-05 - 23500 100 0.0028543876 0.0028543876 0.002842845 0.00012566665 - 23600 100 0.0036979234 0.0036979234 0.0032448309 8.6321879e-05 - 23700 100 0.0030503565 0.0030503565 0.0027392305 5.9716835e-05 - 23800 100 0.0021564041 0.0021564041 0.0022097768 0.00028317769 - 23900 100 0.0018905956 0.0018905956 0.0020002233 4.5205733e-05 - 24000 100 0.0015705513 0.0015705513 0.0017262538 0.00026550225 - 24100 100 0.0013341334 0.0013341334 0.0015663921 4.8307183e-05 - 24200 100 0.0012426828 0.0012426828 0.0014960127 5.5195907e-05 - 24300 100 0.0011933799 0.0011933799 0.0014508697 5.2781568e-05 - 24400 100 0.0010126015 0.0010126015 0.0012821281 0.00011096457 - 24500 100 0.00094102576 0.00094102576 0.0012265703 3.3454252e-05 - 24600 100 0.00092243997 0.00092243997 0.0011970533 3.7288789e-05 - 24700 100 0.00080565605 0.00080565605 0.0010864406 0.00015797228 - 24800 100 0.00075303124 0.00075303124 0.0010103671 5.4727635e-05 - 24900 100 0.00074808599 0.00074808599 0.0010053951 8.6607732e-05 - 25000 100 0.00071720457 0.00071720457 0.00096622937 0.00015861964 -Loop time of 0.0845534 on 1 procs for 5000 steps with 100 atoms - -Performance: 25545994.179 tau/day, 59134.246 timesteps/s, 5.913 Matom-step/s -90.2% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0091411 | 0.0091411 | 0.0091411 | 0.0 | 10.81 -Neigh | 0.013557 | 0.013557 | 0.013557 | 0.0 | 16.03 -Comm | 0.0056205 | 0.0056205 | 0.0056205 | 0.0 | 6.65 -Output | 0.0005087 | 0.0005087 | 0.0005087 | 0.0 | 0.60 -Modify | 0.045578 | 0.045578 | 0.045578 | 0.0 | 53.90 -Other | | 0.01015 | | | 12.00 - -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 = 286 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/granregion/log.15Sep22.granregion.box.g++.4 b/examples/granregion/log.15Sep22.granregion.box.g++.4 deleted file mode 100644 index 3e83d3bb04..0000000000 --- a/examples/granregion/log.15Sep22.granregion.box.g++.4 +++ /dev/null @@ -1,493 +0,0 @@ -LAMMPS (15 Sep 2022) -# 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: Less insertions than requested (../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: Less insertions than requested (../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: Less insertions than requested (../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 0.0046170774 - 1500 99 0.31486691 0.31486691 0.17429054 0.0064903404 - 1600 99 0.26369 0.26369 0.15095263 0.0045226821 - 1700 100 0.19259352 0.19259352 0.11308184 0.0073603886 - 1800 100 0.1372448 0.1372448 0.083273652 0.0058163062 - 1900 100 0.077253038 0.077253038 0.053166156 0.0017440856 - 2000 100 0.065472093 0.065472093 0.04375349 0.0018416047 - 2100 100 0.057213469 0.057213469 0.037773954 0.001226231 - 2200 100 0.058857437 0.058857437 0.0372655 0.00090812381 - 2300 100 0.035066108 0.035066108 0.025934054 0.00072114554 - 2400 100 0.021272125 0.021272125 0.016635107 0.0018506654 - 2500 100 0.015530432 0.015530432 0.012533546 0.0013883971 - 2600 100 0.012603946 0.012603946 0.0096981459 0.00038648118 - 2700 100 0.0097347475 0.0097347475 0.0076016624 0.00057313888 - 2800 100 0.0067081771 0.0067081771 0.0056944431 0.00085080075 - 2900 100 0.0089177981 0.0089177981 0.0065036822 0.00028986539 - 3000 100 0.0057840287 0.0057840287 0.0044989265 0.00016111737 - 3100 100 0.0038909621 0.0038909621 0.0031511938 0.0001708892 - 3200 100 0.0029043214 0.0029043214 0.0025807767 9.2473673e-05 - 3300 100 0.0022769336 0.0022769336 0.0021487157 0.00022312666 - 3400 100 0.0015571397 0.0015571397 0.0016669068 0.0003381372 - 3500 100 0.0015978184 0.0015978184 0.001707772 4.9930818e-05 - 3600 100 0.0023358916 0.0023358916 0.0020709426 9.7687609e-05 - 3700 100 0.0011186736 0.0011186736 0.0012146914 9.3338234e-05 - 3800 100 0.0011657036 0.0011657036 0.0012313764 3.1931251e-05 - 3900 100 0.0014998387 0.0014998387 0.0014015491 2.4226798e-05 - 4000 100 0.0010858335 0.0010858335 0.0010623286 1.6359241e-05 - 4100 100 0.0010464314 0.0010464314 0.0010123557 1.2949588e-05 - 4200 100 0.0010022428 0.0010022428 0.00097338971 1.2402332e-05 - 4300 100 0.00080622372 0.00080622372 0.00084329652 0.00033857037 - 4400 100 0.00073613921 0.00073613921 0.00078373608 1.0103949e-05 - 4500 100 0.00071402196 0.00071402196 0.00076658004 8.8360218e-06 - 4600 100 0.00064851765 0.00064851765 0.00071533461 1.0736438e-05 - 4700 100 0.00061146699 0.00061146699 0.00068274687 4.1341755e-06 - 4800 100 0.00059511472 0.00059511472 0.0006625527 7.3645447e-06 - 4900 100 0.00057700347 0.00057700347 0.0006468562 1.5411897e-05 - 5000 100 0.00056205001 0.00056205001 0.00063592505 7.8813845e-06 -Loop time of 0.0856033 on 4 procs for 5000 steps with 100 atoms - -Performance: 25232672.400 tau/day, 58408.964 timesteps/s, 5.841 Matom-step/s -88.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0034695 | 0.0050634 | 0.0068805 | 2.2 | 5.91 -Neigh | 0.0016916 | 0.0024175 | 0.0032212 | 1.5 | 2.82 -Comm | 0.020003 | 0.026482 | 0.033796 | 3.5 | 30.94 -Output | 0.0010864 | 0.001327 | 0.0014374 | 0.4 | 1.55 -Modify | 0.0067352 | 0.015857 | 0.025751 | 7.2 | 18.52 -Other | | 0.03446 | | | 40.25 - -Nlocal: 25 ave 53 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 4 ave 8 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 40.5 ave 92 max 0 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 162 -Ave neighs/atom = 1.62 -Neighbor list builds = 288 -Dangerous builds = 0 - -region container delete -variable theta equal (step-5000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1 -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -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) = 5.609 | 5.672 | 5.734 Mbytes - Step Atoms Temp c_1 c_2 Press - 5000 100 0.00056205001 0.00056205001 0.00063592505 7.871665e-06 - 5100 100 0.59585977 0.59585977 0.32464933 0.0141718 - 5200 100 0.67306764 0.67306764 0.35872096 0.013373672 - 5300 100 0.76065187 0.76065187 0.39925025 0.011460301 - 5400 100 0.87984446 0.87984446 0.45261417 0.013937042 - 5500 100 0.95548319 0.95548319 0.48706892 0.013601658 - 5600 100 0.9993278 0.9993278 0.50830306 0.015663766 - 5700 100 1.0449415 1.0449415 0.52967249 0.016797841 - 5800 100 1.0767598 1.0767598 0.54508699 0.016128855 - 5900 100 1.118688 1.118688 0.56530849 0.016830117 - 6000 100 1.1535698 1.1535698 0.58290663 0.01715335 - 6100 100 1.1753828 1.1753828 0.59419088 0.019273207 - 6200 100 1.1994171 1.1994171 0.60433264 0.018391566 - 6300 100 1.2244707 1.2244707 0.61626199 0.018842556 - 6400 100 1.2507994 1.2507994 0.62829386 0.019538413 - 6500 100 1.2684644 1.2684644 0.63747702 0.020794729 - 6600 100 1.2704726 1.2704726 0.63929889 0.020253985 - 6700 100 1.2737302 1.2737302 0.63970688 0.020858602 - 6800 100 1.287922 1.287922 0.64460894 0.021589773 - 6900 100 1.3028782 1.3028782 0.65197802 0.02135295 - 7000 100 1.306633 1.306633 0.65371741 0.021291182 - 7100 100 1.3161393 1.3161393 0.65785404 0.022554896 - 7200 100 1.3228158 1.3228158 0.6609031 0.021811977 - 7300 100 1.3245632 1.3245632 0.66161966 0.02206776 - 7400 100 1.3266822 1.3266822 0.662738 0.022070761 - 7500 100 1.3265138 1.3265138 0.6624472 0.021944768 - 7600 100 1.3286802 1.3286802 0.66338775 0.0219393 - 7700 100 1.332829 1.332829 0.66547051 0.022142398 - 7800 100 1.3323535 1.3323535 0.66534513 0.022787777 - 7900 100 1.3372424 1.3372424 0.66777556 0.02192759 - 8000 100 1.3396201 1.3396201 0.66910123 0.022439596 - 8100 100 1.3422271 1.3422271 0.67060566 0.023784952 - 8200 100 1.3468062 1.3468062 0.6728991 0.02243345 - 8300 100 1.3439408 1.3439408 0.6717529 0.022312339 - 8400 100 1.3484134 1.3484134 0.67346027 0.022770922 - 8500 100 1.3490032 1.3490032 0.67378177 0.022427863 - 8600 100 1.349789 1.349789 0.67398897 0.022494049 - 8700 100 1.3513512 1.3513512 0.67475613 0.022413559 - 8800 100 1.3535168 1.3535168 0.67589784 0.022356566 - 8900 100 1.3505765 1.3505765 0.67442168 0.022240615 - 9000 100 1.3499918 1.3499918 0.67419831 0.02226049 - 9100 100 1.3518103 1.3518103 0.67489482 0.022399038 - 9200 100 1.3526275 1.3526275 0.67529852 0.022395079 - 9300 100 1.353741 1.353741 0.67585205 0.022471008 - 9400 100 1.3538758 1.3538758 0.67589523 0.022461734 - 9500 100 1.3537199 1.3537199 0.67586527 0.022370169 - 9600 100 1.3539788 1.3539788 0.67602899 0.022400771 - 9700 100 1.3544874 1.3544874 0.67619552 0.022648464 - 9800 100 1.3555422 1.3555422 0.67666186 0.022367319 - 9900 100 1.3560106 1.3560106 0.6768751 0.02236585 - 10000 100 1.3563578 1.3563578 0.6770434 0.022359307 -Loop time of 0.139615 on 4 procs for 5000 steps with 100 atoms - -Performance: 15471121.710 tau/day, 35812.782 timesteps/s, 3.581 Matom-step/s -89.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0034672 | 0.011349 | 0.019511 | 7.2 | 8.13 -Neigh | 0.0032972 | 0.0053674 | 0.0074946 | 2.8 | 3.84 -Comm | 0.011049 | 0.018572 | 0.027876 | 5.6 | 13.30 -Output | 0.0010807 | 0.0015593 | 0.0018738 | 0.8 | 1.12 -Modify | 0.013556 | 0.040435 | 0.066715 | 13.0 | 28.96 -Other | | 0.06233 | | | 44.65 - -Nlocal: 25 ave 52 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 3 ave 6 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 48.25 ave 109 max 0 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 193 -Ave neighs/atom = 1.93 -Neighbor list builds = 626 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes - Step Atoms Temp c_1 c_2 Press - 10000 100 1.3563578 1.3563578 0.6770434 0.022433108 - 10100 100 0.32881547 0.32881547 0.18968913 0.0063460187 - 10200 100 0.19880113 0.19880113 0.12812646 0.0074601538 - 10300 100 0.12614062 0.12614062 0.090121373 0.0028337336 - 10400 100 0.088358363 0.088358363 0.067236815 0.0020269846 - 10500 100 0.071199344 0.071199344 0.055567135 0.0016191769 - 10600 100 0.053909616 0.053909616 0.042301996 0.00098643468 - 10700 100 0.039560745 0.039560745 0.032482256 0.00089240864 - 10800 100 0.032130432 0.032130432 0.02705329 0.00058669881 - 10900 100 0.02462494 0.02462494 0.021121496 0.0017376127 - 11000 100 0.020941068 0.020941068 0.017866781 0.00031112553 - 11100 100 0.016775675 0.016775675 0.014620214 0.00026856842 - 11200 100 0.015005732 0.015005732 0.012803923 0.00067036626 - 11300 100 0.012099209 0.012099209 0.010308221 0.00032666902 - 11400 100 0.010559421 0.010559421 0.0090243729 0.00013645685 - 11500 100 0.0093738615 0.0093738615 0.0080176514 0.00098541099 - 11600 100 0.0081900702 0.0081900702 0.0070256953 0.00025935992 - 11700 100 0.0068100165 0.0068100165 0.0058703223 0.00014866816 - 11800 100 0.0060475708 0.0060475708 0.0052518105 0.00017895168 - 11900 100 0.0055607485 0.0055607485 0.0047184164 0.00011358846 - 12000 100 0.0053149064 0.0053149064 0.0045168418 0.00015222428 - 12100 100 0.0050909525 0.0050909525 0.0043196952 6.3000537e-05 - 12200 100 0.0041810842 0.0041810842 0.0036835522 4.6423956e-05 - 12300 100 0.0034305227 0.0034305227 0.0031222649 0.00020251115 - 12400 100 0.0031763077 0.0031763077 0.0028956456 0.00030307787 - 12500 100 0.0027440829 0.0027440829 0.0025087304 0.00010418607 - 12600 100 0.0024581964 0.0024581964 0.0022200229 3.042018e-05 - 12700 100 0.002259527 0.002259527 0.0020708869 4.192368e-05 - 12800 100 0.0019143448 0.0019143448 0.0018088032 4.6200439e-05 - 12900 100 0.0017935964 0.0017935964 0.0017028317 2.2195756e-05 - 13000 100 0.0017286429 0.0017286429 0.0016396753 2.3108871e-05 - 13100 100 0.0017055291 0.0017055291 0.0016122058 2.2444611e-05 - 13200 100 0.0016539275 0.0016539275 0.0015570166 2.0467353e-05 - 13300 100 0.0015777788 0.0015777788 0.0014852505 1.9525012e-05 - 13400 100 0.0015372199 0.0015372199 0.0014497102 2.3203566e-05 - 13500 100 0.0015066638 0.0015066638 0.0014097203 1.8644964e-05 - 13600 100 0.0012290618 0.0012290618 0.0012056216 1.3235643e-05 - 13700 100 0.0011781948 0.0011781948 0.0011685226 3.4312262e-05 - 13800 100 0.0011530136 0.0011530136 0.0011433171 2.8832126e-05 - 13900 100 0.0011085224 0.0011085224 0.0011052764 1.444139e-05 - 14000 100 0.0010656788 0.0010656788 0.0010702461 1.3187775e-05 - 14100 100 0.001029277 0.001029277 0.0010469537 1.2837267e-05 - 14200 100 0.0009750904 0.0009750904 0.0009915384 1.209089e-05 - 14300 100 0.00094893337 0.00094893337 0.00096909301 1.1743051e-05 - 14400 100 0.00087708427 0.00087708427 0.00087575318 1.9027338e-05 - 14500 100 0.00086229913 0.00086229913 0.0008643568 1.0670952e-05 - 14600 100 0.00084206808 0.00084206808 0.0008268172 3.2391722e-05 - 14700 100 0.00077682873 0.00077682873 0.00077186085 9.6132555e-06 - 14800 100 0.00074736908 0.00074736908 0.00074958372 9.2486924e-06 - 14900 100 0.00074456847 0.00074456847 0.00074779946 9.2140349e-06 - 15000 100 0.00073830282 0.00073830282 0.0007426924 9.1364974e-06 -Loop time of 0.0808149 on 4 procs for 5000 steps with 100 atoms - -Performance: 26727738.394 tau/day, 61869.765 timesteps/s, 6.187 Matom-step/s -86.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0034354 | 0.0050332 | 0.0069329 | 2.2 | 6.23 -Neigh | 0.00051999 | 0.00084906 | 0.0012075 | 0.0 | 1.05 -Comm | 0.0063631 | 0.014527 | 0.023754 | 6.8 | 17.98 -Output | 0.0010373 | 0.001342 | 0.001464 | 0.5 | 1.66 -Modify | 0.0051837 | 0.017338 | 0.031605 | 9.3 | 21.45 -Other | | 0.04173 | | | 51.63 - -Nlocal: 25 ave 53 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 3.75 ave 8 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 39.25 ave 82 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 157 -Ave neighs/atom = 1.57 -Neighbor list builds = 100 -Dangerous builds = 0 - -region container delete -variable theta equal (step-15000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes - Step Atoms Temp c_1 c_2 Press - 15000 100 0.00073830282 0.00073830282 0.0007426924 9.1364974e-06 - 15100 100 1.1048281 1.1048281 0.7023727 0.018379275 - 15200 100 1.2022249 1.2022249 0.77748962 0.015662439 - 15300 100 1.2561351 1.2561351 0.82563065 0.01835048 - 15400 100 1.4372446 1.4372446 0.92907923 0.02087065 - 15500 100 1.6414713 1.6414713 1.0284489 0.025654324 - 15600 100 1.7844655 1.7844655 1.0861866 0.025170346 - 15700 100 2.034248 2.034248 1.2017171 0.040341642 - 15800 100 2.1253699 2.1253699 1.2228657 0.029297194 - 15900 100 2.1940232 2.1940232 1.2470589 0.033866758 - 16000 100 2.2624419 2.2624419 1.2828225 0.030063645 - 16100 100 2.3208536 2.3208536 1.3118956 0.0323489 - 16200 100 2.3564971 2.3564971 1.3261173 0.032882494 - 16300 100 2.3956066 2.3956066 1.3260307 0.03292972 - 16400 100 2.5025831 2.5025831 1.3817693 0.031132988 - 16500 100 2.5947914 2.5947914 1.4152657 0.036126782 - 16600 100 2.7688769 2.7688769 1.4975686 0.037497127 - 16700 100 2.812503 2.812503 1.5216659 0.039316167 - 16800 100 2.8977424 2.8977424 1.5599254 0.039996029 - 16900 100 3.045802 3.045802 1.6332888 0.041406156 - 17000 100 3.2195366 3.2195366 1.7247171 0.040023634 - 17100 100 3.2597294 3.2597294 1.7527958 0.04828292 - 17200 100 3.293587 3.293587 1.7693254 0.044001441 - 17300 100 3.1861836 3.1861836 1.7142076 0.049158822 - 17400 100 3.4593561 3.4593561 1.8426619 0.053469673 - 17500 100 3.3813767 3.3813767 1.8079958 0.058776299 - 17600 100 3.5834203 3.5834203 1.9094759 0.053256842 - 17700 100 3.2243306 3.2243306 1.7425111 0.064354789 - 17800 100 3.358228 3.358228 1.8202932 0.046798524 - 17900 100 3.2257908 3.2257908 1.7678964 0.043655204 - 18000 100 3.237732 3.237732 1.7598181 0.050850672 - 18100 100 3.2042441 3.2042441 1.751979 0.045582006 - 18200 100 3.1562775 3.1562775 1.7336068 0.042210739 - 18300 100 3.2630507 3.2630507 1.7925333 0.046412778 - 18400 100 3.4150588 3.4150588 1.8668408 0.044386435 - 18500 100 3.4913198 3.4913198 1.9125495 0.043329829 - 18600 100 3.5290036 3.5290036 1.9184098 0.048302721 - 18700 100 3.4852698 3.4852698 1.8865833 0.059566124 - 18800 100 3.7157551 3.7157551 2.0082235 0.051356305 - 18900 100 3.9504619 3.9504619 2.1377018 0.051553987 - 19000 100 3.9711274 3.9711274 2.1549121 0.051555312 - 19100 100 3.90954 3.90954 2.1135174 0.0548311 - 19200 100 4.0672819 4.0672819 2.1837089 0.064431553 - 19300 100 3.998355 3.998355 2.1572884 0.056830399 - 19400 100 3.9172127 3.9172127 2.1130164 0.051264041 - 19500 100 3.9120291 3.9120291 2.1088399 0.052545115 - 19600 100 3.8613614 3.8613614 2.0752883 0.055466569 - 19700 100 3.8428824 3.8428824 2.0787804 0.05129261 - 19800 100 3.5686751 3.5686751 1.9356553 0.059177256 - 19900 100 3.5573788 3.5573788 1.9430183 0.054618794 - 20000 100 3.5453022 3.5453022 1.9413343 0.047640543 -Loop time of 0.13841 on 4 procs for 5000 steps with 100 atoms - -Performance: 15605800.739 tau/day, 36124.539 timesteps/s, 3.612 Matom-step/s -89.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0047469 | 0.0062771 | 0.0080644 | 1.5 | 4.54 -Neigh | 0.0062517 | 0.0079248 | 0.0094271 | 1.3 | 5.73 -Comm | 0.047109 | 0.048595 | 0.050543 | 0.6 | 35.11 -Output | 0.0011807 | 0.0013428 | 0.0015517 | 0.4 | 0.97 -Modify | 0.022766 | 0.033256 | 0.039993 | 3.5 | 24.03 -Other | | 0.04101 | | | 29.63 - -Nlocal: 25 ave 36 max 13 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Nghost: 5 ave 9 max 2 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Neighs: 37.5 ave 53 max 15 min -Histogram: 1 0 0 0 0 1 0 1 0 1 - -Total # of neighbors = 150 -Ave neighs/atom = 1.5 -Neighbor list builds = 913 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes - Step Atoms Temp c_1 c_2 Press - 20000 100 3.5453022 3.5453022 1.9413343 0.047178052 - 20100 100 1.0878587 1.0878587 0.68666704 0.016139979 - 20200 100 1.0230655 1.0230655 0.63593494 0.014642345 - 20300 100 0.94958824 0.94958824 0.59306601 0.011745659 - 20400 100 0.93038108 0.93038108 0.57232527 0.01154829 - 20500 100 0.92183816 0.92183816 0.55466942 0.01212559 - 20600 100 1.0175846 1.0175846 0.59940035 0.013815361 - 20700 100 1.0564615 1.0564615 0.60726745 0.013073711 - 20800 100 0.99967869 0.99967869 0.57665019 0.012450813 - 20900 100 0.97051084 0.97051084 0.5574217 0.015686955 - 21000 100 0.639185 0.639185 0.37441942 0.017594616 - 21100 100 0.24979014 0.24979014 0.17121567 0.0084027295 - 21200 100 0.15147941 0.15147941 0.11124349 0.0030435746 - 21300 100 0.13117502 0.13117502 0.091432638 0.0029110318 - 21400 100 0.11158272 0.11158272 0.076264692 0.0021951204 - 21500 100 0.056660993 0.056660993 0.043503807 0.0010993096 - 21600 100 0.028640836 0.028640836 0.026000267 0.0010440792 - 21700 100 0.025816483 0.025816483 0.021922896 0.00081674646 - 21800 100 0.023929555 0.023929555 0.019936972 0.0010383614 - 21900 100 0.022271339 0.022271339 0.017947505 0.0014630387 - 22000 100 0.019277834 0.019277834 0.015483116 0.00058751407 - 22100 100 0.019997809 0.019997809 0.015919504 0.00064176101 - 22200 100 0.015870543 0.015870543 0.01244838 0.0004205505 - 22300 100 0.011797587 0.011797587 0.0096491363 0.00034907063 - 22400 100 0.010745212 0.010745212 0.008874218 0.00035427537 - 22500 100 0.0082372399 0.0082372399 0.0071217811 0.00028179943 - 22600 100 0.007942576 0.007942576 0.0067248822 0.001507115 - 22700 100 0.0061733667 0.0061733667 0.0053092324 0.00056018554 - 22800 100 0.0058287651 0.0058287651 0.004972189 0.00023807695 - 22900 100 0.0051352339 0.0051352339 0.004324157 0.00020849263 - 23000 100 0.0040107769 0.0040107769 0.0035769703 0.00022626101 - 23100 100 0.0040288854 0.0040288854 0.0034355474 0.00019107621 - 23200 100 0.003277858 0.003277858 0.0030013165 0.00016119888 - 23300 100 0.0033633749 0.0033633749 0.0030188927 0.00014459404 - 23400 100 0.003468042 0.003468042 0.0030079205 0.00013778427 - 23500 100 0.0027616702 0.0027616702 0.0024994596 0.00011834915 - 23600 100 0.0022531303 0.0022531303 0.0021182802 0.0002279623 - 23700 100 0.002067768 0.002067768 0.0019631752 0.00014341503 - 23800 100 0.0020069255 0.0020069255 0.0019209587 0.00010673435 - 23900 100 0.0019630617 0.0019630617 0.0018748221 0.00011856923 - 24000 100 0.0018800646 0.0018800646 0.0018190347 0.00010707562 - 24100 100 0.0018028137 0.0018028137 0.0017067233 0.00010884117 - 24200 100 0.0017278932 0.0017278932 0.0016251004 0.00013664683 - 24300 100 0.0016373288 0.0016373288 0.0015529481 0.00010025414 - 24400 100 0.0019876848 0.0019876848 0.0016912033 0.00011235942 - 24500 100 0.0013677345 0.0013677345 0.0012839488 7.8669645e-05 - 24600 100 0.0012852614 0.0012852614 0.0012065052 0.00010172361 - 24700 100 0.0011145002 0.0011145002 0.0010748344 7.5021689e-05 - 24800 100 0.0012860792 0.0012860792 0.0011429675 5.7939624e-05 - 24900 100 0.00097198499 0.00097198499 0.00096175911 5.443837e-05 - 25000 100 0.00096224466 0.00096224466 0.00095159089 5.4245409e-05 -Loop time of 0.0846408 on 4 procs for 5000 steps with 100 atoms - -Performance: 25519602.289 tau/day, 59073.153 timesteps/s, 5.907 Matom-step/s -82.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0035473 | 0.0055294 | 0.0082454 | 2.7 | 6.53 -Neigh | 0.0016391 | 0.0022521 | 0.0028115 | 1.1 | 2.66 -Comm | 0.014697 | 0.021565 | 0.029045 | 4.1 | 25.48 -Output | 0.0010785 | 0.00132 | 0.0014171 | 0.4 | 1.56 -Modify | 0.0059648 | 0.01618 | 0.027615 | 7.9 | 19.12 -Other | | 0.03779 | | | 44.65 - -Nlocal: 25 ave 56 max 0 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 5.5 ave 12 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 40 ave 101 max 0 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 160 -Ave neighs/atom = 1.6 -Neighbor list builds = 275 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/granregion/log.15Sep22.granregion.funnel.g++.1 b/examples/granregion/log.15Sep22.granregion.funnel.g++.1 deleted file mode 100644 index fc60ca4928..0000000000 --- a/examples/granregion/log.15Sep22.granregion.funnel.g++.1 +++ /dev/null @@ -1,633 +0,0 @@ -LAMMPS (15 Sep 2022) -# 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. (../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 (../output.cpp:896) -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 0.39961733 2000 -0 - 2000 0.61811961 2000 -0 - 3000 0.83512725 2000 -0 - 4000 1.0492881 2000 -0 - 5000 1.2650657 2000 -0 - 6000 1.479921 2000 -0 - 7000 1.6970993 2000 -0 - 8000 1.9107924 2000 -0 - 9000 2.1251713 2000 -0 - 10000 2.3403682 2000 -0 - 11000 2.549912 2000 -0 - 12000 2.7584788 2000 -0 - 13000 2.9712482 2000 -0 - 14000 3.1877015 2000 -0 - 15000 3.4017175 2000 -0 - 16000 3.6127477 2000 -0 - 17000 3.8250134 2000 -0 - 18000 4.0320643 2000 -0 - 19000 4.2371057 2000 -0 - 20000 4.4450882 2000 -0 -Loop time of 4.44512 on 1 procs for 20000 steps with 2000 atoms - -98.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40438 | 0.40438 | 0.40438 | 0.0 | 9.10 -Neigh | 0.078634 | 0.078634 | 0.078634 | 0.0 | 1.77 -Comm | 0.01999 | 0.01999 | 0.01999 | 0.0 | 0.45 -Output | 0.00069031 | 0.00069031 | 0.00069031 | 0.0 | 0.02 -Modify | 3.795 | 3.795 | 3.795 | 0.0 | 85.38 -Other | | 0.1464 | | | 3.29 - -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 0.2135317 2000 6807.2201 - 22000 0.4235523 2000 6973.9359 - 23000 0.63502794 2000 7142.3648 - 24000 0.84593615 2000 7276.9717 - 25000 1.0580291 2000 7369.4191 - 26000 1.2719892 2000 7497.6526 - 27000 1.4843056 2000 7638.946 - 28000 1.9685336 2000 7780.0339 - 29000 2.1850097 2000 7881.8177 - 30000 2.4033006 2000 7967.2641 - 31000 2.6219694 2000 7994.9273 - 32000 2.8455468 2000 7937.0671 - 33000 3.0720066 2000 7774.0508 - 34000 3.3070513 2000 7591.1491 - 35000 3.5468777 2000 7357.5176 - 36000 3.7908265 2000 7147.2024 - 37000 4.0388657 2000 6979.1604 - 38000 4.2873223 2000 6813.2152 - 39000 4.5424244 2000 6660.2701 - 40000 4.8055367 2000 6502.8957 - 41000 5.0754561 2000 6324.3951 - 42000 5.3564118 2000 6132.7516 - 43000 5.6357256 2000 5913.1841 - 44000 5.9130645 2000 5732.2095 - 45000 6.1943539 2000 5508.8322 - 46000 6.4862302 2000 5306.8932 - 47000 6.7796417 2000 5152.0521 - 48000 7.0750069 2000 5028.2274 - 49000 7.3705252 2000 4896.102 - 50000 7.6693894 2000 4723.5189 - 51000 7.9685182 2000 4583.7526 - 52000 8.2774033 2000 4447.0187 - 53000 8.591482 2000 4303.2307 - 54000 8.9156439 2000 4168.5251 - 55000 9.2437364 2000 4036.9704 - 56000 9.5745684 2000 3901.1183 - 57000 9.9173689 2000 3716.7071 - 58000 10.270229 2000 3473.5422 - 59000 10.629101 2000 3245.1223 - 60000 10.989479 2000 3039.7845 - 61000 11.349843 2000 2780.0187 - 62000 11.716916 2000 2577.3345 - 63000 12.093666 2000 2346.2488 - 64000 12.474788 2000 2116.7298 - 65000 12.861438 2000 1903.7828 - 66000 13.25464 2000 1631.1676 - 67000 13.658382 2000 1431.0198 - 68000 14.067584 2000 1212.875 - 69000 14.480877 2000 995.45046 - 70000 14.894765 2000 811.54766 - 71000 15.309158 2000 624.08622 - 72000 15.732937 2000 471.00862 - 73000 16.158388 2000 358.33486 - 74000 16.583847 2000 284.39416 - 75000 17.008335 2000 234.26671 - 76000 17.429582 2000 185.61836 - 77000 17.852799 2000 152.95918 - 78000 18.276783 2000 122.49023 - 79000 18.697016 2000 102.29396 - 80000 19.12318 2000 86.284684 - 81000 19.54992 2000 73.984781 - 82000 19.986149 2000 63.042918 - 83000 20.430305 2000 53.338428 - 84000 20.876061 2000 45.89585 - 85000 21.32714 2000 40.412826 - 86000 21.781352 2000 34.183381 - 87000 22.238656 2000 29.671524 - 88000 22.698093 2000 26.90414 - 89000 23.160614 2000 24.362631 - 90000 23.630639 2000 21.887341 - 91000 24.095463 2000 19.985662 - 92000 24.570659 2000 18.728162 - 93000 25.047431 2000 16.99941 - 94000 25.549041 2000 15.71941 - 95000 26.03281 2000 14.744057 - 96000 26.513659 2000 14.214918 - 97000 26.998918 2000 13.450182 - 98000 27.486584 2000 12.79222 - 99000 27.986785 2000 12.10595 - 100000 28.48799 2000 11.281863 - 101000 28.986622 2000 10.025419 - 102000 29.491312 2000 9.9574468 - 103000 29.999421 2000 9.4078117 - 104000 30.507211 2000 8.9079161 - 105000 31.016484 2000 8.6269302 - 106000 31.527511 2000 8.5512649 - 107000 32.042612 2000 8.4703948 - 108000 32.555041 2000 8.2747542 - 109000 33.07064 2000 8.2895118 - 110000 33.593773 2000 8.1785613 - 111000 34.107129 2000 7.8443234 - 112000 34.619185 2000 7.7436124 - 113000 35.13418 2000 7.8118604 - 114000 35.653352 2000 7.3806177 - 115000 36.179577 2000 7.0857235 - 116000 36.69882 2000 7.1346752 - 117000 37.224612 2000 7.0653751 - 118000 37.756738 2000 6.6314104 - 119000 38.283151 2000 6.2169614 - 120000 38.808288 2000 5.8988829 - 121000 39.334913 2000 5.4197277 - 122000 39.862081 2000 4.6381303 - 123000 40.390252 2000 4.4949206 - 124000 40.920744 2000 4.4261118 - 125000 41.4469 2000 4.4223703 - 126000 41.977937 2000 4.4858898 - 127000 42.51483 2000 4.3312536 - 128000 43.046324 2000 3.7124973 - 129000 43.573687 2000 3.5467396 - 130000 44.103102 2000 3.5104139 - 131000 44.629869 2000 3.5725612 - 132000 45.156621 2000 3.669455 - 133000 45.69364 2000 3.6168912 - 134000 46.23133 2000 3.3598517 - 135000 46.765487 2000 3.3743407 - 136000 47.323693 2000 3.1109764 - 137000 47.881617 2000 3.0720146 - 138000 48.439179 2000 3.1303776 - 139000 49.001417 2000 3.2052806 - 140000 49.558061 2000 2.8958882 - 141000 50.097789 2000 2.9931572 - 142000 50.636089 2000 3.0967832 - 143000 51.175873 2000 3.0576365 - 144000 51.706799 2000 3.2016943 - 145000 52.239356 2000 3.3817709 - 146000 52.769944 2000 3.4527239 - 147000 53.30872 2000 3.5928733 - 148000 53.847762 2000 3.7784682 - 149000 54.387455 2000 3.6587944 - 150000 54.931594 2000 3.7945669 - 151000 55.470076 2000 3.5551557 - 152000 56.01448 2000 3.6248848 - 153000 56.552259 2000 3.7361463 - 154000 57.092655 2000 3.8534319 - 155000 57.635767 2000 4.0101408 - 156000 58.180249 2000 3.7670652 - 157000 58.724032 2000 3.1487676 - 158000 59.262015 2000 2.980076 - 159000 59.794312 2000 3.0350592 - 160000 60.331617 2000 3.125389 - 161000 60.861827 2000 2.7516115 - 162000 61.396691 2000 2.413911 - 163000 61.930145 2000 2.297713 - 164000 62.466983 2000 2.3190806 - 165000 63.00535 2000 2.2868879 - 166000 63.546881 2000 2.1658547 - 167000 64.091461 2000 1.7511071 - 168000 64.63141 2000 1.4112478 - 169000 65.17459 2000 1.3623558 - 170000 65.719571 2000 1.3701579 -Loop time of 65.7196 on 1 procs for 150000 steps with 2000 atoms - -98.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 32.424 | 32.424 | 32.424 | 0.0 | 49.34 -Neigh | 0.65326 | 0.65326 | 0.65326 | 0.0 | 0.99 -Comm | 0.14207 | 0.14207 | 0.14207 | 0.0 | 0.22 -Output | 0.26326 | 0.26326 | 0.26326 | 0.0 | 0.40 -Modify | 31.109 | 31.109 | 31.109 | 0.0 | 47.34 -Other | | 1.128 | | | 1.72 - -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 0.54961146 2000 2.3724823 - 172000 1.0905775 2000 3.5881441 - 173000 1.6190656 2000 5.3771633 - 174000 2.1428619 2000 7.5896471 - 175000 2.6623327 2000 10.77251 - 176000 3.1738773 2000 14.806868 - 177000 3.6751053 2000 19.607624 - 178000 4.17465 2000 25.426227 - 179000 4.6736143 2000 32.23584 - 180000 5.1769137 2000 39.930468 - 181000 5.6766809 2000 47.686304 - 182000 6.1722504 2000 56.506806 - 183000 6.6603586 2000 66.514326 - 184000 7.1473381 2000 77.554644 - 185000 7.6343824 2000 89.224002 - 186000 8.1170225 2000 102.07846 - 187000 8.598305 2000 116.08141 - 188000 9.0708108 2000 130.97964 - 189000 9.5435695 2000 146.77806 - 190000 10.015069 2000 162.79858 - 191000 10.480992 2000 179.02052 - 192000 10.941896 2000 196.26683 - 193000 11.398748 2000 214.38928 - 194000 11.856098 2000 232.32068 - 195000 12.314324 2000 251.74644 - 196000 12.765746 2000 272.25231 - 197000 13.216453 2000 294.64075 - 198000 13.663698 2000 318.32895 - 199000 14.109901 2000 342.44005 - 200000 14.560399 2000 368.35469 - 201000 15.008158 2000 395.2465 - 202000 15.460487 2000 422.63599 - 203000 15.913115 2000 450.45248 - 204000 16.363656 2000 479.60812 - 205000 16.816929 2000 510.44155 - 206000 17.265488 2000 543.25751 - 207000 17.707782 2000 577.35928 - 208000 18.151051 2000 612.29718 - 209000 18.588363 2000 647.8951 - 210000 19.027167 2000 683.79409 - 211000 19.463213 2000 720.36556 - 212000 19.901783 2000 759.27331 - 213000 20.340436 2000 798.27302 - 214000 20.775782 2000 837.93849 - 215000 21.207465 2000 877.92945 - 216000 21.641572 2000 919.62532 - 217000 22.077351 2000 962.83509 - 218000 22.517089 2000 1008.5243 - 219000 22.948683 2000 1054.5769 - 220000 23.381029 2000 1103.1843 - 221000 23.809214 2000 1153.0349 - 222000 24.246127 2000 1204.5599 - 223000 24.677676 2000 1257.1367 - 224000 25.113989 2000 1308.6735 -WARNING: Lost atoms: original 2000 current 1999 (../thermo.cpp:486) - 225000 25.549621 1999 1360.1205 - 226000 25.977155 1998 1404.8405 - 227000 26.406475 1996 1448.4869 - 228000 26.832152 1992 1491.8112 - 229000 27.25327 1985 1518.7013 - 230000 27.672907 1971 1507.6699 - 231000 28.086761 1965 1533.5096 - 232000 28.500134 1948 1489.4128 - 233000 28.912212 1933 1477.4536 - 234000 29.320197 1915 1425.8398 - 235000 29.723669 1904 1410.1451 - 236000 30.124339 1892 1401.7595 - 237000 30.523539 1880 1368.893 - 238000 30.919483 1868 1341.8885 - 239000 31.313194 1850 1286.7968 - 240000 31.711659 1833 1219.5123 - 241000 32.106468 1820 1173.3608 - 242000 32.505486 1806 1106.0727 - 243000 32.905579 1788 1035.912 - 244000 33.303155 1779 1021.6147 - 245000 33.696614 1767 969.40032 - 246000 34.083545 1757 939.12022 - 247000 34.472486 1739 840.9396 - 248000 34.858907 1730 822.06575 - 249000 35.248061 1719 762.11057 - 250000 35.639608 1707 708.50308 - 251000 36.029812 1700 692.12647 - 252000 36.428881 1697 694.5812 - 253000 36.821304 1686 652.36951 - 254000 37.203008 1682 662.95256 - 255000 37.576678 1677 637.34619 - 256000 37.952398 1672 630.71277 - 257000 38.336834 1669 641.87365 - 258000 38.719421 1665 635.862 - 259000 39.104236 1664 658.5339 - 260000 39.484223 1662 669.95468 - 261000 39.861203 1660 676.93495 - 262000 40.240183 1657 681.72646 - 263000 40.614974 1655 687.4078 - 264000 40.99447 1651 681.61352 - 265000 41.368018 1647 673.20622 - 266000 41.740288 1644 677.30073 - 267000 42.111704 1641 671.05897 - 268000 42.479868 1639 689.55776 - 269000 42.851008 1637 711.98809 - 270000 43.22438 1633 705.29974 -Loop time of 43.2244 on 1 procs for 100000 steps with 1633 atoms - -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 | 22.312 | 22.312 | 22.312 | 0.0 | 51.62 -Neigh | 0.47451 | 0.47451 | 0.47451 | 0.0 | 1.10 -Comm | 0.093822 | 0.093822 | 0.093822 | 0.0 | 0.22 -Output | 0.0028326 | 0.0028326 | 0.0028326 | 0.0 | 0.01 -Modify | 19.626 | 19.626 | 19.626 | 0.0 | 45.40 -Other | | 0.7152 | | | 1.65 - -Nlocal: 1633 ave 1633 max 1633 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 11358 ave 11358 max 11358 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 11358 -Ave neighs/atom = 6.955297 -Neighbor list builds = 244 -Dangerous builds = 0 -Total wall time: 0:01:53 diff --git a/examples/granregion/log.15Sep22.granregion.funnel.g++.4 b/examples/granregion/log.15Sep22.granregion.funnel.g++.4 deleted file mode 100644 index 3c18217deb..0000000000 --- a/examples/granregion/log.15Sep22.granregion.funnel.g++.4 +++ /dev/null @@ -1,633 +0,0 @@ -LAMMPS (15 Sep 2022) -# 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. (../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 (../output.cpp:896) -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 0.4194951 2000 -0 - 2000 0.61516729 2000 -0 - 3000 0.80702516 2000 -0 - 4000 0.99253349 2000 -0 - 5000 1.172741 2000 -0 - 6000 1.3484682 2000 -0 - 7000 1.5206253 2000 -0 - 8000 1.6875025 2000 -0 - 9000 1.8503087 2000 -0 - 10000 2.0125622 2000 -0 - 11000 2.0890872 2000 -0 - 12000 2.1663582 2000 -0 - 13000 2.2430386 2000 -0 - 14000 2.320045 2000 -0 - 15000 2.3989769 2000 -0 - 16000 2.4824747 2000 -0 - 17000 2.5693391 2000 -0 - 18000 2.6595183 2000 -0 - 19000 2.752627 2000 -0 - 20000 2.8503071 2000 -0 -Loop time of 2.85034 on 4 procs for 20000 steps with 2000 atoms - -98.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.04057 | 0.088166 | 0.18377 | 18.9 | 3.09 -Neigh | 0.0072649 | 0.014273 | 0.025073 | 5.5 | 0.50 -Comm | 0.097843 | 0.19506 | 0.29871 | 19.9 | 6.84 -Output | 0.00099986 | 0.0018246 | 0.0023299 | 1.2 | 0.06 -Modify | 0.68567 | 1.1174 | 1.9527 | 46.8 | 39.20 -Other | | 1.434 | | | 50.30 - -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 0.069761009 2000 6807.2201 - 22000 0.14277925 2000 6973.9359 - 23000 0.21755553 2000 7142.3648 - 24000 0.29656838 2000 7276.9717 - 25000 0.3791331 2000 7369.4191 - 26000 0.46663378 2000 7497.6526 - 27000 0.55670237 2000 7638.946 - 28000 0.65212555 2000 7780.0339 - 29000 0.75032507 2000 7881.8177 - 30000 0.85580942 2000 7967.2641 - 31000 0.93204785 2000 7994.9273 - 32000 1.0168325 2000 7937.0672 - 33000 1.1081585 2000 7774.0508 - 34000 1.2084122 2000 7591.1511 - 35000 1.3164174 2000 7357.5032 - 36000 1.4326847 2000 7147.3776 - 37000 1.5548919 2000 6980.0719 - 38000 1.6806183 2000 6813.0872 - 39000 1.8171138 2000 6657.0693 - 40000 1.9655069 2000 6505.1155 - 41000 2.0788398 2000 6330.2864 - 42000 2.1972941 2000 6147.8022 - 43000 2.3180177 2000 5932.9244 - 44000 2.4424194 2000 5755.296 - 45000 2.5679759 2000 5511.622 - 46000 2.7042099 2000 5332.3171 - 47000 2.8436403 2000 5162.4926 - 48000 2.983017 2000 5044.5764 - 49000 3.1228322 2000 4901.1141 - 50000 3.2614172 2000 4731.1949 - 51000 3.3835559 2000 4575.418 - 52000 3.5097034 2000 4428.9425 - 53000 3.6438561 2000 4291.7282 - 54000 3.7823058 2000 4154.1885 - 55000 3.9269393 2000 3994.9402 - 56000 4.0761939 2000 3855.5977 - 57000 4.2262191 2000 3672.9504 - 58000 4.3809045 2000 3435.3395 - 59000 4.5439971 2000 3200.7379 - 60000 4.7111867 2000 2986.5411 - 61000 4.8700167 2000 2747.3628 - 62000 5.030656 2000 2542.0805 - 63000 5.1932098 2000 2336.7687 - 64000 5.3585095 2000 2151.6388 - 65000 5.5278279 2000 1933.6773 - 66000 5.7032072 2000 1699.0747 - 67000 5.8804545 2000 1467.7209 - 68000 6.0598984 2000 1227.3577 - 69000 6.2471961 2000 1016.2766 - 70000 6.4413532 2000 812.90843 - 71000 6.615215 2000 632.88108 - 72000 6.7897335 2000 470.67731 - 73000 6.964705 2000 360.47748 - 74000 7.1361808 2000 286.10584 - 75000 7.3068097 2000 229.70386 - 76000 7.4771974 2000 179.62654 - 77000 7.6485358 2000 142.40417 - 78000 7.8200771 2000 113.55745 - 79000 7.9923688 2000 93.787669 - 80000 8.164219 2000 80.646319 - 81000 8.3372059 2000 70.944319 - 82000 8.5130035 2000 59.2275 - 83000 8.6877383 2000 49.633808 - 84000 8.8675712 2000 42.882698 - 85000 9.0509682 2000 36.841824 - 86000 9.2393665 2000 31.776681 - 87000 9.4296116 2000 28.25076 - 88000 9.622196 2000 25.228966 - 89000 9.8176023 2000 22.593627 - 90000 10.01325 2000 21.15796 - 91000 10.204474 2000 19.941629 - 92000 10.399553 2000 18.375654 - 93000 10.596683 2000 17.056701 - 94000 10.796988 2000 16.192511 - 95000 10.998545 2000 15.572922 - 96000 11.200614 2000 14.827788 - 97000 11.402484 2000 13.919613 - 98000 11.606219 2000 13.19525 - 99000 11.81042 2000 11.993376 - 100000 12.018294 2000 11.258787 - 101000 12.223702 2000 10.641688 - 102000 12.432026 2000 10.430435 - 103000 12.640962 2000 9.518069 - 104000 12.849109 2000 9.1332086 - 105000 13.05872 2000 9.2151611 - 106000 13.269956 2000 9.0035132 - 107000 13.481882 2000 8.7835861 - 108000 13.693895 2000 8.5124479 - 109000 13.906381 2000 8.2975453 - 110000 14.120217 2000 8.3483043 - 111000 14.332078 2000 8.4658572 - 112000 14.54349 2000 8.4771784 - 113000 14.755719 2000 7.8937975 - 114000 14.968619 2000 7.2472953 - 115000 15.180485 2000 6.5812074 - 116000 15.394405 2000 5.5651566 - 117000 15.607523 2000 5.3015807 - 118000 15.821873 2000 5.0133941 - 119000 16.035675 2000 4.8746036 - 120000 16.24964 2000 4.9133073 - 121000 16.462102 2000 4.3337392 - 122000 16.676371 2000 4.3374836 - 123000 16.890252 2000 4.3721818 - 124000 17.106594 2000 4.3894508 - 125000 17.321433 2000 4.1811774 - 126000 17.536692 2000 4.3011002 - 127000 17.748238 2000 4.442228 - 128000 17.962609 2000 4.6170394 - 129000 18.175315 2000 4.8184318 - 130000 18.389056 2000 4.8442096 - 131000 18.600872 2000 4.9668117 - 132000 18.81412 2000 4.8364562 - 133000 19.027514 2000 4.6658645 - 134000 19.23975 2000 4.5758487 - 135000 19.451085 2000 4.7251949 - 136000 19.663874 2000 4.5846492 - 137000 19.87624 2000 4.7565986 - 138000 20.088654 2000 4.8186623 - 139000 20.29935 2000 4.6571647 - 140000 20.510911 2000 4.0730143 - 141000 20.722072 2000 4.0605542 - 142000 20.933113 2000 4.1457179 - 143000 21.143916 2000 4.3418042 - 144000 21.353873 2000 4.0323813 - 145000 21.567015 2000 3.8064958 - 146000 21.781334 2000 3.1802044 - 147000 21.996799 2000 2.7947641 - 148000 22.209808 2000 2.7384164 - 149000 22.423177 2000 2.7428829 - 150000 22.638044 2000 2.7802186 - 151000 22.851676 2000 2.6703451 - 152000 23.065354 2000 2.3357647 - 153000 23.278882 2000 1.9855305 - 154000 23.494254 2000 1.9442713 - 155000 23.708192 2000 1.7348027 - 156000 23.923005 2000 1.5699942 - 157000 24.13827 2000 1.5224944 - 158000 24.352068 2000 1.4850914 - 159000 24.565616 2000 1.4461048 - 160000 24.779118 2000 1.3759525 - 161000 24.99111 2000 0.83754463 - 162000 25.205935 2000 0.7952922 - 163000 25.420817 2000 0.69670143 - 164000 25.632672 2000 0.66253723 - 165000 25.846901 2000 0.64602969 - 166000 26.060074 2000 0.60229858 - 167000 26.273714 2000 0.5757589 - 168000 26.484855 2000 0.5996023 - 169000 26.698151 2000 0.62130448 - 170000 26.911208 2000 0.63888277 -Loop time of 26.9112 on 4 procs for 150000 steps with 2000 atoms - -95.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.5517 | 8.6135 | 10.872 | 82.7 | 32.01 -Neigh | 0.092491 | 0.15402 | 0.19598 | 9.7 | 0.57 -Comm | 2.0054 | 3.8686 | 4.6494 | 55.0 | 14.38 -Output | 0.0047033 | 0.0096766 | 0.016452 | 4.6 | 0.04 -Modify | 5.6498 | 7.9588 | 9.4012 | 49.7 | 29.57 -Other | | 6.307 | | | 23.43 - -Nlocal: 500 ave 538 max 419 min -Histogram: 1 0 0 0 0 0 0 1 0 2 -Nghost: 445.5 ave 688 max 200 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 4500.25 ave 5610 max 3443 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 18001 -Ave neighs/atom = 9.0005 -Neighbor list builds = 362 -Dangerous builds = 0 - -# remove "plug" - need to redefine cylinder region & union - -region cylreg delete -region hopreg delete -region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open -region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2 - -region hopreg union 2 cylreg conereg - -unfix hopper3 -fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg - -run 100000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes - Step CPU Atoms KinEng - 170000 0 2000 0.63888277 - 171000 0.21419748 2000 1.4139245 - 172000 0.42844271 2000 2.2400138 - 173000 0.64333145 2000 3.8034979 - 174000 0.85456696 2000 6.116727 - 175000 1.0672981 2000 8.9536458 - 176000 1.2790911 2000 12.74348 - 177000 1.491721 2000 17.410816 - 178000 1.7033452 2000 22.879174 - 179000 1.9168047 2000 28.966022 - 180000 2.1329071 2000 35.449239 - 181000 2.3490841 2000 42.694882 - 182000 2.565508 2000 50.913279 - 183000 2.780369 2000 60.098465 - 184000 2.9967771 2000 70.133474 - 185000 3.2116891 2000 80.950013 - 186000 3.4248923 2000 92.495525 - 187000 3.6394206 2000 104.83034 - 188000 3.8527533 2000 118.04659 - 189000 4.0650838 2000 132.7403 - 190000 4.2781031 2000 148.31955 - 191000 4.476226 2000 164.26321 - 192000 4.6750263 2000 180.6933 - 193000 4.8710737 2000 197.72012 - 194000 5.0677642 2000 215.43637 - 195000 5.2639974 2000 234.29738 - 196000 5.4599746 2000 254.03407 - 197000 5.6534894 2000 274.58626 - 198000 5.8462402 2000 296.88915 - 199000 6.0400194 2000 320.45001 - 200000 6.2329415 2000 344.75891 - 201000 6.4235068 2000 370.14016 - 202000 6.6142055 2000 395.72827 - 203000 6.8048206 2000 420.42026 - 204000 6.9987454 2000 446.08079 - 205000 7.1925778 2000 473.62963 - 206000 7.3846227 2000 501.05693 - 207000 7.5775122 2000 530.40427 - 208000 7.77052 2000 560.62015 - 209000 7.964984 2000 593.00113 - 210000 8.1601405 2000 626.36661 - 211000 8.3504978 2000 661.34861 - 212000 8.5425141 2000 697.41001 - 213000 8.736112 2000 735.12299 - 214000 8.9267615 2000 773.89126 - 215000 9.1154738 2000 813.83268 - 216000 9.3019826 2000 854.63669 - 217000 9.4878433 2000 896.59089 - 218000 9.6739682 2000 938.70251 - 219000 9.8566518 2000 982.10773 - 220000 10.042289 2000 1025.2953 - 221000 10.227275 2000 1069.8382 - 222000 10.412363 2000 1115.4449 - 223000 10.602757 2000 1161.6742 - 224000 10.789101 2000 1211.289 - 225000 10.974854 2000 1262.8074 - 226000 11.157089 2000 1316.6353 - 227000 11.337044 2000 1370.7434 -WARNING: Lost atoms: original 2000 current 1991 (../thermo.cpp:486) - 228000 11.518718 1991 1382.0924 - 229000 11.700488 1986 1407.1543 - 230000 11.883057 1975 1415.708 - 231000 12.063962 1968 1430.6498 - 232000 12.246917 1957 1421.0352 - 233000 12.429345 1939 1376.0322 - 234000 12.6113 1925 1350.1292 - 235000 12.791233 1912 1337.0529 - 236000 12.968444 1893 1273.2219 - 237000 13.146668 1879 1207.0473 - 238000 13.327542 1861 1132.0109 - 239000 13.50936 1846 1083.1042 - 240000 13.693504 1826 1004.3265 - 241000 13.863443 1819 989.36186 - 242000 14.03294 1812 983.26132 - 243000 14.20032 1805 985.79932 - 244000 14.366236 1794 936.34844 - 245000 14.532759 1784 889.17423 - 246000 14.703029 1770 846.65018 - 247000 14.873941 1753 751.16306 - 248000 15.045272 1740 709.23095 - 249000 15.217896 1732 687.61586 - 250000 15.388727 1721 638.82967 - 251000 15.558032 1714 618.71543 - 252000 15.725309 1709 611.25444 - 253000 15.888727 1705 606.6846 - 254000 16.050605 1702 601.7236 - 255000 16.212982 1697 575.97244 - 256000 16.378352 1695 577.1712 - 257000 16.547488 1691 576.93668 - 258000 16.718964 1688 586.63687 - 259000 16.892601 1686 581.52487 - 260000 17.066036 1682 566.49544 - 261000 17.22488 1681 586.18628 - 262000 17.379249 1678 582.11927 - 263000 17.534079 1675 589.96041 - 264000 17.690288 1672 577.55581 - 265000 17.847805 1669 570.45998 - 266000 18.006261 1666 574.0576 - 267000 18.1674 1662 578.07385 - 268000 18.326753 1660 587.65705 - 269000 18.488052 1657 584.43358 - 270000 18.647474 1654 591.22601 -Loop time of 18.6475 on 4 procs for 100000 steps with 1654 atoms - -94.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.7714 | 6.1879 | 8.8765 | 88.8 | 33.18 -Neigh | 0.094692 | 0.11244 | 0.13298 | 4.6 | 0.60 -Comm | 1.2471 | 2.918 | 3.5873 | 57.0 | 15.65 -Output | 0.0013438 | 0.0067176 | 0.014709 | 6.0 | 0.04 -Modify | 4.4355 | 5.0416 | 5.5692 | 21.9 | 27.04 -Other | | 4.381 | | | 23.49 - -Nlocal: 413.5 ave 429 max 408 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 408.25 ave 653 max 182 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 3486.25 ave 4367 max 2213 min -Histogram: 1 0 0 0 0 1 0 0 1 1 - -Total # of neighbors = 13945 -Ave neighs/atom = 8.4310762 -Neighbor list builds = 227 -Dangerous builds = 0 -Total wall time: 0:00:48 diff --git a/examples/granregion/log.15Sep22.granregion.mixer.g++.1 b/examples/granregion/log.15Sep22.granregion.mixer.g++.1 deleted file mode 100644 index 2a3402c642..0000000000 --- a/examples/granregion/log.15Sep22.granregion.mixer.g++.1 +++ /dev/null @@ -1,632 +0,0 @@ -LAMMPS (15 Sep 2022) -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. (../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 (../output.cpp:896) -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 0.10672296 444 -0 0.015707963 - 2000 0.2090638 444 -0 0.031415927 - 3000 0.31029663 444 -0 0.04712389 - 4000 0.41047624 444 -0 0.062831853 - 5000 0.51132361 444 -0 0.078539816 - 6000 0.61279172 444 -0 0.09424778 - 7000 0.71396622 444 -0 0.10995574 - 8000 0.81644319 444 -0 0.12566371 - 9000 0.91730959 444 -0 0.14137167 - 10000 1.0181635 444 -0 0.15707963 - 11000 1.1182214 444 -0 0.1727876 - 12000 1.2190013 444 -0 0.18849556 - 13000 1.3196138 444 -0 0.20420352 - 14000 1.4183593 444 -0 0.21991149 - 15000 1.5178458 444 -0 0.23561945 - 16000 1.6169535 444 -0 0.25132741 - 17000 1.7219188 444 -0 0.26703538 - 18000 1.8266303 444 -0 0.28274334 - 19000 1.9331589 444 -0 0.2984513 - 20000 2.0392693 444 -0 0.31415927 - 21000 2.1457521 444 -0 0.32986723 - 22000 2.2507526 444 -0 0.34557519 - 23000 2.3548243 444 -0 0.36128316 - 24000 2.4606335 444 -0 0.37699112 - 25000 2.5657643 444 -0 0.39269908 - 26000 2.6698254 444 -0 0.40840704 - 27000 2.7732221 444 -0 0.42411501 - 28000 2.8766441 444 -0 0.43982297 - 29000 2.9801547 444 -0 0.45553093 - 30000 3.0839748 444 -0 0.4712389 - 31000 3.1880063 444 -0 0.48694686 - 32000 3.2923439 444 -0 0.50265482 - 33000 3.3969501 444 -0 0.51836279 - 34000 3.5012646 444 -0 0.53407075 - 35000 3.6057831 444 -0 0.54977871 - 36000 3.7098273 444 -0 0.56548668 - 37000 3.8146061 444 -0 0.58119464 - 38000 3.9215588 444 -0 0.5969026 - 39000 4.0474026 444 -0 0.61261057 - 40000 4.1544945 444 -0 0.62831853 - 41000 4.2605761 444 -0 0.64402649 - 42000 4.3665287 444 -0 0.65973446 - 43000 4.4728216 444 -0 0.67544242 - 44000 4.5782483 444 -0 0.69115038 - 45000 4.6833043 444 -0 0.70685835 - 46000 4.7902207 444 -0 0.72256631 - 47000 4.8968527 444 -0 0.73827427 - 48000 5.0035027 444 -0 0.75398224 - 49000 5.1117191 444 -0 0.7696902 - 50000 5.2186233 444 -0 0.78539816 - 51000 5.3244005 444 -0 0.80110613 - 52000 5.4316153 444 -0 0.81681409 - 53000 5.5381785 444 -0 0.83252205 - 54000 5.6458179 444 -0 0.84823002 - 55000 5.759203 444 -0 0.86393798 - 56000 5.8779849 444 -0 0.87964594 - 57000 5.9953108 444 -0 0.89535391 - 58000 6.1115532 444 -0 0.91106187 - 59000 6.2298342 444 -0 0.92676983 - 60000 6.3474382 444 -0 0.9424778 - 61000 6.4642217 444 -0 0.95818576 - 62000 6.5815141 444 -0 0.97389372 - 63000 6.6999766 444 -0 0.98960169 - 64000 6.8181369 444 -0 1.0053096 - 65000 6.9368124 444 -0 1.0210176 - 66000 7.0560733 444 -0 1.0367256 - 67000 7.1761749 444 -0 1.0524335 - 68000 7.2942246 444 -0 1.0681415 - 69000 7.4146786 444 -0 1.0838495 - 70000 7.5364025 444 -0 1.0995574 - 71000 7.6565177 444 -0 1.1152654 - 72000 7.7776652 444 -0 1.1309734 - 73000 7.8972494 444 -0 1.1466813 - 74000 8.0183599 444 -0 1.1623893 - 75000 8.1423045 444 -0 1.1780972 - 76000 8.2667013 444 -0 1.1938052 - 77000 8.3876604 444 -0 1.2095132 - 78000 8.5095993 444 -0 1.2252211 - 79000 8.6317663 444 -0 1.2409291 - 80000 8.7562108 444 -0 1.2566371 - 81000 8.8812625 444 -0 1.272345 - 82000 9.006825 444 -0 1.288053 - 83000 9.1310939 444 -0 1.303761 - 84000 9.2540049 444 -0 1.3194689 - 85000 9.4210019 888 -0 1.3351769 - 86000 9.6509014 888 -0 1.3508848 - 87000 9.8827304 888 -0 1.3665928 - 88000 10.113857 888 -0 1.3823008 - 89000 10.34324 888 -0 1.3980087 - 90000 10.574203 888 -0 1.4137167 - 91000 10.806069 888 -0 1.4294247 - 92000 11.037044 888 -0 1.4451326 - 93000 11.262596 888 -0 1.4608406 - 94000 11.490532 888 -0 1.4765485 - 95000 11.716452 888 -0 1.4922565 - 96000 11.943883 888 -0 1.5079645 - 97000 12.171353 888 -0 1.5236724 - 98000 12.396787 888 -0 1.5393804 - 99000 12.623788 888 -0 1.5550884 - 100000 12.849633 888 -0 1.5707963 - 101000 13.082904 888 -0 1.5865043 - 102000 13.316986 888 -0 1.6022123 - 103000 13.54777 888 -0 1.6179202 - 104000 13.77928 888 -0 1.6336282 - 105000 14.014818 888 -0 1.6493361 - 106000 14.250986 888 -0 1.6650441 - 107000 14.485754 888 -0 1.6807521 - 108000 14.720106 888 -0 1.69646 - 109000 14.970869 888 -0 1.712168 - 110000 15.219203 888 -0 1.727876 - 111000 15.469876 888 -0 1.7435839 - 112000 15.721351 888 -0 1.7592919 - 113000 15.972099 888 -0 1.7749998 - 114000 16.222357 888 -0 1.7907078 - 115000 16.474863 888 -0 1.8064158 - 116000 16.725352 888 -0 1.8221237 - 117000 16.979634 888 -0 1.8378317 - 118000 17.231379 888 -0 1.8535397 - 119000 17.483691 888 -0 1.8692476 - 120000 17.737897 888 -0 1.8849556 - 121000 17.991241 888 -0 1.9006636 - 122000 18.245626 888 -0 1.9163715 - 123000 18.499984 888 -0 1.9320795 - 124000 18.754367 888 -0 1.9477874 - 125000 19.006448 888 -0 1.9634954 - 126000 19.260545 888 -0 1.9792034 - 127000 19.513633 888 -0 1.9949113 - 128000 19.769389 888 -0 2.0106193 - 129000 20.025088 888 -0 2.0263273 - 130000 20.277534 888 -0 2.0420352 - 131000 20.529284 888 -0 2.0577432 - 132000 20.785132 888 -0 2.0734512 - 133000 21.038442 888 -0 2.0891591 - 134000 21.293932 888 -0 2.1048671 - 135000 21.545354 888 -0 2.120575 - 136000 21.799547 888 -0 2.136283 - 137000 22.053639 888 -0 2.151991 - 138000 22.310106 888 -0 2.1676989 - 139000 22.569362 888 -0 2.1834069 - 140000 22.829416 888 -0 2.1991149 - 141000 23.089132 888 -0 2.2148228 - 142000 23.345737 888 -0 2.2305308 - 143000 23.60621 888 -0 2.2462387 - 144000 23.867414 888 -0 2.2619467 - 145000 24.132954 888 -0 2.2776547 - 146000 24.39395 888 -0 2.2933626 - 147000 24.657881 888 -0 2.3090706 - 148000 24.918563 888 -0 2.3247786 - 149000 25.177446 888 -0 2.3404865 - 150000 25.446598 888 -0 2.3561945 - 151000 25.715494 888 -0 2.3719025 - 152000 25.985991 888 -0 2.3876104 - 153000 26.256676 888 -0 2.4033184 - 154000 26.525639 888 -0 2.4190263 - 155000 26.82656 888 -0 2.4347343 - 156000 27.157272 888 -0 2.4504423 - 157000 27.481755 888 -0 2.4661502 - 158000 27.80198 888 -0 2.4818582 - 159000 28.123258 888 -0 2.4975662 - 160000 28.437502 888 -0 2.5132741 - 161000 28.756496 888 -0 2.5289821 - 162000 29.080609 888 -0 2.54469 - 163000 29.399252 888 -0 2.560398 - 164000 29.718986 888 -0 2.576106 - 165000 30.045206 888 -0 2.5918139 - 166000 30.365168 888 -0 2.6075219 - 167000 30.684007 888 -0 2.6232299 - 168000 31.006154 888 -0 2.6389378 - 169000 31.330336 888 -0 2.6546458 - 170000 31.681761 1000 -0 2.6703538 - 171000 32.049778 1000 -0 2.6860617 - 172000 32.421067 1000 -0 2.7017697 - 173000 32.79935 1000 -0 2.7174776 - 174000 33.178002 1000 -0 2.7331856 - 175000 33.54236 1000 -0 2.7488936 - 176000 33.904734 1000 -0 2.7646015 - 177000 34.269671 1000 -0 2.7803095 - 178000 34.633106 1000 -0 2.7960175 - 179000 35.001441 1000 -0 2.8117254 - 180000 35.374769 1000 -0 2.8274334 - 181000 35.742362 1000 -0 2.8431414 - 182000 36.115908 1000 -0 2.8588493 - 183000 36.490149 1000 -0 2.8745573 - 184000 36.866289 1000 -0 2.8902652 - 185000 37.252911 1000 -0 2.9059732 - 186000 37.644586 1000 -0 2.9216812 - 187000 38.028002 1000 -0 2.9373891 - 188000 38.40724 1000 -0 2.9530971 - 189000 38.77431 1000 -0 2.9688051 - 190000 39.14138 1000 -0 2.984513 - 191000 39.519083 1000 -0 3.000221 - 192000 39.895243 1000 -0 3.0159289 - 193000 40.237532 1000 -0 3.0316369 - 194000 40.587663 1000 -0 3.0473449 - 195000 40.939032 1000 -0 3.0630528 - 196000 41.290257 1000 -0 3.0787608 - 197000 41.643778 1000 -0 3.0944688 - 198000 41.992818 1000 -0 3.1101767 - 199000 42.335934 1000 -0 3.1258847 - 200000 42.681071 1000 -0 3.1415927 -Loop time of 42.6811 on 1 procs for 200000 steps with 1000 atoms - -Performance: 19130.397 tau/day, 4685.915 timesteps/s, 4.686 Matom-step/s -98.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.6365 | 2.6365 | 2.6365 | 0.0 | 6.18 -Neigh | 0.051681 | 0.051681 | 0.051681 | 0.0 | 0.12 -Comm | 0.52007 | 0.52007 | 0.52007 | 0.0 | 1.22 -Output | 0.02209 | 0.02209 | 0.02209 | 0.0 | 0.05 -Modify | 38.71 | 38.71 | 38.71 | 0.0 | 90.70 -Other | | 0.7407 | | | 1.74 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 183 ave 183 max 183 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3757 ave 3757 max 3757 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3757 -Ave neighs/atom = 3.757 -Neighbor list builds = 200 -Dangerous builds = 0 -unfix ins -run 200000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes - Step CPU Atoms KinEng v_theta - 200000 0 1000 1.0515941 3.1415927 - 201000 0.35477257 1000 1.0348185 3.1573006 - 202000 0.71436123 1000 1.0220859 3.1730086 - 203000 1.0642832 1000 1.0225785 3.1887165 - 204000 1.4165213 1000 1.0206121 3.2044245 - 205000 1.7728133 1000 1.009961 3.2201325 - 206000 2.1279101 1000 0.9993323 3.2358404 - 207000 2.480623 1000 0.99602628 3.2515484 - 208000 2.8321106 1000 0.98341818 3.2672564 - 209000 3.2138945 1000 0.96700718 3.2829643 - 210000 3.5921146 1000 0.95226699 3.2986723 - 211000 3.9643569 1000 0.93911691 3.3143802 - 212000 4.3368151 1000 0.92920029 3.3300882 - 213000 4.7130192 1000 0.91893472 3.3457962 - 214000 5.0881313 1000 0.90873324 3.3615041 - 215000 5.4660106 1000 0.88925817 3.3772121 - 216000 5.8455926 1000 0.89108236 3.3929201 - 217000 6.2204827 1000 0.90176711 3.408628 - 218000 6.6046736 1000 0.90149435 3.424336 - 219000 6.9931145 1000 0.89629307 3.440044 - 220000 7.3771565 1000 0.90390589 3.4557519 - 221000 7.7635603 1000 0.87858148 3.4714599 - 222000 8.1502771 1000 0.88862314 3.4871678 - 223000 8.5393557 1000 0.90394098 3.5028758 - 224000 8.9327212 1000 0.91005462 3.5185838 - 225000 9.315331 1000 0.91753865 3.5342917 - 226000 9.6930994 1000 0.91741233 3.5499997 - 227000 10.077148 1000 0.9041879 3.5657077 - 228000 10.463223 1000 0.9085712 3.5814156 - 229000 10.850271 1000 0.8937854 3.5971236 - 230000 11.230235 1000 0.88740571 3.6128316 - 231000 11.61003 1000 0.88350028 3.6285395 - 232000 11.988134 1000 0.88344474 3.6442475 - 233000 12.365856 1000 0.88003311 3.6599554 - 234000 12.745397 1000 0.87416727 3.6756634 - 235000 13.120344 1000 0.86154585 3.6913714 - 236000 13.489521 1000 0.85705071 3.7070793 - 237000 13.858736 1000 0.85297378 3.7227873 - 238000 14.230242 1000 0.84879486 3.7384953 - 239000 14.609692 1000 0.86978407 3.7542032 - 240000 14.998899 1000 0.86758733 3.7699112 - 241000 15.40773 1000 0.86123097 3.7856191 - 242000 15.81537 1000 0.86088136 3.8013271 - 243000 16.221448 1000 0.85270311 3.8170351 - 244000 16.619008 1000 0.8524395 3.832743 - 245000 17.003986 1000 0.84054009 3.848451 - 246000 17.380362 1000 0.82623612 3.864159 - 247000 17.756477 1000 0.82787746 3.8798669 - 248000 18.136456 1000 0.83027177 3.8955749 - 249000 18.521277 1000 0.83307565 3.9112829 - 250000 18.906407 1000 0.82612362 3.9269908 - 251000 19.28348 1000 0.8404639 3.9426988 - 252000 19.66549 1000 0.83550946 3.9584067 - 253000 20.053842 1000 0.81516472 3.9741147 - 254000 20.451357 1000 0.79127421 3.9898227 - 255000 20.844416 1000 0.78373024 4.0055306 - 256000 21.228637 1000 0.79885661 4.0212386 - 257000 21.613641 1000 0.80322118 4.0369466 - 258000 21.99162 1000 0.79861523 4.0526545 - 259000 22.367158 1000 0.79216962 4.0683625 - 260000 22.746158 1000 0.79543097 4.0840704 - 261000 23.125626 1000 0.79394211 4.0997784 - 262000 23.504282 1000 0.79269346 4.1154864 - 263000 23.883609 1000 0.80022854 4.1311943 - 264000 24.261864 1000 0.79885184 4.1469023 - 265000 24.639269 1000 0.79595018 4.1626103 - 266000 25.016335 1000 0.78191184 4.1783182 - 267000 25.389754 1000 0.76329279 4.1940262 - 268000 25.762053 1000 0.7342663 4.2097342 - 269000 26.133966 1000 0.72303366 4.2254421 - 270000 26.511157 1000 0.70016481 4.2411501 - 271000 26.888842 1000 0.68891731 4.256858 - 272000 27.26804 1000 0.68545775 4.272566 - 273000 27.644067 1000 0.68712156 4.288274 - 274000 28.024704 1000 0.69249813 4.3039819 - 275000 28.404842 1000 0.70187847 4.3196899 - 276000 28.785799 1000 0.70679419 4.3353979 - 277000 29.165857 1000 0.70955357 4.3511058 - 278000 29.545291 1000 0.70183408 4.3668138 - 279000 29.926113 1000 0.69979273 4.3825218 - 280000 30.302095 1000 0.70822139 4.3982297 - 281000 30.684406 1000 0.71629209 4.4139377 - 282000 31.065873 1000 0.73094905 4.4296456 - 283000 31.445972 1000 0.74554115 4.4453536 - 284000 31.828184 1000 0.74390104 4.4610616 - 285000 32.207807 1000 0.74675359 4.4767695 - 286000 32.58802 1000 0.75330713 4.4924775 - 287000 32.964457 1000 0.75525926 4.5081855 - 288000 33.343222 1000 0.75174884 4.5238934 - 289000 33.717663 1000 0.74062375 4.5396014 - 290000 34.094722 1000 0.72784613 4.5553093 - 291000 34.46982 1000 0.72151574 4.5710173 - 292000 34.843777 1000 0.71712409 4.5867253 - 293000 35.208307 1000 0.71803758 4.6024332 - 294000 35.576207 1000 0.71002715 4.6181412 - 295000 35.942972 1000 0.7070911 4.6338492 - 296000 36.3107 1000 0.71082175 4.6495571 - 297000 36.682044 1000 0.70438977 4.6652651 - 298000 37.054664 1000 0.70240345 4.6809731 - 299000 37.424717 1000 0.70525357 4.696681 - 300000 37.796148 1000 0.70636846 4.712389 - 301000 38.166828 1000 0.70443346 4.7280969 - 302000 38.538428 1000 0.71187973 4.7438049 - 303000 38.907221 1000 0.71047139 4.7595129 - 304000 39.280263 1000 0.71405925 4.7752208 - 305000 39.652902 1000 0.71277063 4.7909288 - 306000 40.02752 1000 0.72005331 4.8066368 - 307000 40.402955 1000 0.72466112 4.8223447 - 308000 40.784177 1000 0.72001329 4.8380527 - 309000 41.173226 1000 0.70611982 4.8537606 - 310000 41.559195 1000 0.70810918 4.8694686 - 311000 41.946697 1000 0.70377166 4.8851766 - 312000 42.337059 1000 0.70434458 4.9008845 - 313000 42.728304 1000 0.70707385 4.9165925 - 314000 43.120803 1000 0.71412995 4.9323005 - 315000 43.510705 1000 0.72228946 4.9480084 - 316000 43.901867 1000 0.72715835 4.9637164 - 317000 44.295667 1000 0.73833476 4.9794244 - 318000 44.687503 1000 0.75953014 4.9951323 - 319000 45.077121 1000 0.76413836 5.0108403 - 320000 45.465317 1000 0.76745045 5.0265482 - 321000 45.86931 1000 0.75813288 5.0422562 - 322000 46.277029 1000 0.75324661 5.0579642 - 323000 46.680799 1000 0.75004276 5.0736721 - 324000 47.082361 1000 0.74316264 5.0893801 - 325000 47.481252 1000 0.74087383 5.1050881 - 326000 47.87511 1000 0.73244882 5.120796 - 327000 48.274582 1000 0.73096631 5.136504 - 328000 48.671718 1000 0.72955403 5.152212 - 329000 49.066335 1000 0.73464916 5.1679199 - 330000 49.459765 1000 0.73130257 5.1836279 - 331000 49.850698 1000 0.73008711 5.1993358 - 332000 50.241012 1000 0.72561074 5.2150438 - 333000 50.643245 1000 0.7214495 5.2307518 - 334000 51.039153 1000 0.71274232 5.2464597 - 335000 51.430328 1000 0.71335777 5.2621677 - 336000 51.819148 1000 0.71317423 5.2778757 - 337000 52.202763 1000 0.70965743 5.2935836 - 338000 52.585061 1000 0.69648518 5.3092916 - 339000 52.967678 1000 0.68985842 5.3249995 - 340000 53.351472 1000 0.6846783 5.3407075 - 341000 53.737731 1000 0.69031602 5.3564155 - 342000 54.131413 1000 0.69035259 5.3721234 - 343000 54.526384 1000 0.69843983 5.3878314 - 344000 54.921609 1000 0.69566088 5.4035394 - 345000 55.314258 1000 0.68309182 5.4192473 - 346000 55.701119 1000 0.68360919 5.4349553 - 347000 56.088194 1000 0.68034628 5.4506633 - 348000 56.467878 1000 0.67155093 5.4663712 - 349000 56.857709 1000 0.66504603 5.4820792 - 350000 57.250758 1000 0.66533658 5.4977871 - 351000 57.643438 1000 0.67726804 5.5134951 - 352000 58.04256 1000 0.68880987 5.5292031 - 353000 58.437369 1000 0.71377276 5.544911 - 354000 58.832421 1000 0.71715625 5.560619 - 355000 59.222221 1000 0.71729576 5.576327 - 356000 59.621431 1000 0.71088872 5.5920349 - 357000 60.013262 1000 0.70564615 5.6077429 - 358000 60.406494 1000 0.69291739 5.6234508 - 359000 60.800632 1000 0.68237469 5.6391588 - 360000 61.195364 1000 0.69105856 5.6548668 - 361000 61.588291 1000 0.69563351 5.6705747 - 362000 61.984821 1000 0.69762747 5.6862827 - 363000 62.377158 1000 0.69717346 5.7019907 - 364000 62.77604 1000 0.69413964 5.7176986 - 365000 63.165863 1000 0.68584257 5.7334066 - 366000 63.5503 1000 0.67653762 5.7491146 - 367000 63.930717 1000 0.66880284 5.7648225 - 368000 64.313698 1000 0.66024732 5.7805305 - 369000 64.708193 1000 0.65451701 5.7962384 - 370000 65.10142 1000 0.64352268 5.8119464 - 371000 65.49169 1000 0.63715296 5.8276544 - 372000 65.879115 1000 0.63840106 5.8433623 - 373000 66.268258 1000 0.64537192 5.8590703 - 374000 66.661807 1000 0.64498753 5.8747783 - 375000 67.052521 1000 0.64666103 5.8904862 - 376000 67.443168 1000 0.65957055 5.9061942 - 377000 67.835892 1000 0.65964257 5.9219022 - 378000 68.229282 1000 0.65720396 5.9376101 - 379000 68.623557 1000 0.66304265 5.9533181 - 380000 69.015967 1000 0.67465814 5.969026 - 381000 69.408981 1000 0.68582945 5.984734 - 382000 69.796561 1000 0.69516677 6.000442 - 383000 70.186403 1000 0.69835516 6.0161499 - 384000 70.5765 1000 0.70403284 6.0318579 - 385000 70.966205 1000 0.6955862 6.0475659 - 386000 71.360054 1000 0.704932 6.0632738 - 387000 71.757912 1000 0.71954173 6.0789818 - 388000 72.147544 1000 0.72347529 6.0946897 - 389000 72.535029 1000 0.72738907 6.1103977 - 390000 72.925842 1000 0.74783091 6.1261057 - 391000 73.306871 1000 0.76739039 6.1418136 - 392000 73.692746 1000 0.77184224 6.1575216 - 393000 74.053385 1000 0.76813357 6.1732296 - 394000 74.416323 1000 0.75994091 6.1889375 - 395000 74.777021 1000 0.74970188 6.2046455 - 396000 75.139847 1000 0.7523174 6.2203535 - 397000 75.502888 1000 0.74652931 6.2360614 - 398000 75.865442 1000 0.74418096 6.2517694 - 399000 76.225245 1000 0.75110038 6.2674773 - 400000 76.590032 1000 0.7609274 6.2831853 -Loop time of 76.5901 on 1 procs for 200000 steps with 1000 atoms - -Performance: 10660.735 tau/day, 2611.305 timesteps/s, 2.611 Matom-step/s -99.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 8.693 | 8.693 | 8.693 | 0.0 | 11.35 -Neigh | 0.082655 | 0.082655 | 0.082655 | 0.0 | 0.11 -Comm | 1.1618 | 1.1618 | 1.1618 | 0.0 | 1.52 -Output | 0.0052644 | 0.0052644 | 0.0052644 | 0.0 | 0.01 -Modify | 65.713 | 65.713 | 65.713 | 0.0 | 85.80 -Other | | 0.934 | | | 1.22 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 268 ave 268 max 268 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5015 ave 5015 max 5015 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5015 -Ave neighs/atom = 5.015 -Neighbor list builds = 163 -Dangerous builds = 0 -Total wall time: 0:01:59 diff --git a/examples/granregion/log.15Sep22.granregion.mixer.g++.4 b/examples/granregion/log.15Sep22.granregion.mixer.g++.4 deleted file mode 100644 index 57c517a063..0000000000 --- a/examples/granregion/log.15Sep22.granregion.mixer.g++.4 +++ /dev/null @@ -1,632 +0,0 @@ -LAMMPS (15 Sep 2022) -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. (../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 (../output.cpp:896) -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 0.089993907 444 -0 0.015707963 - 2000 0.14885989 444 -0 0.031415927 - 3000 0.20954563 444 -0 0.04712389 - 4000 0.27002257 444 -0 0.062831853 - 5000 0.33034347 444 -0 0.078539816 - 6000 0.39049526 444 -0 0.09424778 - 7000 0.45002664 444 -0 0.10995574 - 8000 0.50911338 444 -0 0.12566371 - 9000 0.56771745 444 -0 0.14137167 - 10000 0.62699472 444 -0 0.15707963 - 11000 0.67300351 444 -0 0.1727876 - 12000 0.71981356 444 -0 0.18849556 - 13000 0.76697682 444 -0 0.20420352 - 14000 0.81412229 444 -0 0.21991149 - 15000 0.86284749 444 -0 0.23561945 - 16000 0.91199522 444 -0 0.25132741 - 17000 0.96230663 444 -0 0.26703538 - 18000 1.0118327 444 -0 0.28274334 - 19000 1.0617397 444 -0 0.2984513 - 20000 1.111586 444 -0 0.31415927 - 21000 1.1556637 444 -0 0.32986723 - 22000 1.2005913 444 -0 0.34557519 - 23000 1.2455061 444 -0 0.36128316 - 24000 1.2910181 444 -0 0.37699112 - 25000 1.3370577 444 -0 0.39269908 - 26000 1.383595 444 -0 0.40840704 - 27000 1.430922 444 -0 0.42411501 - 28000 1.478627 444 -0 0.43982297 - 29000 1.5278607 444 -0 0.45553093 - 30000 1.576597 444 -0 0.4712389 - 31000 1.6202694 444 -0 0.48694686 - 32000 1.6646667 444 -0 0.50265482 - 33000 1.7092726 444 -0 0.51836279 - 34000 1.7535573 444 -0 0.53407075 - 35000 1.7985995 444 -0 0.54977871 - 36000 1.8440346 444 -0 0.56548668 - 37000 1.8900841 444 -0 0.58119464 - 38000 1.9368772 444 -0 0.5969026 - 39000 1.9842867 444 -0 0.61261057 - 40000 2.0318482 444 -0 0.62831853 - 41000 2.0753049 444 -0 0.64402649 - 42000 2.1196274 444 -0 0.65973446 - 43000 2.1647071 444 -0 0.67544242 - 44000 2.2101195 444 -0 0.69115038 - 45000 2.2564642 444 -0 0.70685835 - 46000 2.3033573 444 -0 0.72256631 - 47000 2.3500515 444 -0 0.73827427 - 48000 2.3972268 444 -0 0.75398224 - 49000 2.4444727 444 -0 0.7696902 - 50000 2.4921003 444 -0 0.78539816 - 51000 2.535088 444 -0 0.80110613 - 52000 2.5785564 444 -0 0.81681409 - 53000 2.6221392 444 -0 0.83252205 - 54000 2.6664169 444 -0 0.84823002 - 55000 2.7108951 444 -0 0.86393798 - 56000 2.7560522 444 -0 0.87964594 - 57000 2.8010254 444 -0 0.89535391 - 58000 2.8484456 444 -0 0.91106187 - 59000 2.8951674 444 -0 0.92676983 - 60000 2.9424205 444 -0 0.9424778 - 61000 2.9885999 444 -0 0.95818576 - 62000 3.0338676 444 -0 0.97389372 - 63000 3.0793674 444 -0 0.98960169 - 64000 3.1253557 444 -0 1.0053096 - 65000 3.1723823 444 -0 1.0210176 - 66000 3.2203846 444 -0 1.0367256 - 67000 3.2690443 444 -0 1.0524335 - 68000 3.317707 444 -0 1.0681415 - 69000 3.3670196 444 -0 1.0838495 - 70000 3.4160505 444 -0 1.0995574 - 71000 3.4621197 444 -0 1.1152654 - 72000 3.5086434 444 -0 1.1309734 - 73000 3.555691 444 -0 1.1466813 - 74000 3.6032072 444 -0 1.1623893 - 75000 3.6514849 444 -0 1.1780972 - 76000 3.7002713 444 -0 1.1938052 - 77000 3.7497321 444 -0 1.2095132 - 78000 3.7997711 444 -0 1.2252211 - 79000 3.8504338 444 -0 1.2409291 - 80000 3.9020416 444 -0 1.2566371 - 81000 3.9496762 444 -0 1.272345 - 82000 3.9968215 444 -0 1.288053 - 83000 4.04496 444 -0 1.303761 - 84000 4.0936477 444 -0 1.3194689 - 85000 4.1618384 888 -0 1.3351769 - 86000 4.2472086 888 -0 1.3508848 - 87000 4.3322855 888 -0 1.3665928 - 88000 4.4169835 888 -0 1.3823008 - 89000 4.5014588 888 -0 1.3980087 - 90000 4.5861842 888 -0 1.4137167 - 91000 4.653654 888 -0 1.4294247 - 92000 4.7217642 888 -0 1.4451326 - 93000 4.791842 888 -0 1.4608406 - 94000 4.8601789 888 -0 1.4765485 - 95000 4.92849 888 -0 1.4922565 - 96000 4.9976811 888 -0 1.5079645 - 97000 5.0687073 888 -0 1.5236724 - 98000 5.1387234 888 -0 1.5393804 - 99000 5.2086037 888 -0 1.5550884 - 100000 5.2786924 888 -0 1.5707963 - 101000 5.3466895 888 -0 1.5865043 - 102000 5.417132 888 -0 1.6022123 - 103000 5.4865633 888 -0 1.6179202 - 104000 5.5565911 888 -0 1.6336282 - 105000 5.6266394 888 -0 1.6493361 - 106000 5.6975394 888 -0 1.6650441 - 107000 5.7687753 888 -0 1.6807521 - 108000 5.8408498 888 -0 1.69646 - 109000 5.9132618 888 -0 1.712168 - 110000 5.9872629 888 -0 1.727876 - 111000 6.0588115 888 -0 1.7435839 - 112000 6.1308729 888 -0 1.7592919 - 113000 6.2047311 888 -0 1.7749998 - 114000 6.2780757 888 -0 1.7907078 - 115000 6.3528542 888 -0 1.8064158 - 116000 6.4277704 888 -0 1.8221237 - 117000 6.5034683 888 -0 1.8378317 - 118000 6.5795779 888 -0 1.8535397 - 119000 6.655928 888 -0 1.8692476 - 120000 6.7335119 888 -0 1.8849556 - 121000 6.806827 888 -0 1.9006636 - 122000 6.881052 888 -0 1.9163715 - 123000 6.9559647 888 -0 1.9320795 - 124000 7.0300829 888 -0 1.9477874 - 125000 7.1047925 888 -0 1.9634954 - 126000 7.1797025 888 -0 1.9792034 - 127000 7.2556934 888 -0 1.9949113 - 128000 7.3317803 888 -0 2.0106193 - 129000 7.4088096 888 -0 2.0263273 - 130000 7.4862461 888 -0 2.0420352 - 131000 7.5633585 888 -0 2.0577432 - 132000 7.641939 888 -0 2.0734512 - 133000 7.7192741 888 -0 2.0891591 - 134000 7.7970156 888 -0 2.1048671 - 135000 7.8760712 888 -0 2.120575 - 136000 7.9563099 888 -0 2.136283 - 137000 8.0381808 888 -0 2.151991 - 138000 8.1210957 888 -0 2.1676989 - 139000 8.20401 888 -0 2.1834069 - 140000 8.2871705 888 -0 2.1991149 - 141000 8.364321 888 -0 2.2148228 - 142000 8.4426744 888 -0 2.2305308 - 143000 8.5238377 888 -0 2.2462387 - 144000 8.6050517 888 -0 2.2619467 - 145000 8.6865872 888 -0 2.2776547 - 146000 8.767621 888 -0 2.2933626 - 147000 8.8496616 888 -0 2.3090706 - 148000 8.9329599 888 -0 2.3247786 - 149000 9.0165929 888 -0 2.3404865 - 150000 9.1015214 888 -0 2.3561945 - 151000 9.1847289 888 -0 2.3719025 - 152000 9.2689185 888 -0 2.3876104 - 153000 9.3518862 888 -0 2.4033184 - 154000 9.4367057 888 -0 2.4190263 - 155000 9.5227466 888 -0 2.4347343 - 156000 9.6087196 888 -0 2.4504423 - 157000 9.6955661 888 -0 2.4661502 - 158000 9.7838227 888 -0 2.4818582 - 159000 9.8731804 888 -0 2.4975662 - 160000 9.9626648 888 -0 2.5132741 - 161000 10.050473 888 -0 2.5289821 - 162000 10.137725 888 -0 2.54469 - 163000 10.227259 888 -0 2.560398 - 164000 10.318501 888 -0 2.576106 - 165000 10.409218 888 -0 2.5918139 - 166000 10.502055 888 -0 2.6075219 - 167000 10.593786 888 -0 2.6232299 - 168000 10.688536 888 -0 2.6389378 - 169000 10.786033 888 -0 2.6546458 - 170000 10.886377 1000 -0 2.6703538 - 171000 10.987493 1000 -0 2.6860617 - 172000 11.084584 1000 -0 2.7017697 - 173000 11.181502 1000 -0 2.7174776 - 174000 11.28434 1000 -0 2.7331856 - 175000 11.387838 1000 -0 2.7488936 - 176000 11.490915 1000 -0 2.7646015 - 177000 11.595473 1000 -0 2.7803095 - 178000 11.699823 1000 -0 2.7960175 - 179000 11.803927 1000 -0 2.8117254 - 180000 11.90548 1000 -0 2.8274334 - 181000 12.00857 1000 -0 2.8431414 - 182000 12.112787 1000 -0 2.8588493 - 183000 12.217943 1000 -0 2.8745573 - 184000 12.322668 1000 -0 2.8902652 - 185000 12.428332 1000 -0 2.9059732 - 186000 12.535414 1000 -0 2.9216812 - 187000 12.642404 1000 -0 2.9373891 - 188000 12.749332 1000 -0 2.9530971 - 189000 12.856872 1000 -0 2.9688051 - 190000 12.965335 1000 -0 2.984513 - 191000 13.073275 1000 -0 3.000221 - 192000 13.180122 1000 -0 3.0159289 - 193000 13.288112 1000 -0 3.0316369 - 194000 13.394688 1000 -0 3.0473449 - 195000 13.501251 1000 -0 3.0630528 - 196000 13.607472 1000 -0 3.0787608 - 197000 13.71396 1000 -0 3.0944688 - 198000 13.821133 1000 -0 3.1101767 - 199000 13.929192 1000 -0 3.1258847 - 200000 14.036724 1000 -0 3.1415927 -Loop time of 14.0368 on 4 procs for 200000 steps with 1000 atoms - -Performance: 58169.166 tau/day, 14248.307 timesteps/s, 14.248 Matom-step/s -95.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.47004 | 0.75698 | 1.1 | 33.1 | 5.39 -Neigh | 0.0078501 | 0.010659 | 0.013902 | 2.7 | 0.08 -Comm | 3.9589 | 4.4102 | 4.9322 | 21.6 | 31.42 -Output | 0.0031054 | 0.0046208 | 0.0069341 | 2.1 | 0.03 -Modify | 6.1829 | 6.8363 | 7.6135 | 24.8 | 48.70 -Other | | 2.018 | | | 14.38 - -Nlocal: 250 ave 260 max 242 min -Histogram: 1 0 1 0 0 1 0 0 0 1 -Nghost: 279.25 ave 325 max 232 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 939.75 ave 1397 max 509 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 3759 -Ave neighs/atom = 3.759 -Neighbor list builds = 201 -Dangerous builds = 0 -unfix ins -run 200000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.88 | 11.89 Mbytes - Step CPU Atoms KinEng v_theta - 200000 0 1000 1.0071568 3.1415927 - 201000 0.099357585 1000 1.0036239 3.1573006 - 202000 0.19922889 1000 0.99846844 3.1730086 - 203000 0.29896537 1000 0.98236169 3.1887165 - 204000 0.39875771 1000 0.98625572 3.2044245 - 205000 0.49759454 1000 0.9893407 3.2201325 - 206000 0.59609243 1000 1.0012123 3.2358404 - 207000 0.69408206 1000 1.0231892 3.2515484 - 208000 0.79216806 1000 1.0265912 3.2672564 - 209000 0.8902274 1000 1.0190202 3.2829643 - 210000 0.98909509 1000 1.0267754 3.2986723 - 211000 1.0882901 1000 1.0186847 3.3143802 - 212000 1.1895753 1000 1.0159848 3.3300882 - 213000 1.2891277 1000 0.99326329 3.3457962 - 214000 1.387486 1000 0.97263135 3.3615041 - 215000 1.4850078 1000 0.97246409 3.3772121 - 216000 1.58405 1000 0.96000626 3.3929201 - 217000 1.6853829 1000 0.95730432 3.408628 - 218000 1.7911163 1000 0.95605591 3.424336 - 219000 1.8974141 1000 0.94983 3.440044 - 220000 2.0029829 1000 0.95291888 3.4557519 - 221000 2.108723 1000 0.93612997 3.4714599 - 222000 2.2151561 1000 0.93414081 3.4871678 - 223000 2.3220866 1000 0.93321246 3.5028758 - 224000 2.4285504 1000 0.93026943 3.5185838 - 225000 2.5356173 1000 0.930478 3.5342917 - 226000 2.6415516 1000 0.92909096 3.5499997 - 227000 2.747634 1000 0.92308495 3.5657077 - 228000 2.8524082 1000 0.91075986 3.5814156 - 229000 2.9570172 1000 0.9006662 3.5971236 - 230000 3.0627535 1000 0.88869212 3.6128316 - 231000 3.1683919 1000 0.8877611 3.6285395 - 232000 3.2749534 1000 0.89409636 3.6442475 - 233000 3.3824185 1000 0.90866091 3.6599554 - 234000 3.4917899 1000 0.90454601 3.6756634 - 235000 3.6009156 1000 0.89408327 3.6913714 - 236000 3.7111309 1000 0.8881044 3.7070793 - 237000 3.8197619 1000 0.89322168 3.7227873 - 238000 3.9302291 1000 0.89018045 3.7384953 - 239000 4.0407242 1000 0.88771268 3.7542032 - 240000 4.1521989 1000 0.88957717 3.7699112 - 241000 4.2639861 1000 0.89362036 3.7856191 - 242000 4.3782856 1000 0.90967472 3.8013271 - 243000 4.4925107 1000 0.91366381 3.8170351 - 244000 4.6057342 1000 0.9150959 3.832743 - 245000 4.7199383 1000 0.92725789 3.848451 - 246000 4.8346784 1000 0.93024722 3.864159 - 247000 4.9515438 1000 0.93297974 3.8798669 - 248000 5.0696512 1000 0.94755869 3.8955749 - 249000 5.1838845 1000 0.94761679 3.9112829 - 250000 5.297991 1000 0.92701064 3.9269908 - 251000 5.412562 1000 0.91365252 3.9426988 - 252000 5.5274859 1000 0.90918381 3.9584067 - 253000 5.6418647 1000 0.90612685 3.9741147 - 254000 5.7593721 1000 0.90352142 3.9898227 - 255000 5.8759086 1000 0.90421567 4.0055306 - 256000 5.993588 1000 0.90024688 4.0212386 - 257000 6.1142027 1000 0.88540341 4.0369466 - 258000 6.2318882 1000 0.87890423 4.0526545 - 259000 6.3502765 1000 0.86833748 4.0683625 - 260000 6.4677878 1000 0.85465694 4.0840704 - 261000 6.5875341 1000 0.83941242 4.0997784 - 262000 6.7063481 1000 0.81790404 4.1154864 - 263000 6.8249742 1000 0.82284562 4.1311943 - 264000 6.9421188 1000 0.80961447 4.1469023 - 265000 7.0588866 1000 0.80567073 4.1626103 - 266000 7.1763855 1000 0.79577448 4.1783182 - 267000 7.295632 1000 0.78489106 4.1940262 - 268000 7.4144463 1000 0.77348757 4.2097342 - 269000 7.5333839 1000 0.76606696 4.2254421 - 270000 7.6527119 1000 0.7649744 4.2411501 - 271000 7.7704222 1000 0.76050309 4.256858 - 272000 7.8903012 1000 0.75378759 4.272566 - 273000 8.0106197 1000 0.75633811 4.288274 - 274000 8.1309707 1000 0.75703106 4.3039819 - 275000 8.2522837 1000 0.75227453 4.3196899 - 276000 8.3730898 1000 0.76003902 4.3353979 - 277000 8.4955037 1000 0.76274661 4.3511058 - 278000 8.6153206 1000 0.75888482 4.3668138 - 279000 8.7339569 1000 0.75071875 4.3825218 - 280000 8.8515447 1000 0.75454927 4.3982297 - 281000 8.9685253 1000 0.75617824 4.4139377 - 282000 9.0856168 1000 0.75230835 4.4296456 - 283000 9.2018894 1000 0.75417571 4.4453536 - 284000 9.3179777 1000 0.74559345 4.4610616 - 285000 9.4341721 1000 0.73274661 4.4767695 - 286000 9.5498722 1000 0.72385193 4.4924775 - 287000 9.6651326 1000 0.72398899 4.5081855 - 288000 9.7810274 1000 0.72009027 4.5238934 - 289000 9.8959471 1000 0.72026686 4.5396014 - 290000 10.010007 1000 0.72330145 4.5553093 - 291000 10.123304 1000 0.71630656 4.5710173 - 292000 10.238277 1000 0.71089192 4.5867253 - 293000 10.351465 1000 0.70584923 4.6024332 - 294000 10.464794 1000 0.71350398 4.6181412 - 295000 10.57818 1000 0.72781836 4.6338492 - 296000 10.692249 1000 0.72285512 4.6495571 - 297000 10.80741 1000 0.71649517 4.6652651 - 298000 10.923694 1000 0.71132209 4.6809731 - 299000 11.039173 1000 0.73602072 4.696681 - 300000 11.157002 1000 0.74400837 4.712389 - 301000 11.272462 1000 0.76618562 4.7280969 - 302000 11.386581 1000 0.77476041 4.7438049 - 303000 11.499191 1000 0.77124283 4.7595129 - 304000 11.611585 1000 0.7625748 4.7752208 - 305000 11.725012 1000 0.74979361 4.7909288 - 306000 11.838032 1000 0.74515733 4.8066368 - 307000 11.949194 1000 0.74302741 4.8223447 - 308000 12.060586 1000 0.73732959 4.8380527 - 309000 12.171445 1000 0.73368237 4.8537606 - 310000 12.283518 1000 0.72374292 4.8694686 - 311000 12.393447 1000 0.72107784 4.8851766 - 312000 12.505136 1000 0.72944426 4.9008845 - 313000 12.616959 1000 0.73958637 4.9165925 - 314000 12.730312 1000 0.75160847 4.9323005 - 315000 12.846163 1000 0.74419683 4.9480084 - 316000 12.960328 1000 0.74652593 4.9637164 - 317000 13.073994 1000 0.74933482 4.9794244 - 318000 13.186549 1000 0.74200509 4.9951323 - 319000 13.296925 1000 0.7346024 5.0108403 - 320000 13.406825 1000 0.72806145 5.0265482 - 321000 13.51703 1000 0.72147888 5.0422562 - 322000 13.628261 1000 0.71460041 5.0579642 - 323000 13.74063 1000 0.70255075 5.0736721 - 324000 13.853826 1000 0.70640327 5.0893801 - 325000 13.968533 1000 0.70643428 5.1050881 - 326000 14.081456 1000 0.69751794 5.120796 - 327000 14.195505 1000 0.69035108 5.136504 - 328000 14.310048 1000 0.68068243 5.152212 - 329000 14.426048 1000 0.69123492 5.1679199 - 330000 14.543349 1000 0.70326515 5.1836279 - 331000 14.662021 1000 0.70551726 5.1993358 - 332000 14.782194 1000 0.70514444 5.2150438 - 333000 14.901573 1000 0.71102045 5.2307518 - 334000 15.020642 1000 0.71336747 5.2464597 - 335000 15.136739 1000 0.70816388 5.2621677 - 336000 15.252554 1000 0.69502472 5.2778757 - 337000 15.368496 1000 0.69314289 5.2935836 - 338000 15.483744 1000 0.68565794 5.3092916 - 339000 15.599584 1000 0.67268053 5.3249995 - 340000 15.717342 1000 0.68313196 5.3407075 - 341000 15.835594 1000 0.68782815 5.3564155 - 342000 15.954546 1000 0.6989326 5.3721234 - 343000 16.074184 1000 0.694926 5.3878314 - 344000 16.193902 1000 0.7006474 5.4035394 - 345000 16.314878 1000 0.70783177 5.4192473 - 346000 16.434704 1000 0.71334276 5.4349553 - 347000 16.554708 1000 0.72917419 5.4506633 - 348000 16.673034 1000 0.74315705 5.4663712 - 349000 16.791269 1000 0.76731311 5.4820792 - 350000 16.912554 1000 0.79761434 5.4977871 - 351000 17.03323 1000 0.80447724 5.5134951 - 352000 17.155644 1000 0.80118728 5.5292031 - 353000 17.281134 1000 0.77990459 5.544911 - 354000 17.406672 1000 0.76453299 5.560619 - 355000 17.532346 1000 0.76538392 5.576327 - 356000 17.657256 1000 0.76310698 5.5920349 - 357000 17.782477 1000 0.75897095 5.6077429 - 358000 17.909642 1000 0.75071115 5.6234508 - 359000 18.035032 1000 0.74034801 5.6391588 - 360000 18.160696 1000 0.72671924 5.6548668 - 361000 18.285089 1000 0.72111017 5.6705747 - 362000 18.408849 1000 0.71875181 5.6862827 - 363000 18.533901 1000 0.71469706 5.7019907 - 364000 18.659326 1000 0.70470493 5.7176986 - 365000 18.784109 1000 0.70863047 5.7334066 - 366000 18.911344 1000 0.70850561 5.7491146 - 367000 19.039756 1000 0.71413452 5.7648225 - 368000 19.169907 1000 0.71314184 5.7805305 - 369000 19.299066 1000 0.71309549 5.7962384 - 370000 19.428116 1000 0.71132937 5.8119464 - 371000 19.553027 1000 0.70788039 5.8276544 - 372000 19.678121 1000 0.71780071 5.8433623 - 373000 19.804465 1000 0.72352571 5.8590703 - 374000 19.92949 1000 0.71723739 5.8747783 - 375000 20.053554 1000 0.71556941 5.8904862 - 376000 20.177991 1000 0.70935312 5.9061942 - 377000 20.301972 1000 0.71551157 5.9219022 - 378000 20.427612 1000 0.7235163 5.9376101 - 379000 20.554742 1000 0.73896421 5.9533181 - 380000 20.680899 1000 0.74906169 5.969026 - 381000 20.805515 1000 0.75303336 5.984734 - 382000 20.931483 1000 0.75359492 6.000442 - 383000 21.05731 1000 0.75579354 6.0161499 - 384000 21.184712 1000 0.75178368 6.0318579 - 385000 21.310667 1000 0.74412159 6.0475659 - 386000 21.433509 1000 0.7360955 6.0632738 - 387000 21.554251 1000 0.73461103 6.0789818 - 388000 21.674477 1000 0.72496617 6.0946897 - 389000 21.794698 1000 0.7219047 6.1103977 - 390000 21.914083 1000 0.71837013 6.1261057 - 391000 22.033188 1000 0.71495923 6.1418136 - 392000 22.152689 1000 0.71436707 6.1575216 - 393000 22.271183 1000 0.71447834 6.1732296 - 394000 22.389775 1000 0.71334298 6.1889375 - 395000 22.509106 1000 0.71510229 6.2046455 - 396000 22.628068 1000 0.7121714 6.2203535 - 397000 22.746926 1000 0.70818894 6.2360614 - 398000 22.865086 1000 0.70059455 6.2517694 - 399000 22.982394 1000 0.69960089 6.2674773 - 400000 23.100381 1000 0.70261998 6.2831853 -Loop time of 23.1004 on 4 procs for 200000 steps with 1000 atoms - -Performance: 35345.963 tau/day, 8657.854 timesteps/s, 8.658 Matom-step/s -92.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.263 | 2.1388 | 3.0295 | 58.6 | 9.26 -Neigh | 0.012633 | 0.017793 | 0.023147 | 3.7 | 0.08 -Comm | 7.8521 | 9.0474 | 10.284 | 39.6 | 39.17 -Output | 0.0029549 | 0.004916 | 0.0068506 | 2.0 | 0.02 -Modify | 8.3635 | 9.8066 | 11.142 | 41.0 | 42.45 -Other | | 2.085 | | | 9.03 - -Nlocal: 250 ave 258 max 241 min -Histogram: 1 0 0 0 1 0 0 1 0 1 -Nghost: 412 ave 492 max 332 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 1258.5 ave 1588 max 953 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 5034 -Ave neighs/atom = 5.034 -Neighbor list builds = 159 -Dangerous builds = 0 -Total wall time: 0:00:37 diff --git a/examples/granregion/log.16Mar23.granregion.box.g++.1 b/examples/granregion/log.16Mar23.granregion.box.g++.1 new file mode 100644 index 0000000000..b7bdeda1d4 --- /dev/null +++ b/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 diff --git a/examples/granregion/log.16Mar23.granregion.box.g++.4 b/examples/granregion/log.16Mar23.granregion.box.g++.4 new file mode 100644 index 0000000000..0874981da4 --- /dev/null +++ b/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 diff --git a/examples/granregion/log.16Mar23.granregion.funnel.g++.1 b/examples/granregion/log.16Mar23.granregion.funnel.g++.1 new file mode 100644 index 0000000000..0ead1ddd41 --- /dev/null +++ b/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 diff --git a/examples/granregion/log.16Mar23.granregion.funnel.g++.4 b/examples/granregion/log.16Mar23.granregion.funnel.g++.4 new file mode 100644 index 0000000000..451e508fe3 --- /dev/null +++ b/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 diff --git a/examples/granregion/log.16Mar23.granregion.mixer.g++.1 b/examples/granregion/log.16Mar23.granregion.mixer.g++.1 new file mode 100644 index 0000000000..3fc012d20c --- /dev/null +++ b/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 diff --git a/examples/granregion/log.16Mar23.granregion.mixer.g++.4 b/examples/granregion/log.16Mar23.granregion.mixer.g++.4 new file mode 100644 index 0000000000..b601f3f13a --- /dev/null +++ b/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 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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 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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 diff --git a/examples/pour/log.16Mar23.pour.2d.g++.1 b/examples/pour/log.16Mar23.pour.2d.g++.1 new file mode 100644 index 0000000000..76533e5cbf --- /dev/null +++ b/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 diff --git a/examples/pour/log.16Mar23.pour.2d.g++.4 b/examples/pour/log.16Mar23.pour.2d.g++.4 new file mode 100644 index 0000000000..9ced9784dc --- /dev/null +++ b/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 diff --git a/examples/pour/log.16Mar23.pour.2d.molecule.g++.1 b/examples/pour/log.16Mar23.pour.2d.molecule.g++.1 new file mode 100644 index 0000000000..0c5cbd9dc3 --- /dev/null +++ b/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 diff --git a/examples/pour/log.16Mar23.pour.2d.molecule.g++.4 b/examples/pour/log.16Mar23.pour.2d.molecule.g++.4 new file mode 100644 index 0000000000..f0d3cd2db1 --- /dev/null +++ b/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 diff --git a/examples/pour/log.16Mar23.pour.g++.1 b/examples/pour/log.16Mar23.pour.g++.1 new file mode 100644 index 0000000000..4896a1e4e4 --- /dev/null +++ b/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 diff --git a/examples/pour/log.16Mar23.pour.g++.4 b/examples/pour/log.16Mar23.pour.g++.4 new file mode 100644 index 0000000000..f0ffbd8001 --- /dev/null +++ b/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 diff --git a/examples/pour/log.27Nov18.pour.2d.g++.1 b/examples/pour/log.27Nov18.pour.2d.g++.1 deleted file mode 100644 index d8b615816f..0000000000 --- a/examples/pour/log.27Nov18.pour.2d.g++.1 +++ /dev/null @@ -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 diff --git a/examples/pour/log.27Nov18.pour.2d.g++.4 b/examples/pour/log.27Nov18.pour.2d.g++.4 deleted file mode 100644 index a491cf4866..0000000000 --- a/examples/pour/log.27Nov18.pour.2d.g++.4 +++ /dev/null @@ -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 diff --git a/examples/pour/log.27Nov18.pour.2d.molecule.g++.1 b/examples/pour/log.27Nov18.pour.2d.molecule.g++.1 deleted file mode 100644 index 38d3778b01..0000000000 --- a/examples/pour/log.27Nov18.pour.2d.molecule.g++.1 +++ /dev/null @@ -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 diff --git a/examples/pour/log.27Nov18.pour.2d.molecule.g++.4 b/examples/pour/log.27Nov18.pour.2d.molecule.g++.4 deleted file mode 100644 index 397149fb6a..0000000000 --- a/examples/pour/log.27Nov18.pour.2d.molecule.g++.4 +++ /dev/null @@ -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 diff --git a/examples/pour/log.27Nov18.pour.g++.1 b/examples/pour/log.27Nov18.pour.g++.1 deleted file mode 100644 index a1ebc335cd..0000000000 --- a/examples/pour/log.27Nov18.pour.g++.1 +++ /dev/null @@ -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 diff --git a/examples/pour/log.27Nov18.pour.g++.4 b/examples/pour/log.27Nov18.pour.g++.4 deleted file mode 100644 index 004bf92608..0000000000 --- a/examples/pour/log.27Nov18.pour.g++.4 +++ /dev/null @@ -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 From 4a7ab34568a4413cafe888b84c4ff4e690e2c207 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 22:57:56 -0400 Subject: [PATCH 20/21] lift restriction to Sphinx version < 6.0, enable jquery extension --- doc/utils/requirements.txt | 3 ++- doc/utils/sphinx-config/conf.py.in | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt index 8bec6d4148..a7a03e6e41 100644 --- a/doc/utils/requirements.txt +++ b/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 diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index e8a67cc4f6..0da553d755 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/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', From 21c71bf35d72875202e2d2b615db84eec7437fb2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 16 Mar 2023 23:36:13 -0400 Subject: [PATCH 21/21] mention project boards. remove reference to milestones. --- doc/github-development-workflow.md | 32 +++++++++++++++++------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md index 830ce85f48..fccd75d29a 100644 --- a/doc/github-development-workflow.md +++ b/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_` 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. -These have seen additional, manual testing and review of -results from testing with instrumented code and static code analysis. -Also, the last few feature releases before a stable release are "release -candidate" versions which only contain bug fixes, feature additions to -peripheral functionality, and documentation updates. In between stable -releases, bug fixes and infrastructure updates are back-ported from the -"develop" branch to the "maintenance" branch and occasionally merged -into "stable" and published as update releases. +About once each year, there is a "stable" release of LAMMPS. These have +seen additional, manual testing and review of results from testing with +instrumented code and static code analysis. Also, the last few feature +releases before a stable release are "release candidate" versions which +only contain bug fixes, feature additions to peripheral functionality, +and documentation updates. In between stable releases, bug fixes and +infrastructure updates are back-ported from the "develop" branch to the +"maintenance" branch and occasionally merged into "stable" and published +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", -which corresponds to the next stable release or the stable release after -that, with a tentative release date. +and pull requests are being managed with GitHub Project Boards. There +are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports, +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.