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Merge branch 'develop' into rheo

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jtclemm
2024-10-30 08:24:54 -06:00
parent e1f14e1ee8 6d634dc646
commit 9e25c8610c
442 changed files with 41147 additions and 14830 deletions
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92
.github/workflows/check-cpp23.yml vendored Normal file
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@ -0,0 +1,92 @@
# GitHub action to build LAMMPS on Linux with gcc and C++23
name: "Check for C++23 Compatibility"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build with C++23 support enabled
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache \
libeigen3-dev \
libcurl4-openssl-dev \
mold \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-cpp23-ccache-${{ github.sha }}
restore-keys: linux-cpp23-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/most.cmake \
-C cmake/presets/kokkos-openmp.cmake \
-D CMAKE_CXX_STANDARD=23 \
-D CMAKE_CXX_COMPILER=g++ \
-D CMAKE_C_COMPILER=gcc \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D CMAKE_BUILD_TYPE=Debug \
-D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
-D DOWNLOAD_POTENTIALS=off \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=on \
-D BUILD_TOOLS=off \
-D ENABLE_TESTING=off \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_AWPMD=on \
-D PKG_GPU=on \
-D GPU_API=opencl \
-D PKG_KOKKOS=on \
-D PKG_LATBOLTZ=on \
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_MOLFILE=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s

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

15
cmake/CMakeLists.txt
View File

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

1
cmake/Modules/Documentation.cmake
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@ -110,6 +110,7 @@ if(BUILD_DOC)
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
COMMAND ${Python3_EXECUTABLE} ${LAMMPS_DOC_DIR}/utils/make-globbed-tocs.py -d ${LAMMPS_DOC_DIR}/src
COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF

6
cmake/Modules/FindVORO.cmake
View File

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

2
cmake/Modules/Packages/H5MD.cmake
View File

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

2
cmake/Modules/Packages/VORONOI.cmake
View File

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

15
cmake/presets/kokkos-sycl-intel.cmake
View File

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

21
cmake/presets/oneapi.cmake
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@ -3,26 +3,9 @@
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
# force using internal BLAS/LAPCK since external ones may not be ABI compatible
set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)

7
doc/.gitignore vendored
View File

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

13
doc/Makefile
View File

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

1
doc/src/Commands_fix.rst
View File

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

3
doc/src/Commands_pair.rst
View File

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

41
doc/src/Howto_bioFF.rst
View File

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

8
doc/src/Howto_bpm.rst
View File

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

67
doc/src/Howto_chunk.rst
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@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
Note that this compute allows the per-atom output of other
:doc:`computes <compute>`, :doc:`fixes <fix>`, and
:doc:`variables <variable>` to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See the :doc:`Modify <Modify>`
doc pages for info on how to do this. You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
generate a chunk ID for each atom.
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
<variable>` to be used to define chunk IDs for each atom. This means
you can write your own compute or fix to output a per-atom quantity to
use as chunk ID. See the :doc:`Modify <Modify>` doc pages for info on
how to do this. You can also define a :doc:`per-atom variable
<variable>` in the input script that uses a formula to generate a chunk
ID for each atom.
Fix ave/chunk command:
----------------------
This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
This fix takes the ID of a :doc:`compute chunk/atom
<compute_chunk_atom>` command as input. For each chunk, it then sums
one or more specified per-atom values over the atoms in each chunk. The
per-atom values can be any atom property, such as velocity, force,
charge, potential energy, kinetic energy, stress, etc. Additional
keywords are defined for per-chunk properties like density and
temperature. More generally any per-atom value generated by other
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
variables <variable>`, can be summed over atoms in each chunk.
Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
fix produces a global array as output with one row of values per chunk.
Compute \*/chunk commands:
--------------------------
@ -97,17 +99,20 @@ category:
* :doc:`compute torque/chunk <compute_vcm_chunk>`
* :doc:`compute vcm/chunk <compute_vcm_chunk>`
They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
count of atoms in each chunk and extract other per-chunk properties.
They each take the ID of a :doc:`compute chunk/atom
<compute_chunk_atom>` command as input. As their names indicate, they
calculate the center-of-mass, radius of gyration, moments of inertia,
mean-squared displacement, temperature, torque, and velocity of
center-of-mass for each chunk of atoms. The :doc:`compute
property/chunk <compute_property_chunk>` command can tally the count of
atoms in each chunk and extract other per-chunk properties.
The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
The reason these various calculations are not part of the :doc:`fix
ave/chunk command <fix_ave_chunk>`, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass\*position over the
atoms and then dividing by summed mass.
values in each chunk. For example, many of them require calculation of
a center of mass, which requires summing mass\*position over the atoms
and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, with one or more values per chunk. The output can be used in
@ -118,9 +123,10 @@ various ways:
* As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates.
* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave(). E.g. to
find the largest cluster or fastest diffusing molecule or average
radius-of-gyration of a set of molecules (chunks).
* As input to special functions of :doc:`equal-style variables
<variable>`, like sum() and max() and ave(). E.g. to find the largest
cluster or fastest diffusing molecule or average radius-of-gyration of
a set of molecules (chunks).
Other chunk commands:
---------------------
@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
peratom value across the atoms in each chunk to produce a value per
chunk. When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
create peratom values that induce a new set of chunks with a second
:doc:`compute chunk/atom <compute_chunk_atom>` command.
chunk. When used with the :doc:`compute chunk/spread/atom
<compute_chunk_spread_atom>` command it can create peratom values that
induce a new set of chunks with a second :doc:`compute chunk/atom
<compute_chunk_atom>` command.
Example calculations with chunks
--------------------------------

13
doc/src/Intro_portability.rst
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@ -31,18 +31,19 @@ Operating systems
^^^^^^^^^^^^^^^^^
The primary development platform for LAMMPS is Linux. Thus, the chances
for LAMMPS to compile without problems on Linux machines are the best.
for LAMMPS to compile without problems are the best on Linux machines.
Also, compilation and correct execution on macOS and Windows (using
Microsoft Visual C++) is checked automatically for largest part of the
source code. Some (optional) features are not compatible with all
Microsoft Visual C++) is checked automatically for the largest part of
the source code. Some (optional) features are not compatible with all
operating systems, either through limitations of the corresponding
LAMMPS source code or through source code or build system
incompatibilities of required libraries.
LAMMPS source code or through incompatibilities of source code or
build system of required external libraries or packages.
Executables for Windows may be created natively using either Cygwin or
Visual Studio or with a Linux to Windows MinGW cross-compiler.
Additionally, FreeBSD and Solaris have been tested successfully.
Additionally, FreeBSD and Solaris have been tested successfully to
run LAMMPS and produce results consistent with those on Linux.
Compilers
^^^^^^^^^

2
doc/src/Packages_details.rst
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@ -880,7 +880,7 @@ groups of atoms that interact with the remaining atoms as electrolyte.
**Authors:** The ELECTRODE package is written and maintained by Ludwig
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
Robert Meissner (TUHH, Hamburg, Germany).
Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
.. versionadded:: 4May2022

81
doc/src/Run_windows.rst
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@ -3,71 +3,70 @@ Running LAMMPS on Windows
To run a serial (non-MPI) executable, follow these steps:
* Get a command prompt by going to Start->Run... ,
then typing "cmd".
* Move to the directory where you have your input script,
* Install a LAMMPS installer package from https://packages.lammps.org/windows.html
* Open the "Command Prompt" or "Terminal" app.
* Change to the directory where you have your input script,
(e.g. by typing: cd "Documents").
* At the command prompt, type "lmp -in in.file", where
in.file is the name of your LAMMPS input script.
* At the command prompt, type "lmp -in in.file.lmp", where
``in.file.lmp`` is the name of your LAMMPS input script.
Note that the serial executable includes support for multi-threading
parallelization from the styles in the OPENMP packages. To run with
4 threads, you can type this:
parallelization from the styles in the OPENMP and KOKKOS packages.
To run with 4 threads, you can type this:
.. code-block:: bash
lmp -in in.lj -pk omp 4 -sf omp
lmp -in in.lj.lmp -pk omp 4 -sf omp
lmp -in in.lj.lmp -k on t 4 -sf kk
Alternately, you can also install a package with LAMMPS-GUI included and
open the LAMMPS-GUI app (the package includes the command line version
of LAMMPS as well) and open the input file in the GUI and run it from
there. For details on LAMMPS-GUI, see :doc:`Howto_lammps_gui`.
----------
For the MPI executable, which allows you to run LAMMPS under Windows
in parallel, follow these steps.
For the MS-MPI executables, which allow you to run LAMMPS under Windows
in parallel using MPI rather than multi-threading, follow these steps.
Download and install a compatible MPI library binary package:
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the
installation of the MPICH2 software, it needs to be integrated into
the system. For this you need to start a Command Prompt in
*Administrator Mode* (right click on the icon and select it). Change
into the MPICH2 installation directory, then into the subdirectory
**bin** and execute **smpd.exe -install**\ . Exit the command window.
* Get a new, regular command prompt by going to Start->Run... ,
then typing "cmd".
* Move to the directory where you have your input file
(e.g. by typing: cd "Documents").
Download and install the MS-MPI runtime package ``msmpisetup.exe`` from
https://www.microsoft.com/en-us/download/details.aspx?id=105289 (Note
that the ``msmpisdk.msi`` is **only** required for **compilation** of
LAMMPS from source on Windows using Microsoft Visual Studio). After
installation of MS-MPI perform a reboot.
Then you can run the executable in serial like in the example above
or in parallel using MPI with one of the following commands:
.. code-block:: bash
mpiexec -localonly 4 lmp -in in.file
mpiexec -np 4 lmp -in in.file
mpiexec -localonly 4 lmp -in in.file.lmp
mpiexec -np 4 lmp -in in.file.lmp
where in.file is the name of your LAMMPS input script. For the latter
case, you may be prompted to enter the password that you set during
installation of the MPI library software.
where ``in.file.lmp`` is the name of your LAMMPS input script. For the
latter case, you may be prompted to enter the password that you set
during installation of the MPI library software.
In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up.
The parallel executable can also run on a single processor by typing
something like this:
Note that the parallel executable also includes OpenMP multi-threading
through both the OPENMP and the KOKKOS package, which can be combined
with MPI using something like:
.. code-block:: bash
lmp -in in.lj
mpiexec -localonly 2 lmp -in in.lj.lmp -pk omp 2 -sf omp
mpiexec -localonly 2 lmp -in in.lj.lmp -kokkos on t 2 -sf kk
Note that the parallel executable also includes OpenMP
multi-threading, which can be combined with MPI using something like:
.. code-block:: bash
mpiexec -localonly 2 lmp -in in.lj -pk omp 2 -sf omp
-------------
MPI parallelization will work for *all* functionality in LAMMPS and in
many cases the MPI parallelization is more efficient than
multi-threading since LAMMPS was designed from ground up for MPI
parallelization using domain decomposition. Multi-threading is only
available for selected styles and implemented on top of the MPI
parallelization. Multi-threading is most useful for systems with large
load imbalances when using domain decomposition and a smaller number
of threads (<= 8).

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

60
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@ -10,7 +10,7 @@ Syntax
bond_style bpm/spring keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor*
.. parsed-literal::
@ -36,6 +36,9 @@ Syntax
*break* value = *yes* or *no*
indicates whether bonds break during a run
*volume/factor* value = *yes* or *no*
indicates whether forces include the volumetric contribution
Examples
""""""""
@ -44,6 +47,9 @@ Examples
bond_style bpm/spring
bond_coeff 1 1.0 0.05 0.1
bond_style bpm/spring volume/factor yes
bond_coeff 1 1.0 0.05 0.1 0.5
bond_style bpm/spring myfix 1000 time id1 id2
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
dump_modify 1 write_header no
@ -97,15 +103,6 @@ approach the critical strain
w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* :math:`k` (force/distance units)
* :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units)
If the *normalize* keyword is set to *yes*, the elastic bond force will be
normalized by :math:`r_0` such that :math:`k` must be given in force units.
@ -123,6 +120,43 @@ during a simulation run. This will prevent some unnecessary calculation.
However, if a bond reaches a strain greater than :math:`\epsilon_c`,
it will trigger an error.
.. versionadded:: TBD
The *volume/factor* keyword toggles whether an additional multibody
contribution is added to he force using the formulation in
:ref:`(Clemmer2) <multibody-Clemmer>`,
.. math::
\alpha_v \left(\left[\frac{V_i + V_j}{V_{0,i} + V_{0,j}}\right]^{1/3} - \frac{r_{ij}}{r_{0,ij}}\right)
where :math:`\alpha_v` is a user specified coefficient and :math:`V_i`
and :math:`V_{0,i}` are estimates of the current and local volume
of atom :math:`i`. These volumes are calculated as the sum of current
or initial bond lengths cubed. In 2D, the volume is replaced with an area
calculated using bond lengths squared and the cube root in the above equation
is accordingly replaced with a square root. This approximation assumes bonds
are evenly distributed on a spherical surface and neglects constant prefactors
which are irrelevant since only the ratio of volumes matters. This term may be
used to adjust the Poisson's ratio.
If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
(or adding) that bond's contribution.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* :math:`k` (force/distance units)
* :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units)
Additionally, if *volume/factor* is set to *yes*, a fourth coefficient
must be provided:
* :math:`a_v` (force units)
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the
@ -213,7 +247,7 @@ Related commands
Default
"""""""
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, *break* = *yes*, and *volume/factor* = *no*
----------
@ -224,3 +258,7 @@ The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *
.. _Groot4:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _multibody-Clemmer:
**(Clemmer2)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

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

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

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

4
doc/src/compute_composition_atom.rst
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@ -88,6 +88,10 @@ too frequently.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

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

4
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@ -125,10 +125,6 @@ where thermo_temp is the ID of a similarly defined compute of style
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""

10
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@ -206,11 +206,13 @@ IDs and the bond stretch will be printed with thermodynamic output.
The *inputs* keyword allows selection of whether all the inputs are
per-atom or local quantities. As noted above, all the inputs must be
the same kind (per-atom or local). Per-atom is the default setting.
If a compute or fix is specified as an input, it must produce per-atom
or local data to match this setting. If it produces both, e.g. for
the same kind (per-atom or local). Per-atom is the default setting. If
a compute or fix is specified as an input, it must produce per-atom or
local data to match this setting. If it produces both, like for example
the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
this keyword selects between them.
this keyword selects between them. If a compute *only* produces local
data, like for example the :doc:`compute bond/local command
<compute_bond_local>`, the setting "inputs local" is *required*.
----------

93
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@ -37,55 +37,57 @@ Description
Define a calculation that reduces one or more per-atom vectors into
per-chunk values. This can be useful for diagnostic output. Or when
used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
used to create per-atom values that induce a new set of chunks with a
second :doc:`compute chunk/atom <compute_chunk_atom>` command. An
example is given below.
used in conjunction with the :doc:`compute chunk/spread/atom
<compute_chunk_spread_atom>` command it can be used to create per-atom
values that induce a new set of chunks with a second :doc:`compute
chunk/atom <compute_chunk_atom>` command. An example is given below.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
single chunk (or no chunk). The ID for this command is specified as
chunkID. For example, a single chunk could be the atoms in a molecule
or atoms in a spatial bin. See the :doc:`compute chunk/atom
<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
details of how chunks can be defined and examples of how they can be
used to measure properties of a system.
For each atom, this compute accesses its chunk ID from the specified
*chunkID* compute. The per-atom value from an input contributes
to a per-chunk value corresponding the the chunk ID.
*chunkID* compute. The per-atom value from an input contributes to a
per-chunk value corresponding the chunk ID.
The reduction operation is specified by the *mode* setting and is
performed over all the per-atom values from the atoms in each chunk.
The *sum* option adds the pre-atom values to a per-chunk total. The
*min* or *max* options find the minimum or maximum value of the
per-atom values for each chunk.
The *sum* option adds the per-atom values to a per-chunk total. The
*min* or *max* options find the minimum or maximum value of the per-atom
values for each chunk.
Note that only atoms in the specified group contribute to the
reduction operation. If the *chunkID* compute returns a 0 for the
chunk ID of an atom (i.e., the atom is not in a chunk defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
also not contribute to the reduction operation. An input that is a
compute or fix may define its own group which affects the quantities
it returns. For example, a compute with return a zero value for atoms
that are not in the group specified for that compute.
Note that only atoms in the specified group contribute to the reduction
operation. If the *chunkID* compute returns a 0 for the chunk ID of an
atom (i.e., the atom is not in a chunk defined by the :doc:`compute
chunk/atom <compute_chunk_atom>` command), that atom will also not
contribute to the reduction operation. An input that is a compute or
fix may define its own group which affects the quantities it returns.
For example, a compute will return a zero value for atoms that are not
in the group specified for that compute.
Each listed input is operated on independently. Each input can be the
result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
of an atom-style :doc:`variable <variable>`.
result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
evaluation of an atom-style :doc:`variable <variable>`.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
Note that for values from a compute or fix, the bracketed index I can be
specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or
the number of columns in the array (for *mode* = vector), then an
asterisk with no numeric values means all indices from 1 to :math:`N`.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to :math:`N` (inclusive). A
middle asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. For example, the following two compute reduce/chunk
commands are equivalent, since the
:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
had been listed one by one. For example, the following two compute
reduce/chunk commands are equivalent, since the :doc:`compute
property/chunk <compute_property_chunk>` command creates a per-atom
array with 3 columns:
.. code-block:: LAMMPS
@ -164,13 +166,14 @@ Output info
"""""""""""
This compute calculates a global vector if a single input value is
specified, otherwise a global array is output. The number of columns
in the array is the number of inputs provided. The length of the
vector or the number of vector elements or array rows = the number of
chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The vector or array can
be accessed by any command that uses global values from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
specified, otherwise a global array is output. The number of columns in
the array is the number of inputs provided. The length of the vector or
the number of vector elements or array rows = the number of chunks
*Nchunk* as calculated by the specified :doc:`compute chunk/atom
<compute_chunk_atom>` command. The vector or array can be accessed by
any command that uses global values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The per-atom values for the vector or each column of the array will be
in whatever :doc:`units <units>` the corresponding input value is in.
@ -183,7 +186,9 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
:doc:`compute chunk/atom <compute_chunk_atom>`,
:doc:`compute reduce <compute_reduce>`,
:doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
Default
"""""""

2
doc/src/compute_rheo_property_atom.rst
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@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
Many properties require their respective fixes, listed below in related
commands, be defined. For instance, the *viscosity* attribute is the
viscosity of a particle calculated by
:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
properties is described below.
The *phase* property indicates whether the particle is in a fluid state,

3
doc/src/compute_stress_mop.rst
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@ -129,6 +129,9 @@ package <Build_package>` doc page on for more info.
The method is implemented for orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
Contributions from bonds, angles, and dihedrals are not compatible
with MPI parallel runs.
The method only works with two-body pair interactions, because it
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute

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

6
doc/src/compute_temp_partial.rst
View File

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

8
doc/src/computes.rst
View File

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

8
doc/src/dihedrals.rst
View File

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

1
doc/src/fix.rst
View File

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

106
doc/src/fix_adapt.rst
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@ -322,29 +322,33 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
sub-style name. The bond styles that currently work with fix adapt are:
+---------------------------------------------------+---------------------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
+-----------------------------------------------------+---------------------------+------------+
| :doc:`class2 <bond_class2>` | k2,k3,k4,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`gaussian <bond_gaussian>` | alpha,width,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`morse <bond_morse>` | d0,alpha,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | lamda,epsilon,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
----------
@ -367,31 +371,37 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
sub-style name. The angle styles that currently work with fix adapt are:
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/delta <angle_cosine_delta>` | k | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/squared <angle_cosine_squared>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`gaussian <angle_gaussian>` | alpha,width,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.

4
doc/src/fix_addforce.rst
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@ -115,10 +115,6 @@ correctly, the minimization will not converge properly.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

13
doc/src/fix_atom_swap.rst
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@ -119,15 +119,14 @@ groups of atoms that have different charges, these charges will not be
changed when the atom types change.
Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
OK, including the following:
proposed swaps, even complicated potential energy calculations are
acceptable, including the following:
* long-range electrostatics (:math:`k`-space)
* many body pair styles
* hybrid pair styles
* eam pair styles
* hybrid pair styles (with restrictions)
* EAM pair styles
* triclinic systems
* need to include potential energy contributions from other fixes
Some fixes have an associated potential energy. Examples of such fixes
include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
@ -181,6 +180,10 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
When this fix is used with a :doc:`hybrid pair style <pair_hybrid>`
system, only swaps between atom types of the same sub-style (or
combination of sub-styles) are permitted.
This fix cannot be used with systems that do not have per-type masses
(e.g. atom style sphere) since the implemented algorithm pre-computes
velocity rescaling factors from per-type masses and ignores any per-atom

4
doc/src/fix_aveforce.rst
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@ -71,10 +71,6 @@ to it.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

13
doc/src/fix_gcmc.rst
View File

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

2
doc/src/fix_halt.rst
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@ -101,7 +101,7 @@ hstyle = bondmax option.
.. code-block:: LAMMPS
compute bdist all bond/local dist
compute bmax all reduce max c_bdist
compute bmax all reduce max c_bdist inputs local
variable bondmax equal c_bmax
Thus these two versions of a fix halt command will do the same thing:

6
doc/src/fix_langevin.rst
View File

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

7
doc/src/fix_nonaffine_displacement.rst
View File

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

2
doc/src/fix_nph_body.rst
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@ -79,8 +79,6 @@ It also means that changing attributes of *thermo_temp* or
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/fix_npt_body.rst
View File

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

2
doc/src/fix_nvt_body.rst
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@ -85,8 +85,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

16
doc/src/fix_pour.rst
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@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
for the temperature compute you are using.
.. admonition:: Implementation Notes
:class: Hint
The exact insertion procedure depends on many factors (e.g. the range of
diameters inserted or whether molecules are being inserted). However, in
the simplest scenario of monodisperse atoms, the procedure works as
follows. First, the number of timesteps between two insertion events is
calculated as the time for a particle to fall through the insertion region,
accounting for gravity and any region motion. Next, the target number of
particles inserted per event (assuming no failed insertions due to overlaps)
is calculated as the product of the volume fraction and the volume of the
insertion region divided by the volume of a particle (or area in 2D).
Events are repeated until all N particles have been inserted, where
the final event is likely interrupted upon reaching N. Estimates of this
process are printed to the log/screen at the start of a run.
----------
All other keywords are optional with defaults as shown below.

60
doc/src/fix_qeq.rst
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@ -1,6 +1,7 @@
.. index:: fix qeq/point
.. index:: fix qeq/shielded
.. index:: fix qeq/slater
.. index:: fix qeq/ctip
.. index:: fix qeq/dynamic
.. index:: fix qeq/fire
@ -13,6 +14,9 @@ fix qeq/shielded command
fix qeq/slater command
======================
fix qeq/ctip command
====================
fix qeq/dynamic command
=======================
@ -27,18 +31,20 @@ Syntax
fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/ctip* or *qeq/dynamic* or *qeq/fire*
* Nevery = perform charge equilibration every this many steps
* cutoff = global cutoff for charge-charge interactions (distance unit)
* tolerance = precision to which charges will be equilibrated
* maxiter = maximum iterations to perform charge equilibration
* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
* qfile = a filename with QEq parameters or *coul/streitz* or *coul/ctip* or *reaxff*
* zero or more keyword/value pairs may be appended
* keyword = *alpha* or *qdamp* or *qstep* or *warn*
* keyword = *alpha* or *cdamp* or *maxrepeat* or *qdamp* or *qstep* or *warn*
.. parsed-literal::
*alpha* value = Slater type orbital exponent (qeq/slater only)
*cdamp* value = damping parameter for Coulomb interactions (qeq/ctip only)
*maxrepeat* value = number of equilibration cycles allowed to ensure no atoms cross charge bounds (qeq/ctip only)
*qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
@ -51,6 +57,7 @@ Examples
fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
fix 1 all qeq/ctip 1 12 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
@ -103,7 +110,7 @@ equalizes the derivative of energy with respect to charge of all the
atoms) by adjusting the partial charge on individual atoms based on
interactions with their neighbors within *cutoff*\ . It requires a few
parameters in the appropriate units for each atom type which are read
from a file specified by *qfile*\ . The file has the following format
from a file specified by *qfile*\ . The file has the following format:
.. parsed-literal::
@ -112,20 +119,32 @@ from a file specified by *qfile*\ . The file has the following format
...
Ntype chi eta gamma zeta qcore
except for fix style *qeq/ctip* where the format is:
.. parsed-literal::
1 chi eta gamma zeta qcore qmin qmax omega
2 chi eta gamma zeta qcore qmin qmax omega
...
Ntype chi eta gamma zeta qcore qmin qmax omega
There have to be parameters given for every atom type. Wildcard entries
are possible using the same type range syntax as for "coeff" commands
(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
Empty lines or any text following the pound sign (#) are ignored.
Each line starts with the atom type followed by five parameters.
Only a subset of the parameters is used by each QEq style as described
below, thus the others can be set to 0.0 if desired, but all five
entries per line are required.
Empty lines or any text following the pound sign (#) are ignored. Each
line starts with the atom type followed by eight parameters. Only a
subset of the parameters is used by each QEq style as described below,
thus the others can be set to 0.0 if desired, but all eight entries per
line are required.
* *chi* = electronegativity in energy units
* *eta* = self-Coulomb potential in energy units
* *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
* *qmin* = lower bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
* *qmax* = upper bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
* *omega* = penalty parameter used to enforce charge bounds defined by the :ref:`CTIP <CTIP1>` potential in energy units
The fix qeq styles will print a warning if the charges are not
equilibrated within *tolerance* by *maxiter* steps, unless the
@ -171,6 +190,22 @@ on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
usually a good number. Keyword *alpha* can be used to change the Slater
type orbital exponent.
.. versionadded:: TBD
The *qeq/ctip* style describes partial charges on atoms in the same way
as style *qeq/shielded* but also enables the definition of charge
bounds. Only the *chi*, *eta*, *gamma*, *qmin*, *qmax*, and *omega*
parameters from the *qfile* file are used. When using the string
*coul/ctip* as filename, these parameters are extracted directly from an
active *coul/ctip* pair style. This style solves partial charges on
atoms via the matrix inversion method. Keyword *cdamp* can be used to
change the damping parameter used to calculate Coulomb interactions.
Keyword *maxrepeat* can be used to adjust the number of equilibration
cycles allowed to ensure no atoms have crossed the charge bounds. A
value of 10 is usually a good choice. A tolerance between 1.0e-6 and
1.0e-8 is usually a good choice but should be checked in conjunction
with the timestep for adequate energy conservation during dynamic runs.
The *qeq/dynamic* style describes partial charges on atoms as point
charges that interact through 1/r, but the extended Lagrangian method is
used to solve partial charges on atoms. Only the *chi* and *eta*
@ -186,7 +221,7 @@ minimization algorithm to solve for equilibrium charges. Keyword
*qdamp* can be used to change the damping factor, while keyword *qstep*
can be used to change the time step size.
Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe
Note that *qeq/point*, *qeq/shielded*, *qeq/slater*, and *qeq/ctip* describe
different charge models, whereas the matrix inversion method and the
extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
different solvers.
@ -266,6 +301,11 @@ Chemistry, 95, 3358-3363 (1991).
**(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
16, 11996 (1994)
.. _CTIP1:
**(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
in preparation
.. _vanDuin:
**(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J

3
doc/src/fix_rheo.rst
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@ -16,8 +16,7 @@ Syntax
* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
* zmin = minimal number of neighbors for reproducing kernels
* zero or more keyword/value pairs may be appended to args
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
*shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
.. parsed-literal::

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

8
doc/src/fixes.rst
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@ -1,8 +0,0 @@
Fixes
#####
.. toctree::
:maxdepth: 1
:glob:
fix_*

4
doc/src/group.rst
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@ -162,7 +162,7 @@ potential energy is above the threshold value :math:`-3.0`.
compute 1 all pe/atom
compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0
run 0 post no
variable eatom atom "c_1 > -3.0"
group hienergy variable eatom
@ -173,7 +173,7 @@ Note that these lines
compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0
run 0 post no
are necessary to ensure that the "eatom" variable is current when the
group command invokes it. Because the eatom variable computes the

8
doc/src/impropers.rst
View File

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

2
doc/src/min_style.rst
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@ -3,6 +3,8 @@
min_style cg command
====================
Accelerator Variant: *cg/kk*
min_style hftn command
======================

35
doc/src/pair_bpm_spring.rst
View File

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

3
doc/src/pair_brownian.rst
View File

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

55
doc/src/pair_coul.rst
View File

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

4
doc/src/pair_coul_diel.rst
View File

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

4
doc/src/pair_coul_slater.rst
View File

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

4
doc/src/pair_granular.rst
View File

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

4
doc/src/pair_mesodpd.rst
View File

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

4
doc/src/pair_mie.rst
View File

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

4
doc/src/pair_sph_heatconduction.rst
View File

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

4
doc/src/pair_sph_lj.rst
View File

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

4
doc/src/pair_sph_taitwater.rst
View File

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

1
doc/src/pair_style.rst
View File

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

8
doc/src/pairs.rst
View File

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

51
doc/src/read_dump.rst
View File

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

54
doc/utils/check-styles.py
View File

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

1
doc/utils/converters/.gitignore vendored
View File

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

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

2
doc/utils/requirements.txt
View File

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

4
doc/utils/sphinx-config/false_positives.txt
View File

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

6
examples/ASPHERE/line/in.line
View File

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

22
examples/ASPHERE/line/in.line.srd
View File

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

213
examples/ASPHERE/line/log.1Feb14.line.g++.8
View File

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

244
examples/ASPHERE/line/log.1Feb14.line.srd.g++.8
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@ -1,244 +0,0 @@
LAMMPS (1 Feb 2014)
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
units lj
atom_style line
atom_modify first big
dimension 2
read_data data.line.srd
orthogonal box = (-28.7968 -28.7968 -0.5) to (28.7968 28.7968 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
400 atoms
400 lines
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block INF INF INF INF -0.001 0.001
lattice sq 10.0
Lattice spacing in x,y,z = 0.316228 0.316228 0.316228
create_atoms 2 region plane
Created 33489 atoms
group big type 1
400 atoms in group big
group small type 2
33489 atoms in group small
set group small mass 0.01
33489 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
Deleted 13605 atoms, new total = 20284
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 400 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.35 y scale 0.35
fix 4 all enforce2d
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step temp c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
compute 10 big property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.99882 0.503306
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 230 230 1
SRD grid size: request, actual (xyz) = 0.25, 0.250407 0.250407 1
SRD per actual grid cell = 0.444963
SRD viscosity = 4.2356
big/SRD mass density ratio = 14.0918
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 15.906 29.1054
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 7.79007 Mbytes
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
0 0 1.4528554 0 0 0 0 0 0
1000 0 1.1122612 1.1071958 0.00058011072 0 0 0 0.32625408
2000 0 1.0254475 1.0231236 0.00072347646 -2.3144253e-06 -0.00011736451 -0.00011736451 0.44526308
3000 0 1.0089214 0.99966408 0.00061511441 -0.00023298189 -0.011814512 -0.011814512 0.87208025
4000 0 1.0066185 0.99391102 0.00079065587 -0.0021630644 -0.10968899 -0.10968899 1.3901494
5000 0 1.0109003 1.0009124 0.00071588733 -0.0040023493 -0.20295913 -0.20295913 1.2736445
6000 0 1.0119642 1.0105049 0.00080741361 -0.0067908165 -0.34436231 -0.34436231 2.5492857
7000 0 1.0048989 0.98912274 0.00098851463 -0.010933999 -0.55446309 -0.55446309 3.5707613
8000 0 1.0021597 0.99377939 0.0008405671 -0.015690841 -0.79568252 -0.79568252 6.685381
9000 0 1.0197546 1.00114 0.0012645557 -0.021124602 -1.0712286 -1.0712286 18.907993
10000 0 1.0401079 1.0184189 0.0036111452 0.0099395852 0.50403637 0.50403637 96.909257
Loop time of 3.93391 on 8 procs for 10000 steps with 20284 atoms
Pair time (%) = 0.110261 (2.80284)
Neigh time (%) = 0.32853 (8.35124)
Comm time (%) = 0.199613 (5.07416)
Outpt time (%) = 0.00108692 (0.0276295)
Other time (%) = 3.29442 (83.7441)
Nlocal: 2535.5 ave 2850 max 2226 min
Histogram: 1 0 1 1 1 1 1 0 1 1
Nghost: 109.25 ave 117 max 102 min
Histogram: 1 0 2 0 1 1 1 1 0 1
Neighs: 526 ave 665 max 407 min
Histogram: 1 2 0 1 0 1 1 1 0 1
Total # of neighbors = 4208
Ave neighs/atom = 0.207454
Neighbor list builds = 522
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-10.0789 -10.0789 -0.5) to (10.0789 10.0789 0.5) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.99882 0.503306
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 81 81 1
SRD grid size: request, actual (xyz) = 0.25, 0.248861 0.248861 1
SRD per actual grid cell = -11.3331
SRD viscosity = -1920.36
big/SRD mass density ratio = -0.546468
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 12.724 40
ave/max big velocity = 1.54523 5.36901
Memory usage per processor = 4.23847 Mbytes
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
10000 0 1.0277413 0 0.0036111452 0.010135973 0.51399517 0.51399517 60.794865
11000 0 1.0024742 1 0.00040482851 -0.031643325 -1.604633 -1.604633 55.531632
12000 0 1.0036177 1 0.00036416993 -0.030844063 -1.5641024 -1.5641024 56.694788
13000 0 1.0043067 1 0.00068862721 -0.030673787 -1.5554677 -1.5554677 56.852537
14000 0 1.0042533 1 0.00050997053 -0.035967153 -1.8238943 -1.8238943 51.254109
15000 0 1.003956 1 0.00048458218 -0.038060147 -1.9300301 -1.9300301 50.346943
16000 0 1.0059929 1 0.0004740426 -0.037433402 -1.8982478 -1.8982478 49.82532
17000 0 1.0042401 1 0.00039855238 -0.034314446 -1.7400855 -1.7400855 48.430648
18000 0 1.0025952 1 0.00046207703 -0.034166102 -1.732563 -1.732563 53.883613
19000 0 1.0025881 1 0.00034818943 -0.037341367 -1.8935807 -1.8935807 48.90662
20000 0 1.0009932 1 0.00031244041 -0.035274728 -1.7887814 -1.7887814 47.665935
21000 0 1.0025603 1 0.0005514826 -0.034350221 -1.7418997 -1.7418997 63.290704
22000 0 1.0038575 1 0.00034453716 -0.03576596 -1.8136918 -1.8136918 49.805726
23000 0 1.0030321 1 0.00049535709 -0.035873083 -1.819124 -1.819124 48.973244
24000 0 1.0048593 1 0.00034225992 -0.03322158 -1.6846663 -1.6846663 52.557383
25000 0 1.0024423 1 0.00059157362 -0.030152319 -1.5290241 -1.5290241 56.733821
26000 0 1.0022703 1 0.00047512976 -0.029563064 -1.499143 -1.499143 56.271943
27000 0 1.0024537 1 0.00054158319 -0.02957039 -1.4995145 -1.4995145 55.246787
28000 0 1.0023325 1 0.00051129428 -0.035115211 -1.7806924 -1.7806924 49.718172
29000 0 1.002865 1 0.00056728135 -0.035484703 -1.7994293 -1.7994293 48.387401
30000 0 1.0022693 1 0.00040284402 -0.033844303 -1.7162446 -1.7162446 50.486676
31000 0 1.0037106 1 0.00056291948 -0.036529699 -1.852421 -1.852421 52.011803
32000 0 1.0022542 1 0.00041877447 -0.036903458 -1.8713743 -1.8713743 52.712289
33000 0 1.0021364 1 0.00040871451 -0.033616728 -1.7047043 -1.7047043 55.199593
34000 0 1.003779 1 0.00040667148 -0.031745412 -1.6098098 -1.6098098 51.055261
35000 0 1.0015547 1 0.00042509365 -0.033603064 -1.7040114 -1.7040114 53.887389
36000 0 1.0024849 1 0.00040589851 -0.032151258 -1.6303903 -1.6303903 55.673615
37000 0 1.0038204 1 0.00040542177 -0.033643242 -1.7060488 -1.7060488 51.834694
38000 0 1.0031777 1 0.00040237126 -0.034711811 -1.7602359 -1.7602359 56.275778
39000 0 1.002777 1 0.00051021239 -0.034375104 -1.7431615 -1.7431615 48.461145
40000 0 1.0053762 1 0.00041566465 -0.036016384 -1.8263908 -1.8263908 48.937456
41000 0 1.0039078 1 0.00049726673 -0.036481888 -1.8499966 -1.8499966 49.290465
42000 0 1.0033408 1 0.00045236191 -0.034254524 -1.7370469 -1.7370469 52.146603
43000 0 1.0039893 1 0.00048362351 -0.032519474 -1.6490625 -1.6490625 53.320599
44000 0 1.0036667 1 0.00046834006 -0.031099875 -1.5770747 -1.5770747 55.907531
45000 0 1.0035765 1 0.0005195031 -0.029559708 -1.4989728 -1.4989728 56.191165
46000 0 1.004514 1 0.00050134348 -0.028852909 -1.463131 -1.463131 57.547696
47000 0 1.003864 1 0.00038963389 -0.031339229 -1.5892123 -1.5892123 55.775764
48000 0 1.003145 1 0.00035436452 -0.032390682 -1.6425315 -1.6425315 55.233354
49000 0 1.0042615 1 0.00053161075 -0.029960468 -1.5192953 -1.5192953 54.611685
50000 0 1.0037096 1 0.00031191389 -0.02942011 -1.4918938 -1.4918938 58.653762
Loop time of 27.1275 on 8 procs for 40000 steps with 20284 atoms
Pair time (%) = 1.54277 (5.68709)
Neigh time (%) = 1.26864 (4.67658)
Comm time (%) = 1.19871 (4.4188)
Outpt time (%) = 0.00421953 (0.0155544)
Other time (%) = 23.1132 (85.202)
Nlocal: 2535.5 ave 2670 max 2406 min
Histogram: 1 1 1 0 0 2 1 1 0 1
Nghost: 114.5 ave 124 max 103 min
Histogram: 1 0 1 0 2 1 0 1 0 2
Neighs: 521.5 ave 692 max 442 min
Histogram: 3 1 1 1 0 0 0 1 0 1
Total # of neighbors = 4172
Ave neighs/atom = 0.205679
Neighbor list builds = 2002
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

189
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
units lj
atom_style line
dimension 2
read_data data.line
Reading data file ...
orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
350 atoms
350 lines
read_data CPU = 0.003 seconds
velocity all create 1.44 320984 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra all
pair_style line/lj 2.5
pair_coeff * * 0.25 0.25 1.0 0.25 2.5
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
100 rigid bodies with 350 atoms
fix 3 all deform 5 x scale 0.8 y scale 0.8
fix 4 all enforce2d
compute 10 all property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
#dump 2 all custom 500 dump1.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
timestep 0.001
compute 1 all erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
compute_modify thermo_temp extra/dof -350
thermo 1000
thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 33 33 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes
Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
0 1.1872976 0 0.46543528 0.03617212 0.46543528 0 0.5016074
1000 1.9084412 -0.001043719 0.71003395 0.089891202 0.71003395 -0.001043719 0.79888143
2000 2.31668 -0.020711665 0.83611544 0.13062287 0.83611544 -0.020711665 0.94602664
3000 2.3094506 -0.062018072 0.80584123 0.15326943 0.80584123 -0.062018072 0.8970926
4000 2.4383442 -0.053659995 0.86864073 0.14696993 0.86864073 -0.053659995 0.96195067
5000 2.5885917 -0.15612821 0.90351683 0.17156633 0.90351683 -0.15612821 0.91895495
6000 2.1187379 -0.072041135 0.76933527 0.11557939 0.76933527 -0.072041135 0.81287353
7000 2.1407592 -0.057727294 0.75154343 0.13827066 0.75154343 -0.057727294 0.8320868
8000 2.0661844 -0.097529608 0.71093839 0.14547433 0.71093839 -0.097529608 0.75888311
9000 2.1574445 -0.052890857 0.78826145 0.11363136 0.78826145 -0.052890857 0.84900195
10000 2.473097 -0.092376489 0.85756337 0.16861278 0.85756337 -0.092376489 0.93379965
Loop time of 1.16704 on 1 procs for 10000 steps with 350 atoms
Performance: 740334.372 tau/day, 8568.685 timesteps/s, 2.999 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.80757 | 0.80757 | 0.80757 | 0.0 | 69.20
Neigh | 0.0090046 | 0.0090046 | 0.0090046 | 0.0 | 0.77
Comm | 0.011808 | 0.011808 | 0.011808 | 0.0 | 1.01
Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.02
Modify | 0.3317 | 0.3317 | 0.3317 | 0.0 | 28.42
Other | | 0.006768 | | | 0.58
Nlocal: 350 ave 350 max 350 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 101 ave 101 max 101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 853 ave 853 max 853 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 853
Ave neighs/atom = 2.4371429
Neighbor list builds = 274
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
#dump 2 all custom 500 dump2.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.01 units box
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton/tri
stencil: half/bin/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.756 | 4.756 | 4.756 Mbytes
Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
10000 2.473097 -0.092380532 0.85753671 0.16863499 0.85753671 -0.092380532 0.93379117
11000 2.5185915 -0.1015737 0.84230876 0.197573 0.84230876 -0.1015737 0.93830806
12000 2.5971728 -0.13087195 0.90608898 0.17248755 0.90608898 -0.13087195 0.94770458
13000 2.5065714 -0.14666584 0.83804307 0.19683483 0.83804307 -0.14666584 0.88821206
14000 2.1672357 -0.10720878 0.79713452 0.10973398 0.79713452 -0.10720878 0.79965972
15000 2.3444438 -0.14780285 0.81642139 0.15695019 0.81642139 -0.14780285 0.82556873
16000 2.2672973 -0.12590007 0.76672668 0.17081014 0.76672668 -0.12590007 0.81163675
17000 2.3999651 -0.15464102 0.85708567 0.14289234 0.85708567 -0.15464102 0.84533699
18000 2.2024356 -0.14077779 0.76727873 0.14718521 0.76727873 -0.14077779 0.77368615
19000 2.5411572 -0.092014576 0.85750101 0.19297197 0.85750101 -0.092014576 0.95845841
20000 2.2113691 -0.11944862 0.77295445 0.14564597 0.77295445 -0.11944862 0.79915181
Loop time of 1.76388 on 1 procs for 10000 steps with 350 atoms
Performance: 489827.896 tau/day, 5669.304 timesteps/s, 1.984 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3668 | 1.3668 | 1.3668 | 0.0 | 77.49
Neigh | 0.018849 | 0.018849 | 0.018849 | 0.0 | 1.07
Comm | 0.013338 | 0.013338 | 0.013338 | 0.0 | 0.76
Output | 0.00020434 | 0.00020434 | 0.00020434 | 0.0 | 0.01
Modify | 0.35698 | 0.35698 | 0.35698 | 0.0 | 20.24
Other | | 0.007667 | | | 0.43
Nlocal: 350 ave 350 max 350 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 119 ave 119 max 119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 997 ave 997 max 997 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 997
Ave neighs/atom = 2.8485714
Neighbor list builds = 283
Dangerous builds = 0
Total wall time: 0:00:02

189
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
units lj
atom_style line
dimension 2
read_data data.line
Reading data file ...
orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
350 atoms
350 lines
read_data CPU = 0.003 seconds
velocity all create 1.44 320984 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra all
pair_style line/lj 2.5
pair_coeff * * 0.25 0.25 1.0 0.25 2.5
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
100 rigid bodies with 350 atoms
fix 3 all deform 5 x scale 0.8 y scale 0.8
fix 4 all enforce2d
compute 10 all property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
#dump 2 all custom 500 dump1.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
timestep 0.001
compute 1 all erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
compute_modify thermo_temp extra/dof -350
thermo 1000
thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 33 33 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.736 | 4.736 | 4.736 Mbytes
Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
0 1.1872976 0 0.46543528 0.03617212 0.46543528 0 0.5016074
1000 1.9084412 -0.001043719 0.71003395 0.089891202 0.71003395 -0.001043719 0.79888143
2000 2.31668 -0.020711665 0.83611544 0.13062287 0.83611544 -0.020711665 0.94602664
3000 2.3094506 -0.062018072 0.80584123 0.15326943 0.80584123 -0.062018072 0.8970926
4000 2.4383442 -0.053659995 0.86864073 0.14696993 0.86864073 -0.053659995 0.96195067
5000 2.5885917 -0.15612821 0.90351683 0.17156633 0.90351683 -0.15612821 0.91895494
6000 2.118738 -0.072041141 0.76933528 0.1155794 0.76933528 -0.072041141 0.81287354
7000 2.1407609 -0.057727453 0.75154404 0.13827078 0.75154404 -0.057727453 0.83208737
8000 2.066348 -0.097639137 0.71096217 0.14551295 0.71096217 -0.097639137 0.75883597
9000 2.1969096 -0.050133795 0.8028133 0.11559948 0.8028133 -0.050133795 0.86827899
10000 2.3932442 -0.098008752 0.83753779 0.15678193 0.83753779 -0.098008752 0.89631097
Loop time of 0.596624 on 4 procs for 10000 steps with 350 atoms
Performance: 1448149.372 tau/day, 16760.988 timesteps/s, 5.866 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17419 | 0.21073 | 0.27006 | 7.8 | 35.32
Neigh | 0.0015899 | 0.0018079 | 0.0020932 | 0.5 | 0.30
Comm | 0.041688 | 0.101 | 0.13805 | 11.3 | 16.93
Output | 0.00011945 | 0.0001262 | 0.000143 | 0.0 | 0.02
Modify | 0.26906 | 0.27183 | 0.27467 | 0.4 | 45.56
Other | | 0.01113 | | | 1.87
Nlocal: 87.5 ave 94 max 80 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 54.5 ave 67 max 42 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 212.75 ave 286 max 122 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 851
Ave neighs/atom = 2.4314286
Neighbor list builds = 273
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
#dump 2 all custom 500 dump2.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.01 units box
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton/tri
stencil: half/bin/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
10000 2.3932442 -0.098029446 0.83751359 0.1568021 0.83751359 -0.098029446 0.89628624
11000 2.4541893 -0.15538223 0.82053681 0.19271549 0.82053681 -0.15538223 0.85787007
12000 2.4124449 -0.14024177 0.84559598 0.15692416 0.84559598 -0.14024177 0.86227837
13000 2.2095814 -0.10822636 0.73930104 0.173052 0.73930104 -0.10822636 0.80412668
14000 2.0946831 -0.087303541 0.77743494 0.10023865 0.77743494 -0.087303541 0.79037005
15000 2.0911016 -0.11524594 0.74044758 0.12978235 0.74044758 -0.11524594 0.75498398
16000 1.9736428 -0.17259563 0.67852978 0.13943094 0.67852978 -0.17259563 0.64536509
17000 2.3284367 -0.17673537 0.77018991 0.1897596 0.77018991 -0.17673537 0.78321414
18000 2.3178564 -0.16634746 0.81488323 0.1487365 0.81488323 -0.16634746 0.79727227
19000 2.7497251 -0.18254513 1.0041125 0.14528424 1.0041125 -0.18254513 0.96685165
20000 2.3897059 -0.12664177 0.8390411 0.15426546 0.8390411 -0.12664177 0.86666479
Loop time of 0.79519 on 4 procs for 10000 steps with 350 atoms
Performance: 1086533.223 tau/day, 12575.616 timesteps/s, 4.401 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26601 | 0.35051 | 0.443 | 12.3 | 44.08
Neigh | 0.0029891 | 0.0036725 | 0.0040631 | 0.7 | 0.46
Comm | 0.049744 | 0.14268 | 0.22734 | 19.3 | 17.94
Output | 0.00013783 | 0.00014503 | 0.00016304 | 0.0 | 0.02
Modify | 0.27963 | 0.28446 | 0.29049 | 0.8 | 35.77
Other | | 0.01372 | | | 1.73
Nlocal: 87.5 ave 101 max 75 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 61.5 ave 67 max 50 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 244.75 ave 268 max 198 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 979
Ave neighs/atom = 2.7971429
Neighbor list builds = 289
Dangerous builds = 0
Total wall time: 0:00:01

363
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
units lj
atom_style line
atom_modify first big
dimension 2
read_data data.line.srd
Reading data file ...
orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
400 atoms
400 lines
read_data CPU = 0.003 seconds
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region plane block INF INF INF INF -0.001 0.001
lattice sq 10.0
Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
create_atoms 2 region plane
Created 33489 atoms
using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
create_atoms CPU = 0.003 seconds
group big type 1
400 atoms in group big
group small type 2
33489 atoms in group small
set group small mass 0.01
Setting atom values ...
33489 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 1.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 64 64 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:313)
Deleted 13605 atoms, new total = 20284
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.8 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
pair_coeff 1 2 1.0 0.2 1.0 0.2 2.5
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0001
fix 1 big rigid molecule
100 rigid bodies with 400 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 1.25 y scale 1.25
fix 4 all enforce2d
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -350
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
compute 10 big property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.02
SRD max distance & max velocity = 0.08 40
SRD grid counts: 230 230 1
SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
SRD per actual grid cell = 0.45503978
SRD viscosity = 0.92062623
big/SRD mass density ratio = 12.298053
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 15.906001 29.105426
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 35 35 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 43.18 | 43.18 | 43.18 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
0 1.6084386 0 0 0 0 0 0
1000 1.4566787 1.2042825 0.00015900089 0.0011955837 0 0.060628048 0.75322967
2000 1.3561018 1.2092936 0.00026739313 0.0020783306 0 0.10539215 0.53247025
3000 1.3327447 1.1696777 0.0003215116 0.0024935719 0 0.12644903 0.32024668
4000 1.3031273 1.1385596 0.00037337107 0.0031214473 0 0.15828859 0.64066244
5000 1.28204 1.0983763 0.00047966362 0.0033295434 0 0.16884114 0.32103666
6000 1.2654396 1.0969562 0.00049917373 0.0037382387 0 0.18956609 0.16211614
7000 1.2401503 1.1232046 0.00045137168 0.0037522201 0 0.19027508 0.014071672
8000 1.2349025 1.059008 0.00056648801 0.0039664742 0 0.20113991 0.24483817
9000 1.2272907 1.0371006 0.00056271544 0.0037847074 0 0.19192251 0.032968056
10000 1.2153817 1.0209113 0.00053291164 0.0037197691 0 0.18862949 0.3237698
Loop time of 6.0346 on 1 procs for 10000 steps with 20284 atoms
Performance: 14317.424 tau/day, 1657.109 timesteps/s, 33.613 Matom-step/s
96.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10636 | 0.10636 | 0.10636 | 0.0 | 1.76
Neigh | 0.01905 | 0.01905 | 0.01905 | 0.0 | 0.32
Comm | 0.041223 | 0.041223 | 0.041223 | 0.0 | 0.68
Output | 0.0017015 | 0.0017015 | 0.0017015 | 0.0 | 0.03
Modify | 5.8165 | 5.8165 | 5.8165 | 0.0 | 96.39
Other | | 0.04976 | | | 0.82
Nlocal: 20284 ave 20284 max 20284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 500
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip #tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.0002 units box remap v
run 30000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.02
SRD max distance & max velocity = 0.08 40
SRD grid counts: 288 288 1
SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
SRD per actual grid cell = 0.26976265
SRD viscosity = 1.0312189
big/SRD mass density ratio = 20.672578
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 12.805429 40
ave/max big velocity = 0.50400801 2.1697856
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 44 44 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 58.85 | 58.85 | 58.85 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
10000 1.0423767 0 0.00053289774 0.0037197858 0 0.18863034 0.014558088
11000 1.0333923 1.0309908 0.00058283908 0.0042336078 0 0.21468625 0.13036048
12000 1.0268543 1.0290122 0.00055294944 0.0044278861 0 0.2245381 0.53275676
13000 1.0257856 1.0140434 0.00051520803 0.0042888387 0 0.21748701 0.2066835
14000 1.0239497 1.0321558 0.00054742053 0.004259664 0 0.21600756 0.24430097
15000 1.0194475 1.0119806 0.00053619565 0.0041113765 0 0.2084879 0.18420434
16000 1.016421 1.0309991 0.00049553642 0.0041338645 0 0.20962827 0.18298406
17000 1.0088527 0.99723694 0.00049824173 0.0044777581 0 0.22706711 0.65557023
18000 1.0073877 1.0136962 0.00058327835 0.0045355884 0 0.22999969 0.13700737
19000 1.0026916 1.0253129 0.00056760151 0.0045138437 0 0.22889701 0.16443344
20000 1.0024042 0.98988084 0.00057568118 0.0048644983 0 0.24667871 0.060864322
21000 0.99500641 0.99075324 0.00062187543 0.0050480594 0 0.25598709 0.18428384
22000 0.99286446 0.98642266 0.00061024492 0.0050497174 0 0.25607117 0.18499738
23000 0.99204086 0.98869005 0.00064013575 0.0052921112 0 0.26836296 0.046987646
24000 0.98768375 1.0110613 0.00065868636 0.0049285304 0 0.24992578 0.22623751
25000 0.98763308 0.98752678 0.00067070463 0.0049364253 0 0.25032613 0.022819382
26000 0.9844889 1.0059918 0.00075364589 0.0053381778 0 0.270699 0.089735771
27000 0.98574608 0.99094039 0.00080711088 0.0054137233 0 0.27452991 0.14477885
28000 0.98139419 0.97487219 0.00071242405 0.0053315389 0 0.27036234 -0.016357088
29000 0.98458705 0.98600894 0.00068355573 0.0050157315 0 0.25434775 0.015749835
30000 0.98440759 1.0010793 0.00067594666 0.0048121267 0 0.24402295 0.20422918
31000 0.98060632 0.9825933 0.00069529947 0.0050649881 -0.00010700206 0.25684555 0.0014601267
32000 0.97616624 0.94976641 0.00067682494 0.0052111319 -0.00013230279 0.2642565 0.013738873
33000 0.97926122 0.95756794 0.00071774059 0.0053716513 -0.00024804252 0.27239644 0.10643895
34000 0.97227771 0.94365547 0.00080885359 0.0055744144 -0.00063217879 0.28267856 0.12472959
35000 0.97295679 0.98103625 0.0008130852 0.0057598371 -0.00097218501 0.29208134 0.88422099
36000 0.97131919 0.97164636 0.0008345433 0.0062212675 -0.001543055 0.31548048 0.22389401
37000 0.96988732 0.98589058 0.00083271625 0.0062999411 -0.0026064482 0.31947001 0.11797226
38000 0.97135512 0.96486494 0.00076943974 0.0057397763 -0.0041174109 0.29106406 0.072790492
39000 0.97386738 0.95218062 0.00079594844 0.0056308358 -0.0069006312 0.28553968 0.12417837
40000 0.97914045 1.0033941 0.000830798 0.0055952714 -0.0086705514 0.28373621 0.1976663
Loop time of 15.944 on 1 procs for 30000 steps with 20284 atoms
Performance: 16256.931 tau/day, 1881.589 timesteps/s, 38.166 Matom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.31871 | 0.31871 | 0.31871 | 0.0 | 2.00
Neigh | 0.082974 | 0.082974 | 0.082974 | 0.0 | 0.52
Comm | 0.16092 | 0.16092 | 0.16092 | 0.0 | 1.01
Output | 0.0047257 | 0.0047257 | 0.0047257 | 0.0 | 0.03
Modify | 15.189 | 15.189 | 15.189 | 0.0 | 95.27
Other | | 0.1871 | | | 1.17
Nlocal: 20284 ave 20284 max 20284 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 76 ave 76 max 76 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38 ave 38 max 38 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38
Ave neighs/atom = 0.0018733978
Neighbor list builds = 1500
Dangerous builds = 0
Total wall time: 0:00:22

363
examples/ASPHERE/line/log.21Sep24.line.srd.g++.4 Normal file
View File

@ -0,0 +1,363 @@
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
units lj
atom_style line
atom_modify first big
dimension 2
read_data data.line.srd
Reading data file ...
orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
400 atoms
400 lines
read_data CPU = 0.003 seconds
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region plane block INF INF INF INF -0.001 0.001
lattice sq 10.0
Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
create_atoms 2 region plane
Created 33489 atoms
using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
create_atoms CPU = 0.001 seconds
group big type 1
400 atoms in group big
group small type 2
33489 atoms in group small
set group small mass 0.01
Setting atom values ...
33489 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 1.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 64 64 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:313)
Deleted 13605 atoms, new total = 20284
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.8 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
pair_coeff 1 2 1.0 0.2 1.0 0.2 2.5
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0001
fix 1 big rigid molecule
100 rigid bodies with 400 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 1.25 y scale 1.25
fix 4 all enforce2d
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -350
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
compute 10 big property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.02
SRD max distance & max velocity = 0.08 40
SRD grid counts: 230 230 1
SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
SRD per actual grid cell = 0.45503978
SRD viscosity = 0.92062623
big/SRD mass density ratio = 12.298053
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 15.906001 29.105426
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 35 35 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 13.44 | 13.45 | 13.47 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
0 1.6084386 0 0 0 0 0 0
1000 1.4539924 1.2578325 0.0001679809 0.0010497614 0 0.053233399 0.69841607
2000 1.3516746 1.1693535 0.00031932331 0.0021450754 0 0.10877677 0.058141137
3000 1.3294093 1.1539986 0.00032558495 0.0022345521 0 0.11331414 0.085892255
4000 1.3049311 1.1174444 0.00039637116 0.0026520968 0 0.13448783 0.10574422
5000 1.2790124 1.1209176 0.0004519172 0.0032635257 0 0.16549339 0.59225702
6000 1.2631214 1.0868777 0.00052274216 0.003527049 0 0.17885666 0.26093936
7000 1.2520054 1.0780954 0.00051683183 0.0038111141 0 0.1932616 -0.0014733978
8000 1.2412037 1.0587149 0.00056620143 0.0038329297 0 0.19436786 0.31576462
9000 1.2242125 1.0699712 0.00065335672 0.0039948578 0 0.20257924 0.19755012
10000 1.2155758 1.0279682 0.00059730828 0.004142635 0 0.21007302 0.30022953
Loop time of 1.92412 on 4 procs for 10000 steps with 20284 atoms
Performance: 44903.607 tau/day, 5197.177 timesteps/s, 105.420 Matom-step/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026855 | 0.027529 | 0.028377 | 0.4 | 1.43
Neigh | 0.0073723 | 0.007433 | 0.0075693 | 0.1 | 0.39
Comm | 0.062837 | 0.065574 | 0.066747 | 0.6 | 3.41
Output | 0.00072894 | 0.00076558 | 0.00083361 | 0.0 | 0.04
Modify | 1.7861 | 1.7926 | 1.8 | 0.4 | 93.16
Other | | 0.03026 | | | 1.57
Nlocal: 5071 ave 5096 max 5051 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 44 ave 51 max 40 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 500
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip #tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.0002 units box remap v
run 30000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.02
SRD max distance & max velocity = 0.08 40
SRD grid counts: 288 288 1
SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
SRD per actual grid cell = 0.26976265
SRD viscosity = 1.0312189
big/SRD mass density ratio = 20.672578
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 12.826666 40
ave/max big velocity = 0.53469722 1.7415554
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 44 44 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 17.6 | 17.6 | 17.61 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
10000 1.0416233 0 0.0005972922 0.0041426543 0 0.210074 0.016213064
11000 1.0366852 1.0236717 0.00066926382 0.004404743 0 0.22336452 0.097686059
12000 1.028695 1.0023004 0.00065323121 0.0043971164 0 0.22297777 0.30007875
13000 1.0223214 1.0296267 0.00060201395 0.0041815724 0 0.21204754 0.17307062
14000 1.0210601 1.0092227 0.00057020066 0.0041936718 0 0.2126611 0.13379405
15000 1.0169223 1.003359 0.00060818329 0.0046120335 0 0.23387622 0.39144341
16000 1.012222 0.99937463 0.00060471571 0.004533278 0 0.22988253 0.16026051
17000 1.0087993 0.98937449 0.00061843646 0.0048888197 0 0.24791205 0.095507016
18000 1.0030288 0.94092316 0.00054252694 0.0046740839 0 0.2370228 -0.070838649
19000 1.0010739 0.99759814 0.00054041829 0.0045481798 0 0.2306382 0.1944996
20000 1.004189 1.0157285 0.00053330893 0.0044999261 0 0.22819125 0.14452619
21000 0.99601133 1.003771 0.00053282188 0.0048954851 0 0.24825005 0.20196263
22000 0.99445408 1.0163465 0.00059954941 0.0051668276 0 0.26200983 0.21332194
23000 0.99663947 0.94920707 0.00057729723 0.0051052499 0 0.25888722 0.19282224
24000 0.99500015 1.0021742 0.00064312956 0.0053430656 0 0.27094686 0.18044164
25000 0.99388189 0.98446723 0.00060150964 0.0054017824 0 0.27392438 0.18844037
26000 0.99632932 0.94670024 0.00052479857 0.004905147 0 0.24874 0.17961314
27000 0.99112962 1.0247118 0.00053159824 0.004752248 0 0.2409865 0.12037737
28000 0.98887153 0.97734068 0.00052255365 0.0050199491 0 0.25456162 0.29110866
29000 0.98938025 0.99467239 0.00053095044 0.0050303107 0 0.25508706 0.59776339
30000 0.99081592 0.98822122 0.00056693985 0.0052452228 0 0.26598525 0.0150843
31000 0.99050903 1.0184912 0.00056742049 0.0056515686 0 0.28659104 0.07877756
32000 0.98929926 0.99257634 0.00058111732 0.005740055 0 0.29107819 0.19146041
33000 0.98698723 0.94872564 0.00056547335 0.0057628447 0 0.29223385 0.076755599
34000 0.98967998 0.98777081 0.00056045905 0.0055645603 0 0.28217885 0.095025284
35000 0.98777734 0.95746323 0.00050104756 0.0055630681 -4.7847642e-05 0.28210318 0.25667997
36000 0.98661597 0.98801246 0.00047074618 0.0054500805 -5.8956193e-05 0.27637358 0.18221607
37000 0.98390111 0.9837894 0.00044581144 0.0054703357 -7.4197741e-05 0.27740072 0.11959303
38000 0.98092646 1.0142057 0.0004945556 0.0056372628 -8.6736668e-05 0.2858656 0.017325263
39000 0.98125957 0.94219822 0.00059691168 0.0060914156 -9.9726556e-05 0.30889569 0.0081217281
40000 0.98362942 0.9649582 0.00062286697 0.0063736358 -0.00010700337 0.32320707 0.293121
Loop time of 5.08621 on 4 procs for 30000 steps with 20284 atoms
Performance: 50961.296 tau/day, 5898.298 timesteps/s, 119.641 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.084321 | 0.084948 | 0.086233 | 0.3 | 1.67
Neigh | 0.027521 | 0.029247 | 0.030632 | 0.7 | 0.58
Comm | 0.19101 | 0.20262 | 0.2068 | 1.5 | 3.98
Output | 0.0019581 | 0.0020369 | 0.0022544 | 0.3 | 0.04
Modify | 4.681 | 4.6884 | 4.7051 | 0.4 | 92.18
Other | | 0.07891 | | | 1.55
Nlocal: 5071 ave 5197 max 4951 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 44 ave 50 max 41 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 5.75 ave 12 max 0 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 23
Ave neighs/atom = 0.0011338986
Neighbor list builds = 1500
Dangerous builds = 0
Total wall time: 0:00:07

323
examples/ASPHERE/line/log.21Sep24.line.srd.g++.8 Normal file
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@ -0,0 +1,323 @@
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
units lj
atom_style line
atom_modify first big
dimension 2
read_data data.line.srd
Reading data file ...
orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
400 atoms
400 lines
read_data CPU = 0.002 seconds
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region plane block INF INF INF INF -0.001 0.001
lattice sq 10.0
Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
create_atoms 2 region plane
Created 33489 atoms
using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
create_atoms CPU = 0.001 seconds
group big type 1
400 atoms in group big
group small type 2
33489 atoms in group small
set group small mass 0.01
Setting atom values ...
33489 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 1.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 64 64 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:313)
Deleted 13605 atoms, new total = 20284
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.8 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
pair_coeff 1 2 1.0 0.2 1.0 0.2 2.5
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0002
fix 1 big rigid molecule
100 rigid bodies with 400 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 1.25 y scale 1.25
fix 4 all enforce2d
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -350
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
compute 10 big property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.04
SRD max distance & max velocity = 0.16 40
SRD grid counts: 230 230 1
SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
SRD per actual grid cell = 0.45503978
SRD viscosity = 1.0732692
big/SRD mass density ratio = 12.298053
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 15.906001 29.105426
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 35 35 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 9.752 | 9.762 | 9.781 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
0 1.4809886 0 0 0 0 0 0
1000 1.2265081 1.1522909 0.00027866069 0.0022427232 0 0.1137285 0.58262976
2000 1.1757141 1.1251323 0.00040597152 0.003287261 0 0.16669701 0.27109853
3000 1.126304 1.0646585 0.00050542958 0.0040748897 0 0.20663766 0.36959653
4000 1.1140297 1.0761435 0.00060430927 0.0052863645 0 0.26807154 0.35099205
5000 1.0823307 1.0256814 0.00066557681 0.0051213284 0 0.25970256 0.28491631
6000 1.0656188 1.0387091 0.00066454105 0.005213537 0 0.26437846 0.2150581
7000 1.0600108 1.0099931 0.0007238719 0.005470459 0 0.27740698 0.21846568
8000 1.0464374 1.0049819 0.00061068366 0.0053702582 0 0.27232579 0.1326171
9000 1.0381097 1.0126049 0.00057318728 0.0055976321 0 0.28385592 0.16797796
10000 1.0312982 1.0018962 0.00050597007 0.0051153126 0 0.2593975 0.15281043
Loop time of 1.2997 on 8 procs for 10000 steps with 20284 atoms
Performance: 132953.355 tau/day, 7694.060 timesteps/s, 156.066 Matom-step/s
96.7% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01406 | 0.014495 | 0.01532 | 0.3 | 1.12
Neigh | 0.0051916 | 0.0053424 | 0.0054386 | 0.1 | 0.41
Comm | 0.062053 | 0.065305 | 0.069014 | 0.9 | 5.02
Output | 0.00062289 | 0.00065254 | 0.00077243 | 0.0 | 0.05
Modify | 1.169 | 1.178 | 1.1905 | 0.6 | 90.64
Other | | 0.03589 | | | 2.76
Nlocal: 2535.5 ave 2637 max 2476 min
Histogram: 1 3 1 1 0 0 0 0 1 1
Nghost: 31.125 ave 42 max 25 min
Histogram: 3 0 1 2 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 500
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip #tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.0002 units box remap v
run 40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.9988171 0.50330564
SRD temperature & lamda = 1 0.04
SRD max distance & max velocity = 0.16 40
SRD grid counts: 288 288 1
SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
SRD per actual grid cell = 0.26976265
SRD viscosity = 1.5799049
big/SRD mass density ratio = 20.672578
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 1
ave/max small velocity = 12.481632 40
ave/max big velocity = 0.58815233 1.5489134
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.3
ghost atom cutoff = 3.3
binsize = 1.65, bins = 44 44 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair line/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.95 | 11.95 | 11.95 Mbytes
Step c_tsmall f_2[9] c_1 TotEng v_pebig v_ebig Press
10000 0.98889306 0 0.00050595647 0.0051153289 0 0.25939833 0.020019811
11000 0.98995417 0.99721412 0.0005166709 0.0054320552 0 0.27545952 0.03376188
12000 0.99401168 0.95502319 0.00053659416 0.0054974426 0 0.27877531 0.056856034
13000 0.98790692 0.96488357 0.00061076364 0.0053196554 0 0.26975972 0.2677228
14000 0.98939233 0.98809694 0.00052317779 0.0050536922 0 0.25627273 0.20381427
15000 0.99046365 0.97048828 0.00056914402 0.0053274908 0 0.27015706 0.082163088
16000 0.99743447 1.0111983 0.00053706165 0.0048068384 0 0.24375478 0.06429569
17000 0.99622359 1.0124982 0.0005905197 0.0055966416 -7.4541903e-05 0.2838057 0.25418037
18000 0.99283929 0.99581721 0.00061730878 0.0059098964 -0.00014754106 0.29969084 0.12701702
19000 0.99175517 1.0115581 0.0005128714 0.0059214809 -0.00046203987 0.30027829 0.2640506
20000 0.98895811 0.97731528 0.00052294314 0.0055670021 -0.0016029702 0.28230268 0.26239209
21000 0.98904093 0.98120258 0.00054169978 0.0052762731 -0.0026834879 0.26755981 0.15432481
22000 0.98773149 0.99217218 0.00056091602 0.0052754729 -0.0044093345 0.26751923 0.2208051
23000 0.98802862 0.96564549 0.00062226338 0.0053263454 -0.008790914 0.27009898 0.18058977
24000 0.98754002 1.024015 0.00057178953 0.0054083382 -0.0094859317 0.27425683 0.01598147
25000 0.98656341 0.94647246 0.00066215791 0.0053555849 -0.014877058 0.27158171 0.28794628
26000 0.98750471 1.0077626 0.00058955769 0.0057081639 -0.013151869 0.28946099 0.20814911
27

1
examples/COUPLE/plugin/liblammpsplugin.c
View File

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

1
examples/COUPLE/plugin/liblammpsplugin.h
View File

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

4
examples/bpm/impact/in.bpm.impact.rotational
View File

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

4
examples/bpm/impact/in.bpm.impact.spring
View File

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

484
examples/granregion/log.16Mar23.granregion.box.g++.1
View File

@ -1,484 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170772
1500 99 0.31486693 0.31486693 0.17429055 0.0064903432
1600 99 0.26369001 0.26369001 0.15095266 0.0045226847
1700 100 0.1925923 0.1925923 0.11308104 0.007362313
1800 100 0.13724978 0.13724978 0.083276845 0.0058136373
1900 100 0.077212636 0.077212636 0.053159386 0.0016509598
2000 100 0.065294031 0.065294031 0.04372752 0.0020346467
2100 100 0.057431398 0.057431398 0.037977068 0.0012681098
2200 100 0.059093045 0.059093045 0.037435193 0.00096610799
2300 100 0.03422338 0.03422338 0.025491304 0.00069886052
2400 100 0.020558284 0.020558284 0.016163009 0.0017260663
2500 100 0.015339709 0.015339709 0.012329236 0.00041308031
2600 100 0.012891354 0.012891354 0.009766054 0.00030356722
2700 100 0.0092634449 0.0092634449 0.0073580108 0.00077723051
2800 100 0.0073925841 0.0073925841 0.0059932218 0.00016466767
2900 100 0.0081228267 0.0081228267 0.006281761 0.00013828388
3000 100 0.0041833223 0.0041833223 0.0035147096 0.00013160599
3100 100 0.0035930775 0.0035930775 0.0030039922 0.00060639771
3200 100 0.0030824465 0.0030824465 0.0026541293 0.00047391014
3300 100 0.0035087522 0.0035087522 0.0027664508 0.00014080317
3400 100 0.0018537868 0.0018537868 0.0017099705 6.3326674e-05
3500 100 0.0015371228 0.0015371228 0.0014155433 0.00021612522
3600 100 0.001708556 0.001708556 0.0014369892 8.1034202e-05
3700 100 0.00095948652 0.00095948652 0.0009788528 3.4694023e-05
3800 100 0.00091875668 0.00091875668 0.00086805146 3.9373686e-05
3900 100 0.001557068 0.001557068 0.001159526 2.5178607e-05
4000 100 0.00062012451 0.00062012451 0.00066806922 5.6680551e-06
4100 100 0.00060940771 0.00060940771 0.00065614741 1.0137901e-05
4200 100 0.00059538437 0.00059538437 0.00064501521 7.3679744e-06
4300 100 0.00052946048 0.00052946048 0.00059353641 5.9225081e-06
4400 100 0.00051202281 0.00051202281 0.00057524772 3.6198435e-05
4500 100 0.00049986632 0.00049986632 0.00055754521 2.2275519e-05
4600 100 0.00048187334 0.00048187334 0.00053988815 2.2015243e-05
4700 100 0.00045261491 0.00045261491 0.00050298355 8.9681339e-05
4800 100 0.00034965427 0.00034965427 0.0004278781 1.0983535e-05
4900 100 0.00033555621 0.00033555621 0.00041435167 2.9266598e-05
5000 100 0.00031387148 0.00031387148 0.00039605781 2.5628425e-05
Loop time of 0.073938 on 1 procs for 5000 steps with 100 atoms
Performance: 29213677.752 tau/day, 67624.254 timesteps/s, 6.762 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0084547 | 0.0084547 | 0.0084547 | 0.0 | 11.43
Neigh | 0.011399 | 0.011399 | 0.011399 | 0.0 | 15.42
Comm | 0.00077205 | 0.00077205 | 0.00077205 | 0.0 | 1.04
Output | 0.00042663 | 0.00042663 | 0.00042663 | 0.0 | 0.58
Modify | 0.049692 | 0.049692 | 0.049692 | 0.0 | 67.21
Other | | 0.003194 | | | 4.32
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 164 ave 164 max 164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 164
Ave neighs/atom = 1.64
Neighbor list builds = 281
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00031387148 0.00031387148 0.00039605781 2.6174978e-05
5100 100 0.54537023 0.54537023 0.30042175 0.0087427352
5200 100 0.57210852 0.57210852 0.3192468 0.0098134067
5300 100 0.7168108 0.7168108 0.38577893 0.011004584
5400 100 0.78895524 0.78895524 0.41889428 0.013555713
5500 100 0.87797874 0.87797874 0.45689223 0.01565356
5600 100 0.95424379 0.95424379 0.48830429 0.014707858
5700 100 1.0046012 1.0046012 0.51054927 0.01469179
5800 100 1.0371453 1.0371453 0.5262568 0.015576788
5900 100 1.0545743 1.0545743 0.5361173 0.01589889
6000 100 1.0932949 1.0932949 0.55402214 0.017484573
6100 100 1.1148364 1.1148364 0.56241126 0.01721788
6200 100 1.1315267 1.1315267 0.57050887 0.017961246
6300 100 1.1506124 1.1506124 0.58009471 0.017159062
6400 100 1.1663328 1.1663328 0.5876586 0.017935311
6500 100 1.1821086 1.1821086 0.59595161 0.018005316
6600 100 1.2039397 1.2039397 0.60567523 0.021604661
6700 100 1.2269912 1.2269912 0.61770225 0.018907995
6800 100 1.2447034 1.2447034 0.62576519 0.020537655
6900 100 1.2625323 1.2625323 0.63486698 0.02010613
7000 100 1.2617127 1.2617127 0.63318163 0.019670429
7100 100 1.260715 1.260715 0.63311254 0.01981063
7200 100 1.2790404 1.2790404 0.64079 0.020218912
7300 100 1.2760228 1.2760228 0.6395331 0.021749952
7400 100 1.2799657 1.2799657 0.64139078 0.020472917
7500 100 1.2846472 1.2846472 0.64343076 0.020610029
7600 100 1.2883963 1.2883963 0.6449186 0.020748906
7700 100 1.2926891 1.2926891 0.64684538 0.020599574
7800 100 1.3033565 1.3033565 0.65126214 0.021822145
7900 100 1.3025797 1.3025797 0.65069472 0.02121384
8000 100 1.3052551 1.3052551 0.65209898 0.021398725
8100 100 1.3069868 1.3069868 0.65304899 0.021246465
8200 100 1.3091964 1.3091964 0.65438143 0.021222398
8300 100 1.3101277 1.3101277 0.65518554 0.021329556
8400 100 1.3117162 1.3117162 0.65551056 0.021468306
8500 100 1.3143892 1.3143892 0.65683087 0.021610874
8600 100 1.3164123 1.3164123 0.65789423 0.021564818
8700 100 1.3186854 1.3186854 0.65914031 0.021745193
8800 100 1.3216944 1.3216944 0.66041385 0.022178553
8900 100 1.3207558 1.3207558 0.65988071 0.021810027
9000 100 1.3213131 1.3213131 0.66020938 0.021890893
9100 100 1.3224905 1.3224905 0.66088289 0.021824994
9200 100 1.3240681 1.3240681 0.66183168 0.021784616
9300 100 1.3254174 1.3254174 0.66279883 0.021664485
9400 100 1.3326916 1.3326916 0.66633358 0.021979709
9500 100 1.3405062 1.3405062 0.66975745 0.022238702
9600 100 1.3363695 1.3363695 0.66742377 0.022104646
9700 100 1.3363391 1.3363391 0.6673032 0.022066628
9800 100 1.334875 1.334875 0.6665532 0.021902669
9900 100 1.3339805 1.3339805 0.66614358 0.022018971
10000 100 1.3337897 1.3337897 0.66609803 0.022184385
Loop time of 0.213875 on 1 procs for 5000 steps with 100 atoms
Performance: 10099379.673 tau/day, 23378.194 timesteps/s, 2.338 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031863 | 0.031863 | 0.031863 | 0.0 | 14.90
Neigh | 0.026844 | 0.026844 | 0.026844 | 0.0 | 12.55
Comm | 0.0011059 | 0.0011059 | 0.0011059 | 0.0 | 0.52
Output | 0.00072907 | 0.00072907 | 0.00072907 | 0.0 | 0.34
Modify | 0.14874 | 0.14874 | 0.14874 | 0.0 | 69.54
Other | | 0.004595 | | | 2.15
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 186 ave 186 max 186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 186
Ave neighs/atom = 1.86
Neighbor list builds = 626
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3337897 1.3337897 0.66609803 0.022303323
10100 100 0.29960521 0.29960521 0.17535846 0.0099382421
10200 100 0.15737069 0.15737069 0.1024212 0.0045555648
10300 100 0.087501771 0.087501771 0.070895975 0.00093482858
10400 100 0.069967301 0.069967301 0.059253397 0.0008760803
10500 100 0.056137153 0.056137153 0.047810947 0.0009202993
10600 100 0.046835352 0.046835352 0.039400006 0.0011343063
10700 100 0.035422167 0.035422167 0.030746587 0.00081816474
10800 100 0.029180739 0.029180739 0.02627693 0.00039292712
10900 100 0.025094915 0.025094915 0.023244435 0.00044742245
11000 100 0.018014893 0.018014893 0.016862375 0.00017018411
11100 100 0.014549072 0.014549072 0.014551468 0.00020988549
11200 100 0.012586232 0.012586232 0.012569333 0.00019035396
11300 100 0.01003586 0.01003586 0.010253286 0.0004598214
11400 100 0.0067515743 0.0067515743 0.0069569741 0.00040592883
11500 100 0.0057834612 0.0057834612 0.0060790719 0.00013993531
11600 100 0.005496335 0.005496335 0.0056855922 0.00013419698
11700 100 0.0051524178 0.0051524178 0.0053354591 7.4388594e-05
11800 100 0.004911096 0.004911096 0.0051415984 0.00010665621
11900 100 0.004687138 0.004687138 0.0049520306 6.7492552e-05
12000 100 0.0041516495 0.0041516495 0.0044351666 4.3841199e-05
12100 100 0.0033948026 0.0033948026 0.0036851466 4.2010682e-05
12200 100 0.0029584231 0.0029584231 0.0031151054 5.1583068e-05
12300 100 0.0028401114 0.0028401114 0.0030094644 4.5499489e-05
12400 100 0.002650861 0.002650861 0.0027699066 0.00015370263
12500 100 0.0026018053 0.0026018053 0.0027178583 3.219734e-05
12600 100 0.0025788693 0.0025788693 0.0026939358 3.6615314e-05
12700 100 0.0024798907 0.0024798907 0.0026181033 3.0688648e-05
12800 100 0.0023930719 0.0023930719 0.0025491721 7.5200629e-05
12900 100 0.0022100795 0.0022100795 0.0024231125 2.3210159e-05
13000 100 0.0021267492 0.0021267492 0.0023312893 2.463758e-05
13100 100 0.0020732193 0.0020732193 0.0022673707 2.5656089e-05
13200 100 0.0020010659 0.0020010659 0.0021834293 2.4913608e-05
13300 100 0.0019645929 0.0019645929 0.0021311636 6.8209063e-05
13400 100 0.0019236711 0.0019236711 0.0020928899 2.3805429e-05
13500 100 0.001857137 0.001857137 0.0020387354 3.1316165e-05
13600 100 0.0018399111 0.0018399111 0.0020204586 2.27689e-05
13700 100 0.0016240252 0.0016240252 0.0017492695 0.00023180963
13800 100 0.0015856393 0.0015856393 0.0017164012 4.2480373e-05
13900 100 0.0014770352 0.0014770352 0.001571278 2.3192512e-05
14000 100 0.0013712974 0.0013712974 0.0014839763 4.7410142e-05
14100 100 0.0012396318 0.0012396318 0.0013778109 1.3867692e-05
14200 100 0.0011502319 0.0011502319 0.0012780584 0.00018410725
14300 100 0.0011020896 0.0011020896 0.0012348357 7.8122446e-05
14400 100 0.0010486644 0.0010486644 0.0011483239 0.00015074963
14500 100 0.00094167471 0.00094167471 0.0010033809 1.9550083e-05
14600 100 0.00080775791 0.00080775791 0.00087434944 4.6043659e-05
14700 100 0.00076176039 0.00076176039 0.00083462461 8.1916038e-05
14800 100 0.00073637901 0.00073637901 0.00081306941 9.1126903e-06
14900 100 0.00072682383 0.00072682383 0.00079396231 8.9944449e-06
15000 100 0.00070207518 0.00070207518 0.00077168127 2.2155171e-05
Loop time of 0.0756704 on 1 procs for 5000 steps with 100 atoms
Performance: 28544845.995 tau/day, 66076.032 timesteps/s, 6.608 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0079484 | 0.0079484 | 0.0079484 | 0.0 | 10.50
Neigh | 0.0043035 | 0.0043035 | 0.0043035 | 0.0 | 5.69
Comm | 0.00064796 | 0.00064796 | 0.00064796 | 0.0 | 0.86
Output | 0.00044137 | 0.00044137 | 0.00044137 | 0.0 | 0.58
Modify | 0.059329 | 0.059329 | 0.059329 | 0.0 | 78.40
Other | | 0.003 | | | 3.97
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 165 ave 165 max 165 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 165
Ave neighs/atom = 1.65
Neighbor list builds = 101
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00070207518 0.00070207518 0.00077168127 2.0192237e-05
15100 100 1.1160127 1.1160127 0.69939857 0.01822663
15200 100 1.2546016 1.2546016 0.78819474 0.017013321
15300 100 1.1930613 1.1930613 0.77429911 0.015607175
15400 100 1.3791371 1.3791371 0.87875984 0.018478669
15500 100 1.6063158 1.6063158 0.98587325 0.027330546
15600 100 1.7719925 1.7719925 1.0773314 0.025651867
15700 100 1.8053439 1.8053439 1.0934572 0.033790716
15800 100 1.959016 1.959016 1.1465659 0.033715025
15900 100 2.1365654 2.1365654 1.2217718 0.03009529
16000 100 2.2883378 2.2883378 1.2768504 0.030582689
16100 100 2.4384012 2.4384012 1.3513708 0.031435936
16200 100 2.3571308 2.3571308 1.29989 0.034824253
16300 100 2.4671092 2.4671092 1.3516798 0.032364282
16400 100 2.4411936 2.4411936 1.3385743 0.031890134
16500 100 2.4930545 2.4930545 1.3635435 0.032601452
16600 100 2.5771906 2.5771906 1.4113993 0.034547128
16700 100 2.723199 2.723199 1.4769168 0.036582811
16800 100 2.8616886 2.8616886 1.5379462 0.036224198
16900 100 2.9517942 2.9517942 1.5872824 0.038757052
17000 100 3.0150335 3.0150335 1.6337001 0.044031411
17100 100 3.2211536 3.2211536 1.7374532 0.041483093
17200 100 3.2509982 3.2509982 1.7512835 0.042718835
17300 100 3.262348 3.262348 1.7648674 0.049291835
17400 100 3.4050702 3.4050702 1.8352043 0.04435958
17500 100 3.5236051 3.5236051 1.9003369 0.045640904
17600 100 3.4005287 3.4005287 1.8404347 0.044832295
17700 100 3.3190992 3.3190992 1.8154147 0.046365998
17800 100 3.2981138 3.2981138 1.811389 0.04607132
17900 100 3.2839466 3.2839466 1.7863773 0.045628167
18000 100 3.1519747 3.1519747 1.7382103 0.041739193
18100 100 3.1205305 3.1205305 1.7101547 0.043511342
18200 100 3.2014874 3.2014874 1.746745 0.04452173
18300 100 3.2739622 3.2739622 1.7796276 0.041345823
18400 100 3.3157359 3.3157359 1.8158932 0.047414
18500 100 3.5592096 3.5592096 1.9307695 0.046458132
18600 100 3.6594352 3.6594352 1.9851626 0.046396953
18700 100 3.6392917 3.6392917 1.9701361 0.047272883
18800 100 3.8490892 3.8490892 2.0832481 0.052344106
18900 100 3.8465732 3.8465732 2.0790411 0.054203126
19000 100 4.010008 4.010008 2.1620722 0.054242542
19100 100 4.0417392 4.0417392 2.168506 0.066484948
19200 100 3.8791541 3.8791541 2.0791914 0.060788142
19300 100 4.1023603 4.1023603 2.1944127 0.056461298
19400 100 4.1294375 4.1294375 2.2009649 0.061099665
19500 100 3.9274112 3.9274112 2.0877398 0.066068401
19600 100 4.066229 4.066229 2.1678487 0.055961003
19700 100 3.9829257 3.9829257 2.1184329 0.061961838
19800 100 4.0303258 4.0303258 2.14544 0.053667616
19900 100 3.9385166 3.9385166 2.1074364 0.060804382
20000 100 3.8534401 3.8534401 2.0796496 0.057588336
Loop time of 0.167801 on 1 procs for 5000 steps with 100 atoms
Performance: 12872385.064 tau/day, 29797.188 timesteps/s, 2.980 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013849 | 0.013849 | 0.013849 | 0.0 | 8.25
Neigh | 0.038108 | 0.038108 | 0.038108 | 0.0 | 22.71
Comm | 0.0011352 | 0.0011352 | 0.0011352 | 0.0 | 0.68
Output | 0.00073125 | 0.00073125 | 0.00073125 | 0.0 | 0.44
Modify | 0.10927 | 0.10927 | 0.10927 | 0.0 | 65.12
Other | | 0.004703 | | | 2.80
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 157 ave 157 max 157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 914
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.8534401 3.8534401 2.0796496 0.057176513
20100 100 1.2993548 1.2993548 0.81360425 0.016153186
20200 100 1.0761427 1.0761427 0.68479926 0.014383682
20300 100 0.95889127 0.95889127 0.61193887 0.01314653
20400 100 0.89684043 0.89684043 0.57475851 0.011106613
20500 100 0.85901565 0.85901565 0.54372093 0.015717834
20600 100 0.98438384 0.98438384 0.6079212 0.013965815
20700 100 1.1061789 1.1061789 0.66511277 0.013698526
20800 100 1.0615292 1.0615292 0.6269413 0.014496973
20900 100 0.92980037 0.92980037 0.54727184 0.014568574
21000 100 0.71248123 0.71248123 0.41945517 0.01199152
21100 100 0.34785801 0.34785801 0.21699877 0.0062324631
21200 100 0.2452514 0.2452514 0.15265503 0.0041094159
21300 100 0.22937209 0.22937209 0.13988978 0.0034016589
21400 100 0.17765021 0.17765021 0.11334596 0.0024169343
21500 100 0.11484505 0.11484505 0.078119393 0.0020987046
21600 100 0.077564645 0.077564645 0.056175123 0.002107237
21700 100 0.049571519 0.049571519 0.039920177 0.00099127481
21800 100 0.0403125 0.0403125 0.032827882 0.00074671903
21900 100 0.02735168 0.02735168 0.023877339 0.0018186225
22000 100 0.02218474 0.02218474 0.01893178 0.00061438633
22100 100 0.021701103 0.021701103 0.0179008 0.00068071664
22200 100 0.01777321 0.01777321 0.014521817 0.00045296506
22300 100 0.016056338 0.016056338 0.01280709 0.00038192299
22400 100 0.013344054 0.013344054 0.010788852 0.0002617289
22500 100 0.011625836 0.011625836 0.0094362641 0.00045947089
22600 100 0.0068875777 0.0068875777 0.0058858647 0.00028566999
22700 100 0.0054081662 0.0054081662 0.0049545239 0.00029291503
22800 100 0.0045080107 0.0045080107 0.0042362636 0.00015217816
22900 100 0.0038090552 0.0038090552 0.0036905284 0.00049430003
23000 100 0.003551951 0.003551951 0.0033639677 0.00022478393
23100 100 0.0033854012 0.0033854012 0.00317485 0.00015179604
23200 100 0.0032951003 0.0032951003 0.0029760374 0.00015363208
23300 100 0.0022995179 0.0022995179 0.0023224311 0.00018791799
23400 100 0.0020834178 0.0020834178 0.0021434342 0.00020683744
23500 100 0.0019221303 0.0019221303 0.0020227484 0.00018960984
23600 100 0.0018393381 0.0018393381 0.0019560681 0.00021375486
23700 100 0.0019027035 0.0019027035 0.0020047598 0.00010932204
23800 100 0.0023612063 0.0023612063 0.0021895633 6.7671176e-05
23900 100 0.0019570853 0.0019570853 0.0018847178 5.6761457e-05
24000 100 0.0013011744 0.0013011744 0.0013899106 3.8847148e-05
24100 100 0.001281115 0.001281115 0.0013737259 3.7559904e-05
24200 100 0.0012136262 0.0012136262 0.0013002937 6.8727546e-05
24300 100 0.0011789934 0.0011789934 0.0012399341 3.7633632e-05
24400 100 0.0011601514 0.0011601514 0.0012186534 4.0077907e-05
24500 100 0.0010660295 0.0010660295 0.0011419405 0.00015757237
24600 100 0.00098862453 0.00098862453 0.0010869455 4.5714503e-05
24700 100 0.00087647136 0.00087647136 0.00091405278 3.3129869e-05
24800 100 0.00063913046 0.00063913046 0.00072298864 3.5424308e-05
24900 100 0.00062195456 0.00062195456 0.00070527087 2.6201396e-05
25000 100 0.00057599538 0.00057599538 0.00065623226 2.0096103e-05
Loop time of 0.0771328 on 1 procs for 5000 steps with 100 atoms
Performance: 28003659.560 tau/day, 64823.286 timesteps/s, 6.482 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0090635 | 0.0090635 | 0.0090635 | 0.0 | 11.75
Neigh | 0.012028 | 0.012028 | 0.012028 | 0.0 | 15.59
Comm | 0.0008345 | 0.0008345 | 0.0008345 | 0.0 | 1.08
Output | 0.00038777 | 0.00038777 | 0.00038777 | 0.0 | 0.50
Modify | 0.051619 | 0.051619 | 0.051619 | 0.0 | 66.92
Other | | 0.0032 | | | 4.15
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158
Ave neighs/atom = 1.58
Neighbor list builds = 310
Dangerous builds = 0
Total wall time: 0:00:00

484
examples/granregion/log.16Mar23.granregion.box.g++.4
View File

@ -1,484 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 2 by 2 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170772
1500 99 0.31486693 0.31486693 0.17429055 0.0064903432
1600 99 0.26369001 0.26369001 0.15095266 0.0045226847
1700 100 0.1925923 0.1925923 0.11308104 0.007362313
1800 100 0.13724978 0.13724978 0.083276845 0.0058136373
1900 100 0.077212636 0.077212636 0.053159386 0.0016509598
2000 100 0.065294031 0.065294031 0.04372752 0.0020346467
2100 100 0.057431398 0.057431398 0.037977068 0.0012681098
2200 100 0.059093046 0.059093046 0.037435194 0.00096610935
2300 100 0.034223376 0.034223376 0.025491303 0.00069886041
2400 100 0.020558283 0.020558283 0.016163008 0.0017260646
2500 100 0.015339698 0.015339698 0.012329233 0.00041312351
2600 100 0.012891357 0.012891357 0.0097660566 0.00030356702
2700 100 0.0092631621 0.0092631621 0.0073576327 0.00077729311
2800 100 0.0073866488 0.0073866488 0.0060126175 0.00018677664
2900 100 0.0081122362 0.0081122362 0.0062557089 0.00013749542
3000 100 0.0042333757 0.0042333757 0.0035407672 0.00016515787
3100 100 0.0035433278 0.0035433278 0.0029683167 0.00033693479
3200 100 0.0030692964 0.0030692964 0.0026495167 0.00043739373
3300 100 0.0033703684 0.0033703684 0.0026931948 0.00014857157
3400 100 0.0018405709 0.0018405709 0.0016990035 6.0202278e-05
3500 100 0.0014788087 0.0014788087 0.0013889916 0.00016730937
3600 100 0.0015932961 0.0015932961 0.0013807898 0.0001418157
3700 100 0.00096238915 0.00096238915 0.00097931829 6.7974535e-05
3800 100 0.00093087985 0.00093087985 0.00087659377 0.0001504142
3900 100 0.0015825065 0.0015825065 0.0011708936 1.9583518e-05
4000 100 0.00062295367 0.00062295367 0.00067129665 3.9455653e-05
4100 100 0.00061259406 0.00061259406 0.00065710963 1.8540759e-05
4200 100 0.00059619666 0.00059619666 0.00064365219 7.3779336e-06
4300 100 0.00051191641 0.00051191641 0.00057870947 6.3349656e-06
4400 100 0.00050668587 0.00050668587 0.00057057233 6.2702376e-06
4500 100 0.00049474942 0.00049474942 0.00055151343 1.5746831e-05
4600 100 0.00049309932 0.00049309932 0.00054086323 6.1021041e-06
4700 100 0.00049263883 0.00049263883 0.00052677244 6.0964056e-06
4800 100 0.00041885021 0.00041885021 0.00047389202 9.5350789e-05
4900 100 0.00035596444 0.00035596444 0.00042522549 5.8036712e-05
5000 100 0.00032946897 0.00032946897 0.00040320773 6.5350005e-06
Loop time of 0.0763179 on 4 procs for 5000 steps with 100 atoms
Performance: 28302682.620 tau/day, 65515.469 timesteps/s, 6.552 Matom-step/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010572 | 0.0039588 | 0.0074661 | 4.6 | 5.19
Neigh | 0.0025868 | 0.0049885 | 0.0075283 | 3.4 | 6.54
Comm | 0.011862 | 0.014631 | 0.018383 | 2.0 | 19.17
Output | 0.0009702 | 0.0012326 | 0.0014234 | 0.5 | 1.62
Modify | 0.0019843 | 0.018558 | 0.036592 | 12.2 | 24.32
Other | | 0.03295 | | | 43.17
Nlocal: 25 ave 54 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 4.5 ave 10 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 40.5 ave 94 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 162
Ave neighs/atom = 1.62
Neighbor list builds = 281
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00032946897 0.00032946897 0.00040320773 6.050219e-06
5100 100 0.54371575 0.54371575 0.29836301 0.008148168
5200 100 0.60281896 0.60281896 0.33161676 0.0083772071
5300 100 0.70823011 0.70823011 0.38289657 0.0099694209
5400 100 0.78467127 0.78467127 0.4133495 0.010119104
5500 100 0.85741178 0.85741178 0.44761254 0.013013239
5600 100 0.93241573 0.93241573 0.47879351 0.017769592
5700 100 1.019104 1.019104 0.51644461 0.015312937
5800 100 1.0550014 1.0550014 0.53450507 0.017227797
5900 100 1.0910946 1.0910946 0.55272891 0.017469625
6000 100 1.1275288 1.1275288 0.56906788 0.018958103
6100 100 1.1545017 1.1545017 0.58324166 0.019220208
6200 100 1.1815817 1.1815817 0.59552677 0.019397271
6300 100 1.1963931 1.1963931 0.60251664 0.018382058
6400 100 1.2084652 1.2084652 0.60776713 0.020027986
6500 100 1.2217215 1.2217215 0.61406339 0.021750945
6600 100 1.2364016 1.2364016 0.62124174 0.021701243
6700 100 1.2739954 1.2739954 0.63930766 0.02025277
6800 100 1.3032733 1.3032733 0.65268105 0.021684843
6900 100 1.3226653 1.3226653 0.66168772 0.021187963
7000 100 1.3464995 1.3464995 0.67431153 0.022066117
7100 100 1.3250485 1.3250485 0.66342366 0.02109487
7200 100 1.3384316 1.3384316 0.67035095 0.021554113
7300 100 1.3280234 1.3280234 0.66553439 0.020829435
7400 100 1.3218971 1.3218971 0.66186263 0.020882591
7500 100 1.3293858 1.3293858 0.66506462 0.020897778
7600 100 1.3386019 1.3386019 0.66909392 0.020754479
7700 100 1.3465327 1.3465327 0.67316081 0.021231547
7800 100 1.3510586 1.3510586 0.67531764 0.021053475
7900 100 1.3508987 1.3508987 0.67535907 0.020769633
8000 100 1.3575635 1.3575635 0.67875993 0.022020776
8100 100 1.3655144 1.3655144 0.68258066 0.021016999
8200 100 1.375187 1.375187 0.68732222 0.021385146
8300 100 1.3799568 1.3799568 0.69000134 0.02114428
8400 100 1.3755871 1.3755871 0.68757909 0.022395102
8500 100 1.3708345 1.3708345 0.68509834 0.021603853
8600 100 1.3689806 1.3689806 0.68388935 0.022127839
8700 100 1.3697516 1.3697516 0.68411868 0.02165119
8800 100 1.3700522 1.3700522 0.68423671 0.021554001
8900 100 1.3705045 1.3705045 0.68451935 0.021470392
9000 100 1.3715107 1.3715107 0.68506443 0.021789844
9100 100 1.3707806 1.3707806 0.68467539 0.021451331
9200 100 1.371112 1.371112 0.68485975 0.021479203
9300 100 1.3716851 1.3716851 0.68516034 0.021515076
9400 100 1.3719031 1.3719031 0.68529221 0.021502802
9500 100 1.3726759 1.3726759 0.68544012 0.021585119
9600 100 1.3746583 1.3746583 0.68636924 0.02206073
9700 100 1.3761662 1.3761662 0.68716579 0.021533719
9800 100 1.3760157 1.3760157 0.687092 0.02163129
9900 100 1.3762626 1.3762626 0.68726404 0.021707045
10000 100 1.376303 1.376303 0.68735031 0.022306557
Loop time of 0.128472 on 4 procs for 5000 steps with 100 atoms
Performance: 16812995.511 tau/day, 38918.971 timesteps/s, 3.892 Matom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012241 | 0.0085024 | 0.016023 | 7.8 | 6.62
Neigh | 0.0051137 | 0.0079745 | 0.011012 | 3.2 | 6.21
Comm | 0.0050448 | 0.009504 | 0.015048 | 4.6 | 7.40
Output | 0.00090309 | 0.0014765 | 0.0019648 | 1.2 | 1.15
Modify | 0.0072253 | 0.041211 | 0.076226 | 16.7 | 32.08
Other | | 0.0598 | | | 46.55
Nlocal: 25 ave 51 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 3.25 ave 7 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 46 ave 101 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 184
Ave neighs/atom = 1.84
Neighbor list builds = 628
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.376303 1.376303 0.68735031 0.022411506
10100 100 0.28192752 0.28192752 0.16298909 0.0041760951
10200 100 0.14576408 0.14576408 0.10117889 0.0058653094
10300 100 0.10070361 0.10070361 0.078060938 0.0041432979
10400 100 0.07455595 0.07455595 0.061163197 0.0029733745
10500 100 0.063531027 0.063531027 0.052515707 0.0015731241
10600 100 0.049259626 0.049259626 0.041321284 0.00073083104
10700 100 0.037377957 0.037377957 0.032017729 0.0022631642
10800 100 0.031849901 0.031849901 0.027079116 0.0014148618
10900 100 0.02795233 0.02795233 0.02461403 0.00037567522
11000 100 0.02597858 0.02597858 0.022516094 0.00054992645
11100 100 0.021812043 0.021812043 0.019276946 0.00043233309
11200 100 0.019318956 0.019318956 0.017224213 0.00035792964
11300 100 0.017760494 0.017760494 0.01578407 0.00056959435
11400 100 0.015485043 0.015485043 0.013703 0.00061308169
11500 100 0.015051781 0.015051781 0.012994991 0.00040607387
11600 100 0.012204953 0.012204953 0.01079191 0.00059482171
11700 100 0.011242847 0.011242847 0.0096811013 0.00018299476
11800 100 0.0089605707 0.0089605707 0.0075086629 0.0012779422
11900 100 0.0065544011 0.0065544011 0.0056480432 0.00039599272
12000 100 0.0048068901 0.0048068901 0.004185961 0.00022434097
12100 100 0.0045272524 0.0045272524 0.0039084556 7.8443821e-05
12200 100 0.0038926209 0.0038926209 0.0033949999 0.00011203445
12300 100 0.0034653 0.0034653 0.0030246557 0.00014999893
12400 100 0.0034031041 0.0034031041 0.0029879474 7.9628343e-05
12500 100 0.0032219984 0.0032219984 0.0028369239 6.1651251e-05
12600 100 0.0031148659 0.0031148659 0.0027543848 5.7332789e-05
12700 100 0.0027407824 0.0027407824 0.0024822578 5.150993e-05
12800 100 0.0026205294 0.0026205294 0.0023576698 8.896122e-05
12900 100 0.0025633289 0.0025633289 0.0023134486 7.0525939e-05
13000 100 0.0025434711 0.0025434711 0.0022833007 5.5638668e-05
13100 100 0.0025046562 0.0025046562 0.002227265 5.2772716e-05
13200 100 0.0023544645 0.0023544645 0.0021086805 0.00030775943
13300 100 0.0022163971 0.0022163971 0.0020107508 4.9204292e-05
13400 100 0.0021307794 0.0021307794 0.0019334987 4.8144132e-05
13500 100 0.0019891796 0.0019891796 0.0018128084 4.8532374e-05
13600 100 0.0018591538 0.0018591538 0.0016721703 4.4781385e-05
13700 100 0.001768055 0.001768055 0.001597222 1.6800418e-05
13800 100 0.001569014 0.001569014 0.0014331265 4.2982654e-05
13900 100 0.0013700893 0.0013700893 0.0012782771 4.8209662e-05
14000 100 0.0012398662 0.0012398662 0.0011606486 5.5766702e-05
14100 100 0.0011707267 0.0011707267 0.0010811523 3.4913501e-05
14200 100 0.0010483984 0.0010483984 0.0009831881 3.4742894e-05
14300 100 0.0010043196 0.0010043196 0.00092474592 3.4196115e-05
14400 100 0.00094238924 0.00094238924 0.00087181843 8.1414071e-05
14500 100 0.00093341457 0.00093341457 0.00086429224 3.3276909e-05
14600 100 0.00086042474 0.00086042474 0.00079524877 3.2260019e-05
14700 100 0.00080525469 0.00080525469 0.00075380989 2.8374703e-05
14800 100 0.00070848512 0.00070848512 0.0006762901 2.9937591e-05
14900 100 0.00060414588 0.00060414588 0.00058494979 2.5684401e-05
15000 100 0.00054251571 0.00054251571 0.00053643753 4.5496354e-05
Loop time of 0.0553238 on 4 procs for 5000 steps with 100 atoms
Performance: 39042861.362 tau/day, 90376.994 timesteps/s, 9.038 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00085556 | 0.0028667 | 0.0052429 | 3.6 | 5.18
Neigh | 0.00076731 | 0.0012173 | 0.0016987 | 1.3 | 2.20
Comm | 0.0016497 | 0.0060965 | 0.010792 | 5.7 | 11.02
Output | 0.00072675 | 0.00099509 | 0.0011615 | 0.0 | 1.80
Modify | 0.00064371 | 0.014719 | 0.030427 | 11.6 | 26.61
Other | | 0.02943 | | | 53.19
Nlocal: 25 ave 54 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 5 ave 11 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 40 ave 88 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 160
Ave neighs/atom = 1.6
Neighbor list builds = 97
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00054251571 0.00054251571 0.00053643753 4.3506263e-05
15100 100 1.1164435 1.1164435 0.7163854 0.017358175
15200 100 1.0384203 1.0384203 0.66790042 0.016095459
15300 100 1.0829984 1.0829984 0.712381 0.015915015
15400 100 1.4187366 1.4187366 0.89537718 0.023771032
15500 100 1.5397547 1.5397547 0.97895571 0.025145916
15600 100 1.7993339 1.7993339 1.1003794 0.026783317
15700 100 1.8858073 1.8858073 1.1481696 0.030802833
15800 100 1.9368129 1.9368129 1.1450129 0.032144729
15900 100 2.0379823 2.0379823 1.1738926 0.031969116
16000 100 2.0655671 2.0655671 1.187038 0.032395513
16100 100 2.1199141 2.1199141 1.2102937 0.028830059
16200 100 2.1819656 2.1819656 1.245147 0.029493813
16300 100 2.2451204 2.2451204 1.2726968 0.029915554
16400 100 2.1697892 2.1697892 1.2342734 0.027495983
16500 100 2.2689358 2.2689358 1.2710223 0.029516621
16600 100 2.3901976 2.3901976 1.3328992 0.030049751
16700 100 2.4731258 2.4731258 1.3763126 0.032663365
16800 100 2.5708338 2.5708338 1.4255635 0.032731991
16900 100 2.7232422 2.7232422 1.5006931 0.036649645
17000 100 2.901986 2.901986 1.5886643 0.037333791
17100 100 2.8787369 2.8787369 1.5752504 0.03582313
17200 100 3.1137189 3.1137189 1.6974538 0.041245422
17300 100 3.1805823 3.1805823 1.7370013 0.040766564
17400 100 3.3215703 3.3215703 1.8109954 0.044269306
17500 100 3.3767256 3.3767256 1.813696 0.048012575
17600 100 3.3618731 3.3618731 1.8004834 0.06103562
17700 100 3.2288285 3.2288285 1.7447885 0.042875761
17800 100 3.2545435 3.2545435 1.7617642 0.04661949
17900 100 3.1162969 3.1162969 1.6850561 0.040086156
18000 100 3.2053719 3.2053719 1.7132296 0.040657811
18100 100 3.2924625 3.2924625 1.7709303 0.048407939
18200 100 3.1682076 3.1682076 1.7136129 0.040996326
18300 100 3.2244534 3.2244534 1.7401102 0.043957312
18400 100 3.1470903 3.1470903 1.7171698 0.043123438
18500 100 3.2690021 3.2690021 1.7803818 0.042693323
18600 100 3.2566233 3.2566233 1.7670476 0.04776305
18700 100 3.384347 3.384347 1.8334885 0.04441225
18800 100 3.6479797 3.6479797 1.9565845 0.047454733
18900 100 3.6894531 3.6894531 1.9767079 0.053222159
19000 100 3.7867788 3.7867788 2.0265223 0.055923793
19100 100 3.9120999 3.9120999 2.0850815 0.053591707
19200 100 3.8255419 3.8255419 2.0517931 0.061034295
19300 100 3.764721 3.764721 2.0089969 0.068118255
19400 100 3.8604884 3.8604884 2.0640292 0.052825172
19500 100 3.7763823 3.7763823 2.0223758 0.054529616
19600 100 3.9158781 3.9158781 2.0873723 0.053130512
19700 100 3.6394071 3.6394071 1.9735106 0.047466529
19800 100 3.5409741 3.5409741 1.9335311 0.047317029
19900 100 3.5961407 3.5961407 1.954696 0.048093129
20000 100 3.4355899 3.4355899 1.8679902 0.0486077
Loop time of 0.107854 on 4 procs for 5000 steps with 100 atoms
Performance: 20026986.271 tau/day, 46358.765 timesteps/s, 4.636 Matom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0025992 | 0.0042158 | 0.0061269 | 1.9 | 3.91
Neigh | 0.0089595 | 0.011254 | 0.012853 | 1.3 | 10.43
Comm | 0.020408 | 0.022579 | 0.024669 | 1.4 | 20.94
Output | 0.0010271 | 0.0011457 | 0.0012268 | 0.2 | 1.06
Modify | 0.019454 | 0.032696 | 0.040003 | 4.4 | 30.31
Other | | 0.03596 | | | 33.34
Nlocal: 25 ave 36 max 16 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 5.5 ave 8 max 2 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 34.25 ave 48 max 19 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 137
Ave neighs/atom = 1.37
Neighbor list builds = 908
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.4355899 3.4355899 1.8679902 0.047866781
20100 100 1.1677914 1.1677914 0.70763342 0.015645481
20200 100 0.99137326 0.99137326 0.61064707 0.012080974
20300 100 0.84603548 0.84603548 0.52093267 0.012501649
20400 100 0.82813609 0.82813609 0.50585936 0.010248184
20500 100 0.86524293 0.86524293 0.5210492 0.011145216
20600 100 0.92229302 0.92229302 0.54567614 0.012838894
20700 100 0.93499886 0.93499886 0.55161401 0.011618713
20800 100 0.95831407 0.95831407 0.56173113 0.014502297
20900 100 0.88486451 0.88486451 0.51926962 0.013847246
21000 100 0.66876325 0.66876325 0.39313901 0.010224296
21100 100 0.46578708 0.46578708 0.28086455 0.0089121873
21200 100 0.21445902 0.21445902 0.14749113 0.0033665892
21300 100 0.12935011 0.12935011 0.09319765 0.002811107
21400 100 0.10572326 0.10572326 0.075154962 0.0034728629
21500 100 0.10952604 0.10952604 0.073864376 0.0017411404
21600 100 0.074321422 0.074321422 0.051368858 0.0037915268
21700 100 0.043324694 0.043324694 0.032954769 0.00092476658
21800 100 0.034911155 0.034911155 0.026843877 0.00061350592
21900 100 0.02261818 0.02261818 0.018357224 0.00049800957
22000 100 0.015096211 0.015096211 0.01390442 0.00059260194
22100 100 0.016119209 0.016119209 0.013990821 0.00038431756
22200 100 0.012184692 0.012184692 0.011062653 0.00030466184
22300 100 0.0090526001 0.0090526001 0.0080893293 0.00082507232
22400 100 0.007155528 0.007155528 0.0067365227 0.00094740021
22500 100 0.0057433117 0.0057433117 0.0057438575 0.00016706605
22600 100 0.0053029734 0.0053029734 0.0050429137 0.00018457156
22700 100 0.0041888319 0.0041888319 0.0039979907 0.00029467329
22800 100 0.0046486843 0.0046486843 0.0042259456 0.00019395675
22900 100 0.0046414295 0.0046414295 0.0040659744 0.00016025205
23000 100 0.0033983576 0.0033983576 0.0033431909 0.00039998961
23100 100 0.0031212625 0.0031212625 0.0031113361 0.00024783655
23200 100 0.0026724347 0.0026724347 0.0026905233 0.00026001445
23300 100 0.0029222876 0.0029222876 0.002946198 0.00012385327
23400 100 0.0023944825 0.0023944825 0.0021829995 0.00016185776
23500 100 0.0020384082 0.0020384082 0.0019106613 9.2139544e-05
23600 100 0.0019773679 0.0019773679 0.0018577006 8.9169073e-05
23700 100 0.0018850072 0.0018850072 0.0017715658 9.1301463e-05
23800 100 0.0020857322 0.0020857322 0.001864009 7.4633597e-05
23900 100 0.0017616498 0.0017616498 0.001680563 4.8547939e-05
24000 100 0.0017183254 0.0017183254 0.0016568629 6.56741e-05
24100 100 0.0014311732 0.0014311732 0.0013829993 6.0743962e-05
24200 100 0.0013434756 0.0013434756 0.001315682 0.00025727478
24300 100 0.0012855885 0.0012855885 0.0012558467 9.0130585e-05
24400 100 0.0012731213 0.0012731213 0.0012408428 8.2008231e-05
24500 100 0.0011333063 0.0011333063 0.001045815 8.8391061e-05
24600 100 0.0010560932 0.0010560932 0.00098304208 5.6725938e-05
24700 100 0.00097698038 0.00097698038 0.00092381967 7.1771848e-05
24800 100 0.00094316799 0.00094316799 0.00089343119 5.5558578e-05
24900 100 0.00082812377 0.00082812377 0.00076615512 5.8668812e-05
25000 100 0.00076097781 0.00076097781 0.00069462801 6.5742694e-05
Loop time of 0.0523621 on 4 procs for 5000 steps with 100 atoms
Performance: 41251226.669 tau/day, 95488.951 timesteps/s, 9.549 Matom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0011166 | 0.0029573 | 0.0049613 | 3.3 | 5.65
Neigh | 0.0026276 | 0.0033989 | 0.0041666 | 1.1 | 6.49
Comm | 0.0054479 | 0.0084136 | 0.01182 | 2.9 | 16.07
Output | 0.00070658 | 0.00092447 | 0.0010421 | 0.0 | 1.77
Modify | 0.0015069 | 0.012796 | 0.025273 | 9.9 | 24.44
Other | | 0.02387 | | | 45.59
Nlocal: 25 ave 55 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 6 ave 14 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 39.25 ave 88 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 280
Dangerous builds = 0
Total wall time: 0:00:00

635
examples/granregion/log.16Mar23.granregion.funnel.g++.1
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@ -1,635 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.52844331 2000 -0
2000 0.76085445 2000 -0
3000 0.99183068 2000 -0
4000 1.2193085 2000 -0
5000 1.4439617 2000 -0
6000 1.6703511 2000 -0
7000 1.9053408 2000 -0
8000 2.1323525 2000 -0
9000 2.3566342 2000 -0
10000 2.5829638 2000 -0
11000 2.8106202 2000 -0
12000 3.0371473 2000 -0
13000 3.2621782 2000 -0
14000 3.4860689 2000 -0
15000 3.7138322 2000 -0
16000 3.9424002 2000 -0
17000 4.1703584 2000 -0
18000 4.3973348 2000 -0
19000 4.6213358 2000 -0
20000 4.8547603 2000 -0
Loop time of 4.85478 on 1 procs for 20000 steps with 2000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52375 | 0.52375 | 0.52375 | 0.0 | 10.79
Neigh | 0.070018 | 0.070018 | 0.070018 | 0.0 | 1.44
Comm | 0.011077 | 0.011077 | 0.011077 | 0.0 | 0.23
Output | 0.00071321 | 0.00071321 | 0.00071321 | 0.0 | 0.01
Modify | 4.1233 | 4.1233 | 4.1233 | 0.0 | 84.93
Other | | 0.126 | | | 2.59
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1607 ave 1607 max 1607 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1607
Ave neighs/atom = 0.8035
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.22761741 2000 6807.2201
22000 0.45508977 2000 6973.9359
23000 0.68132308 2000 7142.3648
24000 0.91084802 2000 7276.9717
25000 1.1397154 2000 7369.4191
26000 1.3724974 2000 7497.6526
27000 1.6037436 2000 7638.946
28000 1.8381254 2000 7780.0339
29000 2.0763695 2000 7881.8177
30000 2.3169444 2000 7967.2641
31000 2.5544704 2000 7994.9273
32000 2.7981688 2000 7937.0671
33000 3.0486439 2000 7774.0508
34000 3.3065315 2000 7591.1491
35000 3.5712927 2000 7357.5176
36000 3.8415508 2000 7147.2024
37000 4.1137466 2000 6979.1604
38000 4.3946186 2000 6813.2152
39000 4.6737386 2000 6660.2701
40000 4.9654287 2000 6502.8957
41000 5.2606376 2000 6324.3951
42000 5.5633065 2000 6132.7516
43000 5.8692745 2000 5913.1841
44000 6.1757115 2000 5732.2095
45000 6.4896845 2000 5508.8322
46000 6.8170163 2000 5306.8932
47000 7.1514543 2000 5152.0521
48000 7.4863157 2000 5028.2274
49000 7.8214974 2000 4896.102
50000 8.1600826 2000 4723.5189
51000 8.4984004 2000 4583.7526
52000 8.8500924 2000 4447.0187
53000 9.2046999 2000 4303.2307
54000 9.5724785 2000 4168.5251
55000 9.9479954 2000 4036.9704
56000 10.324666 2000 3901.1183
57000 10.708944 2000 3716.7071
58000 11.108887 2000 3473.5422
59000 11.515057 2000 3245.1223
60000 11.922119 2000 3039.7845
61000 12.331146 2000 2780.0187
62000 12.745147 2000 2577.3345
63000 13.169644 2000 2346.2488
64000 13.602869 2000 2116.7298
65000 14.044828 2000 1903.7828
66000 14.49159 2000 1631.1676
67000 14.953127 2000 1431.0198
68000 15.428874 2000 1212.875
69000 15.981012 2000 995.45046
70000 16.458356 2000 811.54766
71000 16.936094 2000 624.08622
72000 17.432306 2000 471.00862
73000 17.949423 2000 358.33486
74000 18.467878 2000 284.39416
75000 18.970599 2000 234.26671
76000 19.45957 2000 185.61836
77000 19.959792 2000 152.95918
78000 20.455734 2000 122.49023
79000 20.93849 2000 102.29396
80000 21.430632 2000 86.284684
81000 21.925932 2000 73.984781
82000 22.428573 2000 63.042918
83000 22.945552 2000 53.338428
84000 23.467102 2000 45.89585
85000 23.992243 2000 40.412826
86000 24.512956 2000 34.183381
87000 25.037944 2000 29.671524
88000 25.56622 2000 26.90414
89000 26.102251 2000 24.362631
90000 26.638165 2000 21.887341
91000 27.17863 2000 19.985662
92000 27.72662 2000 18.728162
93000 28.276842 2000 16.99941
94000 28.830281 2000 15.71941
95000 29.389744 2000 14.744057
96000 29.972451 2000 14.214918
97000 30.575245 2000 13.450182
98000 31.141552 2000 12.79222
99000 31.711177 2000 12.10595
100000 32.286609 2000 11.281863
101000 32.879692 2000 10.025419
102000 33.460265 2000 9.9574468
103000 34.040002 2000 9.4078117
104000 34.619096 2000 8.9079161
105000 35.199384 2000 8.6269302
106000 35.784782 2000 8.5512649
107000 36.37489 2000 8.4703948
108000 36.963891 2000 8.2747542
109000 37.551549 2000 8.2895118
110000 38.154561 2000 8.1785613
111000 38.749306 2000 7.8443234
112000 39.344241 2000 7.7436124
113000 39.938878 2000 7.8118604
114000 40.531935 2000 7.3806177
115000 41.130022 2000 7.0857235
116000 41.726772 2000 7.1346752
117000 42.322611 2000 7.0653751
118000 42.927287 2000 6.6314104
119000 43.524125 2000 6.2169614
120000 44.127912 2000 5.8988829
121000 44.724988 2000 5.4197277
122000 45.328051 2000 4.6381303
123000 45.93285 2000 4.4949206
124000 46.54149 2000 4.4261118
125000 47.301723 2000 4.4223703
126000 48.071689 2000 4.4858898
127000 48.834286 2000 4.3312536
128000 49.448737 2000 3.7124973
129000 50.169622 2000 3.5467396
130000 50.867494 2000 3.5104139
131000 51.585563 2000 3.5725612
132000 52.240372 2000 3.669455
133000 52.892134 2000 3.6168912
134000 53.50594 2000 3.3598517
135000 54.114565 2000 3.3743407
136000 54.725082 2000 3.1109764
137000 55.358218 2000 3.0720146
138000 55.977314 2000 3.1303776
139000 56.589791 2000 3.2052806
140000 57.212518 2000 2.8958882
141000 57.867102 2000 2.9931572
142000 58.690342 2000 3.0967832
143000 59.418639 2000 3.0576365
144000 60.035852 2000 3.2016943
145000 60.666569 2000 3.3817709
146000 61.368878 2000 3.4527239
147000 62.159309 2000 3.5928733
148000 62.879677 2000 3.7784682
149000 63.50784 2000 3.6587944
150000 64.129366 2000 3.7945669
151000 64.74324 2000 3.5551557
152000 65.360802 2000 3.6248848
153000 65.979475 2000 3.7361463
154000 66.593554 2000 3.8534319
155000 67.30899 2000 4.0101408
156000 68.295637 2000 3.7670652
157000 69.257704 2000 3.1487676
158000 70.085566 2000 2.980076
159000 70.914218 2000 3.0350592
160000 71.734553 2000 3.125389
161000 72.423913 2000 2.7516115
162000 73.264994 2000 2.413911
163000 74.126424 2000 2.297713
164000 75.050891 2000 2.3190806
165000 75.917063 2000 2.2868879
166000 76.783267 2000 2.1658547
167000 77.516683 2000 1.7511071
168000 78.319102 2000 1.4112478
169000 78.961239 2000 1.3623558
170000 79.578448 2000 1.3701579
Loop time of 79.5785 on 1 procs for 150000 steps with 2000 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 40.78 | 40.78 | 40.78 | 0.0 | 51.25
Neigh | 0.6504 | 0.6504 | 0.6504 | 0.0 | 0.82
Comm | 0.090848 | 0.090848 | 0.090848 | 0.0 | 0.11
Output | 0.0059597 | 0.0059597 | 0.0059597 | 0.0 | 0.01
Modify | 36.939 | 36.939 | 36.939 | 0.0 | 46.42
Other | | 1.112 | | | 1.40
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15308 ave 15308 max 15308 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15308
Ave neighs/atom = 7.654
Neighbor list builds = 367
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
170000 0 2000 1.3701579
171000 0.71457906 2000 2.3724823
172000 1.4067557 2000 3.5881441
173000 2.0500352 2000 5.3771633
174000 2.8020081 2000 7.5896471
175000 3.467807 2000 10.77251
176000 4.064748 2000 14.806868
177000 4.6769962 2000 19.607624
178000 5.26259 2000 25.426227
179000 5.8424937 2000 32.23584
180000 6.4222206 2000 39.930468
181000 6.9910375 2000 47.686304
182000 7.5601562 2000 56.506806
183000 8.1243537 2000 66.514326
184000 8.6871123 2000 77.554644
185000 9.3749051 2000 89.224002
186000 10.008412 2000 102.07846
187000 10.668269 2000 116.08141
188000 11.26663 2000 130.97964
189000 11.874542 2000 146.77806
190000 12.436262 2000 162.79858
191000 12.973297 2000 179.02052
192000 13.532286 2000 196.26683
193000 14.056018 2000 214.38928
194000 14.593726 2000 232.32068
195000 15.115478 2000 251.74644
196000 15.637308 2000 272.25231
197000 16.159144 2000 294.64075
198000 16.676958 2000 318.32895
199000 17.186114 2000 342.44005
200000 17.706244 2000 368.35469
201000 18.221731 2000 395.2465
202000 18.739505 2000 422.63599
203000 19.259645 2000 450.45248
204000 19.769875 2000 479.60812
205000 20.293972 2000 510.44155
206000 20.806658 2000 543.25751
207000 21.348998 2000 577.35928
208000 21.888691 2000 612.29718
209000 22.421596 2000 647.8951
210000 22.922782 2000 683.79409
211000 23.473165 2000 720.36556
212000 24.008952 2000 759.27331
213000 24.56155 2000 798.27302
214000 25.062386 2000 837.93849
215000 25.563743 2000 877.92945
216000 26.066188 2000 919.62532
217000 26.584605 2000 962.83509
218000 27.15076 2000 1008.5243
219000 27.651387 2000 1054.5769
220000 28.146147 2000 1103.1843
221000 28.644239 2000 1153.0349
222000 29.141899 2000 1204.5599
223000 29.636644 2000 1257.1367
224000 30.13786 2000 1308.6735
WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
225000 30.638093 1999 1360.1205
226000 31.127956 1998 1404.8405
227000 31.620394 1996 1448.4869
228000 32.108597 1992 1491.8112
229000 32.592048 1985 1518.7013
230000 33.067462 1971 1507.6699
231000 33.552874 1965 1533.5096
232000 34.037763 1948 1489.4128
233000 34.531058 1933 1477.4536
234000 35.01451 1915 1425.8398
235000 35.495081 1904 1410.1451
236000 35.963357 1892 1401.7595
237000 36.428382 1880 1368.893
238000 36.890459 1868 1341.8885
239000 37.358838 1850 1286.7968
240000 37.828549 1833 1219.5123
241000 38.29428 1820 1173.3608
242000 38.750021 1806 1106.0727
243000 39.206425 1788 1035.912
244000 39.690492 1779 1021.6147
245000 40.138287 1767 969.40032
246000 40.582591 1757 939.12022
247000 41.02378 1739 840.9396
248000 41.472154 1730 822.06575
249000 41.916625 1719 762.11057
250000 42.365019 1707 708.50308
251000 42.804617 1700 692.12647
252000 43.257666 1697 694.5812
253000 43.777656 1686 652.36951
254000 44.244131 1682 662.95256
255000 44.667759 1677 637.34619
256000 45.111967 1672 630.71277
257000 45.550194 1669 641.87365
258000 45.985106 1665 635.862
259000 46.42582 1664 658.5339
260000 46.860965 1662 669.95468
261000 47.298309 1660 676.93495
262000 47.748236 1657 681.72646
263000 48.215018 1655 687.4078
264000 48.657973 1651 681.61352
265000 49.076584 1647 673.20622
266000 49.497823 1644 677.30073
267000 49.917789 1641 671.05897
268000 50.347112 1639 689.55776
269000 50.778062 1637 711.98809
270000 51.226034 1633 705.29974
Loop time of 51.2261 on 1 procs for 100000 steps with 1633 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.462 | 27.462 | 27.462 | 0.0 | 53.61
Neigh | 0.47887 | 0.47887 | 0.47887 | 0.0 | 0.93
Comm | 0.058496 | 0.058496 | 0.058496 | 0.0 | 0.11
Output | 0.0039167 | 0.0039167 | 0.0039167 | 0.0 | 0.01
Modify | 22.566 | 22.566 | 22.566 | 0.0 | 44.05
Other | | 0.6567 | | | 1.28
Nlocal: 1633 ave 1633 max 1633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11358 ave 11358 max 11358 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11358
Ave neighs/atom = 6.955297
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:02:15

635
examples/granregion/log.16Mar23.granregion.funnel.g++.4
View File

@ -1,635 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 4 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.55467905 2000 -0
2000 0.77825615 2000 -0
3000 0.99338813 2000 -0
4000 1.2048904 2000 -0
5000 1.4073987 2000 -0
6000 1.6070452 2000 -0
7000 1.8056594 2000 -0
8000 1.9907326 2000 -0
9000 2.1732359 2000 -0
10000 2.3525506 2000 -0
11000 2.4202338 2000 -0
12000 2.4883928 2000 -0
13000 2.5587335 2000 -0
14000 2.6327822 2000 -0
15000 2.7095893 2000 -0
16000 2.7909032 2000 -0
17000 2.8763781 2000 -0
18000 2.9671807 2000 -0
19000 3.05783 2000 -0
20000 3.1546642 2000 -0
Loop time of 3.1547 on 4 procs for 20000 steps with 2000 atoms
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.045592 | 0.12271 | 0.29398 | 28.5 | 3.89
Neigh | 0.011353 | 0.019401 | 0.032667 | 5.7 | 0.61
Comm | 0.043342 | 0.09899 | 0.1539 | 14.6 | 3.14
Output | 0.00097884 | 0.0019761 | 0.0024333 | 1.3 | 0.06
Modify | 0.8096 | 1.2822 | 2.26 | 50.7 | 40.65
Other | | 1.629 | | | 51.65
Nlocal: 500 ave 510 max 493 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 154 ave 227 max 79 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 415.5 ave 610 max 258 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1662
Ave neighs/atom = 0.831
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.068149031 2000 6807.2201
22000 0.13906682 2000 6973.9359
23000 0.21167896 2000 7142.3648
24000 0.28828482 2000 7276.9717
25000 0.36895294 2000 7369.4191
26000 0.45705665 2000 7497.6526
27000 0.55283141 2000 7638.946
28000 0.65163553 2000 7780.0339
29000 0.75208427 2000 7881.8177
30000 0.85956458 2000 7967.2641
31000 0.94177635 2000 7994.9273
32000 1.0345834 2000 7937.0672
33000 1.1315152 2000 7774.0508
34000 1.2426423 2000 7591.1511
35000 1.3578344 2000 7357.5032
36000 1.4893311 2000 7147.3776
37000 1.6240315 2000 6980.0719
38000 1.7664339 2000 6813.0872
39000 1.91857 2000 6657.0694
40000 2.0835393 2000 6505.1356
41000 2.2038908 2000 6330.3106
42000 2.330345 2000 6148.0635
43000 2.4596185 2000 5933.4808
44000 2.5912876 2000 5759.5507
45000 2.7316375 2000 5510.4729
46000 2.8777238 2000 5332.8673
47000 3.0357893 2000 5164.4197
48000 3.1931582 2000 5027.4099
49000 3.341993 2000 4904.6999
50000 3.4914327 2000 4712.0967
51000 3.6880787 2000 4575.8693
52000 3.8868278 2000 4443.4894
53000 4.0538325 2000 4272.1666
54000 4.2275386 2000 4113.2811
55000 4.3935565 2000 3974.5981
56000 4.6008319 2000 3863.5272
57000 4.8305792 2000 3676.8918
58000 5.1085757 2000 3446.5177
59000 5.3025239 2000 3227.8857
60000 5.5061134 2000 2997.8151
61000 5.6771065 2000 2745.5998
62000 5.8533046 2000 2530.2536
63000 6.0266287 2000 2352.9283
64000 6.1975348 2000 2102.4916
65000 6.375875 2000 1906.3034
66000 6.6008814 2000 1683.179
67000 6.8728018 2000 1440.0663
68000 7.1104699 2000 1220.2743
69000 7.3660591 2000 1012.4596
70000 7.6208232 2000 796.99913
71000 7.8459169 2000 631.28788
72000 8.0433916 2000 459.93641
73000 8.2225178 2000 359.28959
74000 8.3982201 2000 286.19292
75000 8.5769976 2000 235.53259
76000 8.7541865 2000 187.55737
77000 9.0010462 2000 144.42323
78000 9.2721615 2000 116.12613
79000 9.4992863 2000 95.625301
80000 9.7368141 2000 82.645629
81000 9.9462546 2000 72.124657
82000 10.15281 2000 64.266704
83000 10.365519 2000 56.7285
84000 10.55069 2000 49.44393
85000 10.764107 2000 42.434733
86000 10.993211 2000 37.816266
87000 11.243268 2000 33.892006
88000 11.487204 2000 29.898596
89000 11.684173 2000 26.4401
90000 11.880908 2000 23.329056
91000 12.078366 2000 21.291141
92000 12.347446 2000 19.494401
93000 12.582632 2000 18.157646
94000 12.833491 2000 17.176709
95000 13.109452 2000 16.059418
96000 13.34541 2000 15.524934
97000 13.604566 2000 13.887097
98000 13.816696 2000 12.98846
99000 14.043128 2000 12.325347
100000 14.35998 2000 11.567779
101000 14.584033 2000 11.097346
102000 14.793606 2000 10.981696
103000 15.011832 2000 10.914661
104000 15.223053 2000 10.183009
105000 15.435892 2000 9.9825606
106000 15.651946 2000 9.5164341
107000 15.870696 2000 9.4270389
108000 16.237826 2000 9.2752131
109000 16.525601 2000 8.580319
110000 16.74452 2000 8.3138082
111000 16.991527 2000 7.826454
112000 17.322972 2000 7.5958866
113000 17.649386 2000 7.2760339
114000 17.967676 2000 7.2879075
115000 18.27941 2000 6.8298855
116000 18.619507 2000 6.6964815
117000 18.979092 2000 6.490952
118000 19.303215 2000 6.0204595
119000 19.683409 2000 5.9293145
120000 20.034873 2000 5.7244854
121000 20.329374 2000 5.4221021
122000 20.670529 2000 4.8227757
123000 20.970073 2000 4.7914829
124000 21.297132 2000 4.6895984
125000 21.524346 2000 4.4951309
126000 21.742931 2000 4.5186107
127000 21.983039 2000 4.5989696
128000 22.203881 2000 4.5578225
129000 22.428553 2000 4.2667783
130000 22.662049 2000 4.0855202
131000 22.893977 2000 4.129346
132000 23.134398 2000 4.1720282
133000 23.367561 2000 4.3178701
134000 23.614361 2000 4.1047803
135000 23.840139 2000 3.856834
136000 24.095293 2000 4.0099605
137000 24.320746 2000 4.1104868
138000 24.555868 2000 4.1538456
139000 24.798604 2000 4.3079797
140000 25.125474 2000 4.0655486
141000 25.360498 2000 4.1257388
142000 25.597535 2000 4.1180413
143000 25.824173 2000 4.2764691
144000 26.082826 2000 4.3992832
145000 26.307002 2000 4.0978942
146000 26.532413 2000 4.1776805
147000 26.759469 2000 4.2261665
148000 26.989405 2000 4.4049886
149000 27.215826 2000 4.5559941
150000 27.443235 2000 4.7449947
151000 27.670397 2000 4.962558
152000 27.901368 2000 4.8517188
153000 28.148201 2000 4.9263912
154000 28.379071 2000 4.6200149
155000 28.621063 2000 4.8289752
156000 28.870192 2000 5.043235
157000 29.105614 2000 5.2399981
158000 29.330537 2000 5.494424
159000 29.558095 2000 4.9215021
160000 29.785841 2000 4.8938104
161000 30.011182 2000 5.0832139
162000 30.23825 2000 5.2281894
163000 30.464829 2000 5.4710487
164000 30.719854 2000 5.7311326
165000 31.038065 2000 5.9048483
166000 31.340672 2000 6.1177544
167000 31.649901 2000 4.0749212
168000 31.928746 2000 4.0087545
169000 32.153717 2000 2.8333927
170000 32.380796 2000 2.6131424
Loop time of 32.3808 on 4 procs for 150000 steps with 2000 atoms
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.997 | 12.251 | 14.992 | 89.3 | 37.83
Neigh | 0.1358 | 0.20191 | 0.24331 | 9.0 | 0.62
Comm | 1.2102 | 2.0432 | 2.4992 | 36.1 | 6.31
Output | 0.0079578 | 0.012222 | 0.020149 | 4.4 | 0.04
Modify | 7.1333 | 9.974 | 12.03 | 56.2 | 30.80
Other | | 7.899 | | | 24.39
Nlocal: 500 ave 547 max 414 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 447.5 ave 678 max 201 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 4478.75 ave 5715 max 3358 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 17915
Ave neighs/atom = 8.9575
Neighbor list builds = 375
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
Step CPU Atoms KinEng
170000 0 2000 2.6131424
171000 0.22601136 2000 3.529459
172000 0.45221016 2000 4.7071494
173000 0.68427839 2000 6.3480095
174000 0.91114205 2000 8.8055429
175000 1.1431874 2000 12.020148
176000 1.3732197 2000 16.079961
177000 1.6051751 2000 20.911155
178000 1.8346523 2000 26.447901
179000 2.0762403 2000 32.277607
180000 2.3420473 2000 39.374754
181000 2.6328957 2000 46.824434
182000 2.8669203 2000 54.755937
183000 3.1047916 2000 63.957816
184000 3.3310346 2000 74.217343
185000 3.5685015 2000 85.472859
186000 3.7955114 2000 97.586962
187000 4.0326183 2000 110.39658
188000 4.267244 2000 123.54524
189000 4.4987867 2000 137.45798
190000 4.7358838 2000 151.81094
191000 4.9494874 2000 166.91945
192000 5.1552044 2000 182.93379
193000 5.3547002 2000 200.32195
194000 5.5590208 2000 218.31863
195000 5.7575332 2000 237.22122
196000 5.9520759 2000 255.12936
197000 6.1457469 2000 273.87347
198000 6.341216 2000 293.82126
199000 6.5397944 2000 315.13067
200000 6.7418645 2000 337.18517
201000 6.9368245 2000 359.48438
202000 7.1538903 2000 382.76229
203000 7.3864641 2000 408.60338
204000 7.6731476 2000 435.15421
205000 7.9053649 2000 462.53542
206000 8.1480905 2000 490.85791
207000 8.3856692 2000 519.80878
208000 8.6034715 2000 550.44978
209000 8.8046602 2000 581.78594
210000 9.0044136 2000 615.02491
211000 9.2216638 2000 649.34564
212000 9.4269046 2000 684.24357
213000 9.6587854 2000 720.72627
214000 9.8596293 2000 757.96901
215000 10.05877 2000 796.8493
216000 10.256066 2000 836.58839
217000 10.48718 2000 877.81823
218000 10.694787 2000 920.81077
219000 10.891455 2000 963.77552
220000 11.147269 2000 1007.6868
221000 11.400829 2000 1054.0654
222000 11.65238 2000 1102.4934
223000 11.846807 2000 1151.1348
224000 12.040148 2000 1200.6622
225000 12.229259 2000 1251.5126
WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
226000 12.420863 1999 1299.6349
227000 12.635492 1997 1338.1126
228000 12.827738 1987 1354.6661
229000 13.016127 1980 1369.1412
230000 13.211511 1970 1369.1776
231000 13.404909 1963 1377.7863
232000 13.602332 1950 1362.1028
233000 13.796103 1938 1344.4535
234000 13.988442 1924 1318.1397
235000 14.185813 1907 1269.3181
236000 14.378388 1895 1242.269
237000 14.568867 1881 1188.0729
238000 14.75676 1868 1162.8778
239000 14.947894 1854 1111.9974
240000 15.160004 1840 1050.2813
241000 15.340495 1831 1024.5782
242000 15.523597 1816 980.07203
243000 15.725193 1807 973.84606
244000 15.902549 1796 936.95947
245000 16.081382 1790 916.53685
246000 16.261081 1780 893.82891
247000 16.451727 1770 853.09944
248000 16.628641 1755 804.73429
249000 16.804105 1749 773.19378
250000 16.978354 1738 734.78084
251000 17.152527 1725 668.92528
252000 17.328291 1717 651.36038
253000 17.512786 1706 595.48412
254000 17.695931 1699 564.79829
255000 17.874221 1695 558.19897
256000 18.050516 1693 568.02459
257000 18.228697 1692 584.97166
258000 18.400925 1689 574.19701
259000 18.576449 1687 583.36332
260000 18.754006 1684 577.56927
261000 18.946091 1681 582.0375
262000 19.182957 1679 583.29644
263000 19.394795 1676 575.09831
264000 19.604668 1673 575.78272
265000 19.81517 1672 595.66572
266000 20.046658 1670 610.84262
267000 20.332684 1665 588.36505
268000 20.573691 1662 593.44831
269000 20.800574 1660 600.31964
270000 21.058624 1656 588.46212
Loop time of 21.0587 on 4 procs for 100000 steps with 1656 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8632 | 8.4037 | 11.541 | 97.3 | 39.91
Neigh | 0.13431 | 0.15665 | 0.17248 | 3.8 | 0.74
Comm | 0.70516 | 1.4552 | 1.9637 | 40.7 | 6.91
Output | 0.0030904 | 0.0079543 | 0.016722 | 5.9 | 0.04
Modify | 5.3661 | 6.1781 | 6.8249 | 22.0 | 29.34
Other | | 4.857 | | | 23.06
Nlocal: 414 ave 426 max 385 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 408 ave 634 max 183 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 3463 ave 4360 max 2354 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 13852
Ave neighs/atom = 8.3647343
Neighbor list builds = 255
Dangerous builds = 0
Total wall time: 0:00:56

634
examples/granregion/log.16Mar23.granregion.mixer.g++.1
View File

@ -1,634 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.11477344 444 -0 0.015707963
2000 0.21604269 444 -0 0.031415927
3000 0.31421365 444 -0 0.04712389
4000 0.41095902 444 -0 0.062831853
5000 0.50703042 444 -0 0.078539816
6000 0.60585007 444 -0 0.09424778
7000 0.70232419 444 -0 0.10995574
8000 0.80002622 444 -0 0.12566371
9000 0.89464008 444 -0 0.14137167
10000 0.99260726 444 -0 0.15707963
11000 1.090675 444 -0 0.1727876
12000 1.1878107 444 -0 0.18849556
13000 1.2860401 444 -0 0.20420352
14000 1.3830433 444 -0 0.21991149
15000 1.4834023 444 -0 0.23561945
16000 1.5799984 444 -0 0.25132741
17000 1.6758091 444 -0 0.26703538
18000 1.7713554 444 -0 0.28274334
19000 1.8684734 444 -0 0.2984513
20000 1.9661563 444 -0 0.31415927
21000 2.0629748 444 -0 0.32986723
22000 2.1575594 444 -0 0.34557519
23000 2.2530422 444 -0 0.36128316
24000 2.3525179 444 -0 0.37699112
25000 2.4494323 444 -0 0.39269908
26000 2.5454666 444 -0 0.40840704
27000 2.6402269 444 -0 0.42411501
28000 2.7364338 444 -0 0.43982297
29000 2.8349 444 -0 0.45553093
30000 2.9327959 444 -0 0.4712389
31000 3.0304534 444 -0 0.48694686
32000 3.1315005 444 -0 0.50265482
33000 3.2290307 444 -0 0.51836279
34000 3.3243787 444 -0 0.53407075
35000 3.4232964 444 -0 0.54977871
36000 3.5235978 444 -0 0.56548668
37000 3.6214101 444 -0 0.58119464
38000 3.7179412 444 -0 0.5969026
39000 3.8159856 444 -0 0.61261057
40000 3.9121916 444 -0 0.62831853
41000 4.0080794 444 -0 0.64402649
42000 4.1087349 444 -0 0.65973446
43000 4.2059697 444 -0 0.67544242
44000 4.3043867 444 -0 0.69115038
45000 4.4014253 444 -0 0.70685835
46000 4.5000241 444 -0 0.72256631
47000 4.5970258 444 -0 0.73827427
48000 4.6929243 444 -0 0.75398224
49000 4.7894702 444 -0 0.7696902
50000 4.8858098 444 -0 0.78539816
51000 4.985063 444 -0 0.80110613
52000 5.0863877 444 -0 0.81681409
53000 5.181301 444 -0 0.83252205
54000 5.2819523 444 -0 0.84823002
55000 5.3895357 444 -0 0.86393798
56000 5.5225568 444 -0 0.87964594
57000 5.6473901 444 -0 0.89535391
58000 5.7786123 444 -0 0.91106187
59000 5.8932617 444 -0 0.92676983
60000 6.004952 444 -0 0.9424778
61000 6.1168028 444 -0 0.95818576
62000 6.2274784 444 -0 0.97389372
63000 6.341172 444 -0 0.98960169
64000 6.4565154 444 -0 1.0053096
65000 6.5684785 444 -0 1.0210176
66000 6.6836542 444 -0 1.0367256
67000 6.797745 444 -0 1.0524335
68000 6.9091592 444 -0 1.0681415
69000 7.0230958 444 -0 1.0838495
70000 7.140508 444 -0 1.0995574
71000 7.2547153 444 -0 1.1152654
72000 7.3698096 444 -0 1.1309734
73000 7.4846587 444 -0 1.1466813
74000 7.6005538 444 -0 1.1623893
75000 7.715498 444 -0 1.1780972
76000 7.8306339 444 -0 1.1938052
77000 7.9458861 444 -0 1.2095132
78000 8.0608796 444 -0 1.2252211
79000 8.1819612 444 -0 1.2409291
80000 8.3017939 444 -0 1.2566371
81000 8.4206794 444 -0 1.272345
82000 8.5396045 444 -0 1.288053
83000 8.6588178 444 -0 1.303761
84000 8.7939815 444 -0 1.3194689
85000 8.9999511 888 -0 1.3351769
86000 9.2762515 888 -0 1.3508848
87000 9.5497189 888 -0 1.3665928
88000 9.8025426 888 -0 1.3823008
89000 10.063005 888 -0 1.3980087
90000 10.343956 888 -0 1.4137167
91000 10.630004 888 -0 1.4294247
92000 10.865437 888 -0 1.4451326
93000 11.090302 888 -0 1.4608406
94000 11.306921 888 -0 1.4765485
95000 11.525442 888 -0 1.4922565
96000 11.786482 888 -0 1.5079645
97000 12.033336 888 -0 1.5236724
98000 12.258224 888 -0 1.5393804
99000 12.486583 888 -0 1.5550884
100000 12.70566 888 -0 1.5707963
101000 12.934051 888 -0 1.5865043
102000 13.194977 888 -0 1.6022123
103000 13.503561 888 -0 1.6179202
104000 13.737785 888 -0 1.6336282
105000 13.96388 888 -0 1.6493361
106000 14.190156 888 -0 1.6650441
107000 14.416346 888 -0 1.6807521
108000 14.642321 888 -0 1.69646
109000 14.877668 888 -0 1.712168
110000 15.114644 888 -0 1.727876
111000 15.354762 888 -0 1.7435839
112000 15.615795 888 -0 1.7592919
113000 15.854301 888 -0 1.7749998
114000 16.099855 888 -0 1.7907078
115000 16.344044 888 -0 1.8064158
116000 16.60829 888 -0 1.8221237
117000 16.847146 888 -0 1.8378317
118000 17.086787 888 -0 1.8535397
119000 17.324264 888 -0 1.8692476
120000 17.563913 888 -0 1.8849556
121000 17.798333 888 -0 1.9006636
122000 18.033339 888 -0 1.9163715
123000 18.275883 888 -0 1.9320795
124000 18.542879 888 -0 1.9477874
125000 18.790098 888 -0 1.9634954
126000 19.034113 888 -0 1.9792034
127000 19.286183 888 -0 1.9949113
128000 19.574764 888 -0 2.0106193
129000 19.832536 888 -0 2.0263273
130000 20.085705 888 -0 2.0420352
131000 20.327805 888 -0 2.0577432
132000 20.576476 888 -0 2.0734512
133000 20.82021 888 -0 2.0891591
134000 21.063425 888 -0 2.1048671
135000 21.304848 888 -0 2.120575
136000 21.554936 888 -0 2.136283
137000 21.797949 888 -0 2.151991
138000 22.041181 888 -0 2.1676989
139000 22.288509 888 -0 2.1834069
140000 22.539512 888 -0 2.1991149
141000 22.786046 888 -0 2.2148228
142000 23.052553 888 -0 2.2305308
143000 23.321282 888 -0 2.2462387
144000 23.619171 888 -0 2.2619467
145000 23.918581 888 -0 2.2776547
146000 24.200849 888 -0 2.2933626
147000 24.500127 888 -0 2.3090706
148000 24.756357 888 -0 2.3247786
149000 25.015262 888 -0 2.3404865
150000 25.271136 888 -0 2.3561945
151000 25.519846 888 -0 2.3719025
152000 25.780481 888 -0 2.3876104
153000 26.027917 888 -0 2.4033184
154000 26.277021 888 -0 2.4190263
155000 26.54158 888 -0 2.4347343
156000 26.828357 888 -0 2.4504423
157000 27.172993 888 -0 2.4661502
158000 27.454171 888 -0 2.4818582
159000 27.72964 888 -0 2.4975662
160000 28.007464 888 -0 2.5132741
161000 28.28268 888 -0 2.5289821
162000 28.561094 888 -0 2.54469
163000 28.839295 888 -0 2.560398
164000 29.117588 888 -0 2.576106
165000 29.394126 888 -0 2.5918139
166000 29.675102 888 -0 2.6075219
167000 29.951524 888 -0 2.6232299
168000 30.233181 888 -0 2.6389378
169000 30.516798 888 -0 2.6546458
170000 30.818897 1000 -0 2.6703538
171000 31.215403 1000 -0 2.6860617
172000 31.528362 1000 -0 2.7017697
173000 31.844759 1000 -0 2.7174776
174000 32.159787 1000 -0 2.7331856
175000 32.482605 1000 -0 2.7488936
176000 32.798004 1000 -0 2.7646015
177000 33.112668 1000 -0 2.7803095
178000 33.429501 1000 -0 2.7960175
179000 33.74646 1000 -0 2.8117254
180000 34.059172 1000 -0 2.8274334
181000 34.381226 1000 -0 2.8431414
182000 34.697465 1000 -0 2.8588493
183000 35.008892 1000 -0 2.8745573
184000 35.332856 1000 -0 2.8902652
185000 35.650733 1000 -0 2.9059732
186000 35.971328 1000 -0 2.9216812
187000 36.298046 1000 -0 2.9373891
188000 36.622634 1000 -0 2.9530971
189000 36.945728 1000 -0 2.9688051
190000 37.268801 1000 -0 2.984513
191000 37.592615 1000 -0 3.000221
192000 37.915197 1000 -0 3.0159289
193000 38.226138 1000 -0 3.0316369
194000 38.534735 1000 -0 3.0473449
195000 38.844711 1000 -0 3.0630528
196000 39.159518 1000 -0 3.0787608
197000 39.474235 1000 -0 3.0944688
198000 39.786609 1000 -0 3.1101767
199000 40.10213 1000 -0 3.1258847
200000 40.421226 1000 -0 3.1415927
Loop time of 40.4213 on 1 procs for 200000 steps with 1000 atoms
Performance: 20199.903 tau/day, 4947.886 timesteps/s, 4.948 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6681 | 3.6681 | 3.6681 | 0.0 | 9.07
Neigh | 0.050194 | 0.050194 | 0.050194 | 0.0 | 0.12
Comm | 0.53308 | 0.53308 | 0.53308 | 0.0 | 1.32
Output | 0.0071363 | 0.0071363 | 0.0071363 | 0.0 | 0.02
Modify | 35.563 | 35.563 | 35.563 | 0.0 | 87.98
Other | | 0.5999 | | | 1.48
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3812 ave 3812 max 3812 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3812
Ave neighs/atom = 3.812
Neighbor list builds = 205
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0188213 3.1415927
201000 0.31745969 1000 1.0237918 3.1573006
202000 0.6315036 1000 1.0177231 3.1730086
203000 0.9480314 1000 1.0127096 3.1887165
204000 1.2572431 1000 1.0084386 3.2044245
205000 1.5683429 1000 0.9957528 3.2201325
206000 1.8801922 1000 1.0003921 3.2358404
207000 2.1905883 1000 0.99358387 3.2515484
208000 2.4948426 1000 0.99103748 3.2672564
209000 2.8195665 1000 0.98488628 3.2829643
210000 3.1420952 1000 0.98305824 3.2986723
211000 3.4618849 1000 0.97185818 3.3143802
212000 3.7910078 1000 0.96191966 3.3300882
213000 4.1184009 1000 0.95953159 3.3457962
214000 4.4491355 1000 0.95307268 3.3615041
215000 4.7782398 1000 0.95612155 3.3772121
216000 5.1088177 1000 0.96582166 3.3929201
217000 5.4376503 1000 0.96124408 3.408628
218000 5.7707229 1000 0.95705813 3.424336
219000 6.1055922 1000 0.9660222 3.440044
220000 6.4418056 1000 0.97539486 3.4557519
221000 6.7755181 1000 0.97919396 3.4714599
222000 7.104521 1000 0.97448171 3.4871678
223000 7.4368025 1000 0.95742917 3.5028758
224000 7.7623405 1000 0.94218245 3.5185838
225000 8.0932682 1000 0.93056484 3.5342917
226000 8.4217598 1000 0.92009109 3.5499997
227000 8.747426 1000 0.90684871 3.5657077
228000 9.0818038 1000 0.91719046 3.5814156
229000 9.4125504 1000 0.92681746 3.5971236
230000 9.7439963 1000 0.9195493 3.6128316
231000 10.075499 1000 0.93275667 3.6285395
232000 10.404017 1000 0.9494565 3.6442475
233000 10.774786 1000 0.95036607 3.6599554
234000 11.158713 1000 0.9596283 3.6756634
235000 11.566878 1000 0.98314341 3.6913714
236000 11.977294 1000 0.98115865 3.7070793
237000 12.347191 1000 0.9723466 3.7227873
238000 12.686388 1000 0.95267817 3.7384953
239000 13.031631 1000 0.92661956 3.7542032
240000 13.451121 1000 0.92237207 3.7699112
241000 13.855031 1000 0.91301732 3.7856191
242000 14.272001 1000 0.90488754 3.8013271
243000 14.632631 1000 0.90430417 3.8170351
244000 14.97608 1000 0.90179051 3.832743
245000 15.419173 1000 0.89658897 3.848451
246000 15.903699 1000 0.89583335 3.864159
247000 16.312374 1000 0.89409138 3.8798669
248000 16.660472 1000 0.89948364 3.8955749
249000 17.063147 1000 0.90196936 3.9112829
250000 17.423622 1000 0.89616943 3.9269908
251000 17.76439 1000 0.87816303 3.9426988
252000 18.103828 1000 0.86705341 3.9584067
253000 18.454644 1000 0.84494344 3.9741147
254000 18.876297 1000 0.81541663 3.9898227
255000 19.264851 1000 0.80071805 4.0055306
256000 19.669757 1000 0.80290754 4.0212386
257000 20.066097 1000 0.80000385 4.0369466
258000 20.481516 1000 0.80379277 4.0526545
259000 20.851537 1000 0.81091684 4.0683625
260000 21.246226 1000 0.80124855 4.0840704
261000 21.586832 1000 0.79581606 4.0997784
262000 21.968726 1000 0.78415946 4.1154864
263000 22.388474 1000 0.78837276 4.1311943
264000 22.76238 1000 0.78962435 4.1469023
265000 23.13787 1000 0.79388706 4.1626103
266000 23.470742 1000 0.80484385 4.1783182
267000 23.801402 1000 0.79505699 4.1940262
268000 24.14266 1000 0.78663829 4.2097342
269000 24.545281 1000 0.77557297 4.2254421
270000 24.886776 1000 0.76992342 4.2411501
271000 25.218744 1000 0.75955867 4.256858
272000 25.549898 1000 0.76207709 4.272566
273000 25.882738 1000 0.76891185 4.288274
274000 26.212384 1000 0.77380617 4.3039819
275000 26.540612 1000 0.77349795 4.3196899
276000 26.869636 1000 0.77559636 4.3353979
277000 27.200449 1000 0.76806972 4.3511058
278000 27.548549 1000 0.76223861 4.3668138
279000 27.883681 1000 0.76306533 4.3825218
280000 28.221552 1000 0.76369569 4.3982297
281000 28.558479 1000 0.75945303 4.4139377
282000 28.892758 1000 0.75872312 4.4296456
283000 29.224927 1000 0.75354345 4.4453536
284000 29.565477 1000 0.74433058 4.4610616
285000 29.914679 1000 0.7349005 4.4767695
286000 30.265305 1000 0.73182808 4.4924775
287000 30.607982 1000 0.73334122 4.5081855
288000 30.94168 1000 0.73308623 4.5238934
289000 31.276062 1000 0.73620818 4.5396014
290000 31.614934 1000 0.73906492 4.5553093
291000 31.959782 1000 0.73921306 4.5710173
292000 32.296279 1000 0.73919766 4.5867253
293000 32.615262 1000 0.75148875 4.6024332
294000 32.93925 1000 0.76390126 4.6181412
295000 33.266316 1000 0.76421084 4.6338492
296000 33.591115 1000 0.78124272 4.6495571
297000 33.924279 1000 0.78526224 4.6652651
298000 34.256265 1000 0.78279226 4.6809731
299000 34.584382 1000 0.78390001 4.696681
300000 34.910629 1000 0.78017239 4.712389
301000 35.233205 1000 0.77432653 4.7280969
302000 35.55956 1000 0.7627792 4.7438049
303000 35.885484 1000 0.75222273 4.7595129
304000 36.205453 1000 0.73765921 4.7752208
305000 36.525101 1000 0.72338298 4.7909288
306000 36.845236 1000 0.71944975 4.8066368
307000 37.168044 1000 0.71547274 4.8223447
308000 37.491196 1000 0.71267737 4.8380527
309000 37.827079 1000 0.70506173 4.8537606
310000 38.168049 1000 0.70685173 4.8694686
311000 38.504282 1000 0.70327488 4.8851766
312000 38.846152 1000 0.69732519 4.9008845
313000 39.191958 1000 0.70137823 4.9165925
314000 39.532177 1000 0.70613806 4.9323005
315000 39.876728 1000 0.70981591 4.9480084
316000 40.225244 1000 0.72246602 4.9637164
317000 40.573681 1000 0.71946499 4.9794244
318000 40.918134 1000 0.73275857 4.9951323
319000 41.261914 1000 0.74357547 5.0108403
320000 41.607984 1000 0.74138038 5.0265482
321000 41.957822 1000 0.73285846 5.0422562
322000 42.30176 1000 0.72990718 5.0579642
323000 42.644077 1000 0.72024459 5.0736721
324000 42.985509 1000 0.71052943 5.0893801
325000 43.323921 1000 0.69560261 5.1050881
326000 43.664945 1000 0.69939398 5.120796
327000 44.004741 1000 0.71331291 5.136504
328000 44.347204 1000 0.72181082 5.152212
329000 44.689866 1000 0.72534262 5.1679199
330000 45.055673 1000 0.73874292 5.1836279
331000 45.400501 1000 0.74135464 5.1993358
332000 45.743289 1000 0.73578005 5.2150438
333000 46.087061 1000 0.72662516 5.2307518
334000 46.427231 1000 0.72030125 5.2464597
335000 46.767813 1000 0.72801784 5.2621677
336000 47.108619 1000 0.73020974 5.2778757
337000 47.44666 1000 0.7344527 5.2935836
338000 47.784653 1000 0.73826638 5.3092916
339000 48.124114 1000 0.74079395 5.3249995
340000 48.463953 1000 0.74030413 5.3407075
341000 48.804616 1000 0.74815855 5.3564155
342000 49.143226 1000 0.75762011 5.3721234
343000 49.482788 1000 0.76311094 5.3878314
344000 49.822597 1000 0.76394459 5.4035394
345000 50.162186 1000 0.75550163 5.4192473
346000 50.496689 1000 0.7594991 5.4349553
347000 50.831695 1000 0.76650932 5.4506633
348000 51.167201 1000 0.76750437 5.4663712
349000 51.501847 1000 0.77084248 5.4820792
350000 51.841805 1000 0.76487701 5.4977871
351000 52.179907 1000 0.76870148 5.5134951
352000 52.517605 1000 0.77597853 5.5292031
353000 52.850047 1000 0.77929348 5.544911
354000 53.182408 1000 0.7744937 5.560619
355000 53.512931 1000 0.76114616 5.576327
356000 53.845782 1000 0.75392687 5.5920349
357000 54.178336 1000 0.74858889 5.6077429
358000 54.514517 1000 0.75630978 5.6234508
359000 54.850783 1000 0.75781107 5.6391588
360000 55.183323 1000 0.75613713 5.6548668
361000 55.518704 1000 0.75250391 5.6705747
362000 55.851425 1000 0.75790051 5.6862827
363000 56.212376 1000 0.75283475 5.7019907
364000 56.542027 1000 0.7431151 5.7176986
365000 56.874325 1000 0.73274509 5.7334066
366000 57.208926 1000 0.72261631 5.7491146
367000 57.596495 1000 0.71279773 5.7648225
368000 58.007863 1000 0.70452113 5.7805305
369000 58.346944 1000 0.69777381 5.7962384
370000 58.686215 1000 0.69698007 5.8119464
371000 59.030366 1000 0.69322062 5.8276544
372000 59.368607 1000 0.67728454 5.8433623
373000 59.704376 1000 0.67335006 5.8590703
374000 60.044772 1000 0.66920493 5.8747783
375000 60.382875 1000 0.65614401 5.8904862
376000 60.72002 1000 0.65874131 5.9061942
377000 61.058554 1000 0.67072465 5.9219022
378000 61.400078 1000 0.68118419 5.9376101
379000 61.748931 1000 0.68481865 5.9533181
380000 62.098203 1000 0.68840839 5.969026
381000 62.444961 1000 0.69447162 5.984734
382000 62.797286 1000 0.69881397 6.000442
383000 63.154921 1000 0.69610171 6.0161499
384000 63.508448 1000 0.70059329 6.0318579
385000 63.857115 1000 0.71085103 6.0475659
386000 64.207915 1000 0.71532684 6.0632738
387000 64.561127 1000 0.72968624 6.0789818
388000 64.939826 1000 0.74729894 6.0946897
389000 65.284635 1000 0.76268063 6.1103977
390000 65.631752 1000 0.77170089 6.1261057
391000 65.981566 1000 0.77212462 6.1418136
392000 66.328406 1000 0.773784 6.1575216
393000 66.655905 1000 0.7731096 6.1732296
394000 66.993751 1000 0.77245259 6.1889375
395000 67.322842 1000 0.76912533 6.2046455
396000 67.647532 1000 0.76397972 6.2203535
397000 67.977448 1000 0.75736166 6.2360614
398000 68.310064 1000 0.75287599 6.2517694
399000 68.635966 1000 0.75354368 6.2674773
400000 68.963492 1000 0.75582397 6.2831853
Loop time of 68.9635 on 1 procs for 200000 steps with 1000 atoms
Performance: 11839.683 tau/day, 2900.084 timesteps/s, 2.900 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.238 | 11.238 | 11.238 | 0.0 | 16.30
Neigh | 0.077817 | 0.077817 | 0.077817 | 0.0 | 0.11
Comm | 1.5441 | 1.5441 | 1.5441 | 0.0 | 2.24
Output | 0.0082341 | 0.0082341 | 0.0082341 | 0.0 | 0.01
Modify | 55.304 | 55.304 | 55.304 | 0.0 | 80.19
Other | | 0.7909 | | | 1.15
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 278 ave 278 max 278 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5072 ave 5072 max 5072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5072
Ave neighs/atom = 5.072
Neighbor list builds = 166
Dangerous builds = 0
Total wall time: 0:01:49

634
examples/granregion/log.16Mar23.granregion.mixer.g++.4
View File

@ -1,634 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 2 by 2 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.069039547 444 -0 0.015707963
2000 0.12867095 444 -0 0.031415927
3000 0.18791426 444 -0 0.04712389
4000 0.24614388 444 -0 0.062831853
5000 0.30404486 444 -0 0.078539816
6000 0.36105446 444 -0 0.09424778
7000 0.41713358 444 -0 0.10995574
8000 0.47282802 444 -0 0.12566371
9000 0.52742586 444 -0 0.14137167
10000 0.58233488 444 -0 0.15707963
11000 0.62155506 444 -0 0.1727876
12000 0.6605457 444 -0 0.18849556
13000 0.69971591 444 -0 0.20420352
14000 0.73821845 444 -0 0.21991149
15000 0.77860211 444 -0 0.23561945
16000 0.8188072 444 -0 0.25132741
17000 0.85992964 444 -0 0.26703538
18000 0.9008443 444 -0 0.28274334
19000 0.94216466 444 -0 0.2984513
20000 0.98508697 444 -0 0.31415927
21000 1.0241468 444 -0 0.32986723
22000 1.0606191 444 -0 0.34557519
23000 1.0972735 444 -0 0.36128316
24000 1.134726 444 -0 0.37699112
25000 1.1723693 444 -0 0.39269908
26000 1.211349 444 -0 0.40840704
27000 1.250291 444 -0 0.42411501
28000 1.2906408 444 -0 0.43982297
29000 1.3307315 444 -0 0.45553093
30000 1.3704867 444 -0 0.4712389
31000 1.4064392 444 -0 0.48694686
32000 1.4426955 444 -0 0.50265482
33000 1.4789666 444 -0 0.51836279
34000 1.5163037 444 -0 0.53407075
35000 1.5534135 444 -0 0.54977871
36000 1.5907054 444 -0 0.56548668
37000 1.6296055 444 -0 0.58119464
38000 1.6690167 444 -0 0.5969026
39000 1.7082024 444 -0 0.61261057
40000 1.7476796 444 -0 0.62831853
41000 1.7847465 444 -0 0.64402649
42000 1.8216975 444 -0 0.65973446
43000 1.8594424 444 -0 0.67544242
44000 1.8975401 444 -0 0.69115038
45000 1.9361216 444 -0 0.70685835
46000 1.9764821 444 -0 0.72256631
47000 2.0221252 444 -0 0.73827427
48000 2.0635337 444 -0 0.75398224
49000 2.104472 444 -0 0.7696902
50000 2.1447842 444 -0 0.78539816
51000 2.1808558 444 -0 0.80110613
52000 2.2180542 444 -0 0.81681409
53000 2.2547243 444 -0 0.83252205
54000 2.2934546 444 -0 0.84823002
55000 2.3321909 444 -0 0.86393798
56000 2.3732179 444 -0 0.87964594
57000 2.4141133 444 -0 0.89535391
58000 2.455667 444 -0 0.91106187
59000 2.4983196 444 -0 0.92676983
60000 2.5415086 444 -0 0.9424778
61000 2.581342 444 -0 0.95818576
62000 2.6215029 444 -0 0.97389372
63000 2.6633884 444 -0 0.98960169
64000 2.7048848 444 -0 1.0053096
65000 2.7497607 444 -0 1.0210176
66000 2.7952373 444 -0 1.0367256
67000 2.8399748 444 -0 1.0524335
68000 2.8851806 444 -0 1.0681415
69000 2.9303317 444 -0 1.0838495
70000 2.9815632 444 -0 1.0995574
71000 3.0257986 444 -0 1.1152654
72000 3.068788 444 -0 1.1309734
73000 3.1130125 444 -0 1.1466813
74000 3.1558178 444 -0 1.1623893
75000 3.1993327 444 -0 1.1780972
76000 3.2444469 444 -0 1.1938052
77000 3.2901781 444 -0 1.2095132
78000 3.3356302 444 -0 1.2252211
79000 3.3814834 444 -0 1.2409291
80000 3.4290631 444 -0 1.2566371
81000 3.4715671 444 -0 1.272345
82000 3.5136342 444 -0 1.288053
83000 3.5566281 444 -0 1.303761
84000 3.6001405 444 -0 1.3194689
85000 3.6709788 888 -0 1.3351769
86000 3.7652387 888 -0 1.3508848
87000 3.8618109 888 -0 1.3665928
88000 3.9546406 888 -0 1.3823008
89000 4.0475587 888 -0 1.3980087
90000 4.1424919 888 -0 1.4137167
91000 4.2114594 888 -0 1.4294247
92000 4.2842588 888 -0 1.4451326
93000 4.3524161 888 -0 1.4608406
94000 4.4204131 888 -0 1.4765485
95000 4.4886628 888 -0 1.4922565
96000 4.5588224 888 -0 1.5079645
97000 4.6304943 888 -0 1.5236724
98000 4.7018695 888 -0 1.5393804
99000 4.774147 888 -0 1.5550884
100000 4.847776 888 -0 1.5707963
101000 4.9173562 888 -0 1.5865043
102000 4.9886499 888 -0 1.6022123
103000 5.0618801 888 -0 1.6179202
104000 5.1331411 888 -0 1.6336282
105000 5.205209 888 -0 1.6493361
106000 5.2795148 888 -0 1.6650441
107000 5.3523346 888 -0 1.6807521
108000 5.4263886 888 -0 1.69646
109000 5.5029416 888 -0 1.712168
110000 5.5807033 888 -0 1.727876
111000 5.6574852 888 -0 1.7435839
112000 5.7320356 888 -0 1.7592919
113000 5.8097178 888 -0 1.7749998
114000 5.8858974 888 -0 1.7907078
115000 5.9636528 888 -0 1.8064158
116000 6.0421783 888 -0 1.8221237
117000 6.12052 888 -0 1.8378317
118000 6.2016349 888 -0 1.8535397
119000 6.2834058 888 -0 1.8692476
120000 6.3644485 888 -0 1.8849556
121000 6.4398727 888 -0 1.9006636
122000 6.5152081 888 -0 1.9163715
123000 6.5916482 888 -0 1.9320795
124000 6.6694407 888 -0 1.9477874
125000 6.7474201 888 -0 1.9634954
126000 6.8270768 888 -0 1.9792034
127000 6.9060885 888 -0 1.9949113
128000 6.9847809 888 -0 2.0106193
129000 7.0660497 888 -0 2.0263273
130000 7.1468939 888 -0 2.0420352
131000 7.2275386 888 -0 2.0577432
132000 7.3103515 888 -0 2.0734512
133000 7.3904073 888 -0 2.0891591
134000 7.4711333 888 -0 2.1048671
135000 7.5529594 888 -0 2.120575
136000 7.6399017 888 -0 2.136283
137000 7.7263891 888 -0 2.151991
138000 7.815523 888 -0 2.1676989
139000 7.9041642 888 -0 2.1834069
140000 7.9950145 888 -0 2.1991149
141000 8.0776291 888 -0 2.2148228
142000 8.1584715 888 -0 2.2305308
143000 8.2409653 888 -0 2.2462387
144000 8.326064 888 -0 2.2619467
145000 8.4107211 888 -0 2.2776547
146000 8.4946153 888 -0 2.2933626
147000 8.5784663 888 -0 2.3090706
148000 8.6648861 888 -0 2.3247786
149000 8.7503472 888 -0 2.3404865
150000 8.8378801 888 -0 2.3561945
151000 8.9221381 888 -0 2.3719025
152000 9.0101516 888 -0 2.3876104
153000 9.0982387 888 -0 2.4033184
154000 9.1851912 888 -0 2.4190263
155000 9.2744741 888 -0 2.4347343
156000 9.3697509 888 -0 2.4504423
157000 9.4640354 888 -0 2.4661502
158000 9.5594845 888 -0 2.4818582
159000 9.6572972 888 -0 2.4975662
160000 9.7543656 888 -0 2.5132741
161000 9.8485073 888 -0 2.5289821
162000 9.9446493 888 -0 2.54469
163000 10.040013 888 -0 2.560398
164000 10.137116 888 -0 2.576106
165000 10.23506 888 -0 2.5918139
166000 10.335537 888 -0 2.6075219
167000 10.436607 888 -0 2.6232299
168000 10.537429 888 -0 2.6389378
169000 10.642458 888 -0 2.6546458
170000 10.74705 1000 -0 2.6703538
171000 10.857156 1000 -0 2.6860617
172000 10.965939 1000 -0 2.7017697
173000 11.076233 1000 -0 2.7174776
174000 11.184172 1000 -0 2.7331856
175000 11.293846 1000 -0 2.7488936
176000 11.402493 1000 -0 2.7646015
177000 11.513895 1000 -0 2.7803095
178000 11.625438 1000 -0 2.7960175
179000 11.738308 1000 -0 2.8117254
180000 11.854793 1000 -0 2.8274334
181000 11.968344 1000 -0 2.8431414
182000 12.082268 1000 -0 2.8588493
183000 12.196356 1000 -0 2.8745573
184000 12.313359 1000 -0 2.8902652
185000 12.429559 1000 -0 2.9059732
186000 12.545853 1000 -0 2.9216812
187000 12.661447 1000 -0 2.9373891
188000 12.777355 1000 -0 2.9530971
189000 12.894856 1000 -0 2.9688051
190000 13.0103 1000 -0 2.984513
191000 13.126221 1000 -0 3.000221
192000 13.241507 1000 -0 3.0159289
193000 13.356198 1000 -0 3.0316369
194000 13.468168 1000 -0 3.0473449
195000 13.582232 1000 -0 3.0630528
196000 13.700446 1000 -0 3.0787608
197000 13.816948 1000 -0 3.0944688
198000 13.934106 1000 -0 3.1101767
199000 14.053497 1000 -0 3.1258847
200000 14.171799 1000 -0 3.1415927
Loop time of 14.1719 on 4 procs for 200000 steps with 1000 atoms
Performance: 57614.644 tau/day, 14112.479 timesteps/s, 14.112 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46468 | 0.82686 | 1.2428 | 39.9 | 5.83
Neigh | 0.010644 | 0.013047 | 0.015567 | 2.0 | 0.09
Comm | 2.2447 | 2.716 | 3.2525 | 28.2 | 19.16
Output | 0.0040193 | 0.0057101 | 0.0084742 | 2.2 | 0.04
Modify | 7.9913 | 8.6193 | 9.394 | 20.9 | 60.82
Other | | 1.991 | | | 14.05
Nlocal: 250 ave 266 max 237 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 294 ave 335 max 253 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 960.25 ave 1454 max 492 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3841
Ave neighs/atom = 3.841
Neighbor list builds = 201
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.89 | 11.9 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0060272 3.1415927
201000 0.11023112 1000 1.0117513 3.1573006
202000 0.22297119 1000 1.0121624 3.1730086
203000 0.33090251 1000 1.0099707 3.1887165
204000 0.43921623 1000 1.0099624 3.2044245
205000 0.54813391 1000 1.009398 3.2201325
206000 0.6597641 1000 0.99686298 3.2358404
207000 0.76806828 1000 0.96520673 3.2515484
208000 0.88217705 1000 0.96521294 3.2672564
209000 0.99810181 1000 0.96501099 3.2829643
210000 1.1113988 1000 0.96426624 3.2986723
211000 1.2252752 1000 0.9564358 3.3143802
212000 1.3381064 1000 0.95482019 3.3300882
213000 1.4513852 1000 0.9446233 3.3457962
214000 1.5630713 1000 0.92461651 3.3615041
215000 1.6785702 1000 0.92106646 3.3772121
216000 1.7937182 1000 0.92058667 3.3929201
217000 1.9092992 1000 0.91797493 3.408628
218000 2.0251567 1000 0.91351081 3.424336
219000 2.1419482 1000 0.91991749 3.440044
220000 2.258391 1000 0.92943198 3.4557519
221000 2.3747328 1000 0.93176684 3.4714599
222000 2.4930355 1000 0.92625008 3.4871678
223000 2.6111794 1000 0.9216243 3.5028758
224000 2.729971 1000 0.92332955 3.5185838
225000 2.8489286 1000 0.91963985 3.5342917
226000 2.97003 1000 0.91913679 3.5499997
227000 3.0874646 1000 0.92381436 3.5657077
228000 3.2089543 1000 0.93085242 3.5814156
229000 3.3281962 1000 0.92872221 3.5971236
230000 3.4476271 1000 0.92536664 3.6128316
231000 3.5681706 1000 0.92953138 3.6285395
232000 3.6911427 1000 0.93937257 3.6442475
233000 3.8115833 1000 0.95916002 3.6599554
234000 3.9301977 1000 0.96652709 3.6756634
235000 4.0481963 1000 0.96753364 3.6913714
236000 4.1684171 1000 0.96096249 3.7070793
237000 4.2874672 1000 0.97028893 3.7227873
238000 4.4072896 1000 0.95323014 3.7384953
239000 4.5292898 1000 0.94143454 3.7542032
240000 4.6529563 1000 0.9334569 3.7699112
241000 4.7701737 1000 0.93340822 3.7856191
242000 4.8891772 1000 0.93517762 3.8013271
243000 5.0078759 1000 0.92632745 3.8170351
244000 5.1260291 1000 0.91858996 3.832743
245000 5.2472736 1000 0.90006015 3.848451
246000 5.363907 1000 0.8850116 3.864159
247000 5.4838317 1000 0.87807775 3.8798669
248000 5.6039445 1000 0.85981326 3.8955749
249000 5.7262584 1000 0.85764597 3.9112829
250000 5.8488174 1000 0.86748856 3.9269908
251000 5.9665578 1000 0.85889952 3.9426988
252000 6.084021 1000 0.84476495 3.9584067
253000 6.203987 1000 0.84094974 3.9741147
254000 6.3221073 1000 0.82638568 3.9898227
255000 6.441682 1000 0.81449512 4.0055306
256000 6.5625653 1000 0.80130582 4.0212386
257000 6.6860772 1000 0.79100139 4.0369466
258000 6.8117355 1000 0.78531082 4.0526545
259000 6.9379959 1000 0.7678277 4.0683625
260000 7.0606907 1000 0.74798797 4.0840704
261000 7.1846943 1000 0.73902576 4.0997784
262000 7.3084818 1000 0.73326104 4.1154864
263000 7.4304296 1000 0.7370234 4.1311943
264000 7.5536012 1000 0.73817854 4.1469023
265000 7.6792395 1000 0.74675482 4.1626103
266000 7.8061753 1000 0.7480056 4.1783182
267000 7.9331093 1000 0.748671 4.1940262
268000 8.0593048 1000 0.74430146 4.2097342
269000 8.1888555 1000 0.73246199 4.2254421
270000 8.3184687 1000 0.71666285 4.2411501
271000 8.4489277 1000 0.69699332 4.256858
272000 8.5822473 1000 0.69724726 4.272566
273000 8.7148666 1000 0.69752702 4.288274
274000 8.8426159 1000 0.69393439 4.3039819
275000 8.9746848 1000 0.67961922 4.3196899
276000 9.1020134 1000 0.67808365 4.3353979
277000 9.232486 1000 0.66241302 4.3511058
278000 9.3607588 1000 0.65559661 4.3668138
279000 9.4879578 1000 0.64949975 4.3825218
280000 9.6142148 1000 0.65351945 4.3982297
281000 9.7437802 1000 0.66566267 4.4139377
282000 9.87097 1000 0.68284419 4.4296456
283000 9.9975944 1000 0.68906456 4.4453536
284000 10.124724 1000 0.69474503 4.4610616
285000 10.25369 1000 0.71686298 4.4767695
286000 10.38212 1000 0.70966561 4.4924775
287000 10.513274 1000 0.70173402 4.5081855
288000 10.641359 1000 0.69841037 4.5238934
289000 10.765608 1000 0.68947449 4.5396014
290000 10.893738 1000 0.68391661 4.5553093
291000 11.018982 1000 0.69112115 4.5710173
292000 11.146639 1000 0.70208247 4.5867253
293000 11.269392 1000 0.70044553 4.6024332
294000 11.39243 1000 0.69973655 4.6181412
295000 11.517741 1000 0.70719661 4.6338492
296000 11.643013 1000 0.69961909 4.6495571
297000 11.771064 1000 0.7038606 4.6652651
298000 11.899855 1000 0.70651383 4.6809731
299000 12.024499 1000 0.72028817 4.696681
300000 12.151124 1000 0.72141372 4.712389
301000 12.278902 1000 0.73011344 4.7280969
302000 12.402615 1000 0.74750506 4.7438049
303000 12.524021 1000 0.74362139 4.7595129
304000 12.645914 1000 0.73643471 4.7752208
305000 12.766721 1000 0.73250587 4.7909288
306000 12.945373 1000 0.72450933 4.8066368
307000 13.084062 1000 0.71650682 4.8223447
308000 13.210593 1000 0.71012044 4.8380527
309000 13.339536 1000 0.7045498 4.8537606
310000 13.477512 1000 0.69904261 4.8694686
311000 13.617832 1000 0.69370407 4.8851766
312000 13.802532 1000 0.70012261 4.9008845
313000 13.9682 1000 0.69796658 4.9165925
314000 14.139079 1000 0.70673901 4.9323005
315000 14.290205 1000 0.70285296 4.9480084
316000 14.414474 1000 0.69917788 4.9637164
317000 14.541743 1000 0.69153454 4.9794244
318000 14.672817 1000 0.69630312 4.9951323
319000 14.800594 1000 0.70732059 5.0108403
320000 14.982014 1000 0.71069744 5.0265482
321000 15.126459 1000 0.70982909 5.0422562
322000 15.264165 1000 0.70514067 5.0579642
323000 15.391036 1000 0.70591206 5.0736721
324000 15.518096 1000 0.70992653 5.0893801
325000 15.644416 1000 0.70605327 5.1050881
326000 15.772686 1000 0.70492617 5.120796
327000 15.899812 1000 0.69711977 5.136504
328000 16.050906 1000 0.68791974 5.152212
329000 16.197987 1000 0.68350425 5.1679199
330000 16.346901 1000 0.67886559 5.1836279
331000 16.511885 1000 0.6838106 5.1993358
332000 16.666556 1000 0.68570448 5.2150438
333000 16.820557 1000 0.68347768 5.2307518
334000 16.972048 1000 0.67352858 5.2464597
335000 17.171176 1000 0.67154375 5.2621677
336000 17.380218 1000 0.67050288 5.2778757
337000 17.561848 1000 0.66093797 5.2935836
338000 17.746525 1000 0.65261747 5.3092916
339000 17.926411 1000 0.65084314 5.3249995
340000 18.105197 1000 0.65003008 5.3407075
341000 18.235972 1000 0.65397536 5.3564155
342000 18.389741 1000 0.67129271 5.3721234
343000 18.604032 1000 0.68934086 5.3878314
344000 18.788879 1000 0.71225704 5.4035394
345000 18.935273 1000 0.72645711 5.4192473
346000 19.136926 1000 0.73153889 5.4349553
347000 19.310095 1000 0.74047453 5.4506633
348000 19.476545 1000 0.74508084 5.4663712
349000 19.599138 1000 0.74030176 5.4820792
350000 19.753114 1000 0.72037009 5.4977871
351000 19.893497 1000 0.71009934 5.5134951
352000 20.020982 1000 0.69475509 5.5292031
353000 20.149857 1000 0.68883962 5.544911
354000 20.278476 1000 0.68764856 5.560619
355000 20.407747 1000 0.6853423 5.576327
356000 20.53591 1000 0.69528948 5.5920349
357000 20.668654 1000 0.70787069 5.6077429
358000 20.802835 1000 0.70110924 5.6234508
359000 20.950394 1000 0.69356484 5.6391588
360000 21.076061 1000 0.69727901 5.6548668
361000 21.224785 1000 0.69878093 5.6705747
362000 21.416947 1000 0.70063124 5.6862827
363000 21.632619 1000 0.68842038 5.7019907
364000 21.836231 1000 0.68478573 5.7176986
365000 21.963636 1000 0.68232032 5.7334066
366000 22.092926 1000 0.66971225 5.7491146
367000 22.219251 1000 0.67006227 5.7648225
368000 22.344723 1000 0.6694355 5.7805305
369000 22.470654 1000 0.66622377 5.7962384
370000 22.59941 1000 0.66501888 5.8119464
371000 22.732869 1000 0.66108622 5.8276544
372000 22.859824 1000 0.65989005 5.8433623
373000 22.989282 1000 0.65277032 5.8590703
374000 23.116089 1000 0.64599939 5.8747783
375000 23.243733 1000 0.64279675 5.8904862
376000 23.371971 1000 0.64321129 5.9061942
377000 23.505382 1000 0.65596736 5.9219022
378000 23.638755 1000 0.68055295 5.9376101
379000 23.770714 1000 0.71147476 5.9533181
380000 23.906376 1000 0.7478441 5.969026
381000 24.040685 1000 0.76216879 5.984734
382000 24.173446 1000 0.78574658 6.000442
383000 24.30114 1000 0.80947952 6.0161499
384000 24.426872 1000 0.81514681 6.0318579
385000 24.555905 1000 0.81469775 6.0475659
386000 24.684891 1000 0.80579609 6.0632738
387000 24.811946 1000 0.79952446 6.0789818
388000 24.940028 1000 0.78668384 6.0946897
389000 25.061479 1000 0.78375511 6.1103977
390000 25.18315 1000 0.78124583 6.1261057
391000 25.303012 1000 0.77072038 6.1418136
392000 25.423275 1000 0.75748297 6.1575216
393000 25.542996 1000 0.74703682 6.1732296
394000 25.661826 1000 0.74135384 6.1889375
395000 25.782254 1000 0.73344196 6.2046455
396000 25.903156 1000 0.72305463 6.2203535
397000 26.026207 1000 0.71221263 6.2360614
398000 26.145498 1000 0.70602241 6.2517694
399000 26.266146 1000 0.69822375 6.2674773
400000 26.387762 1000 0.69567985 6.2831853
Loop time of 26.3878 on 4 procs for 200000 steps with 1000 atoms
Performance: 30942.580 tau/day, 7579.263 timesteps/s, 7.579 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6871 | 2.8172 | 3.925 | 64.8 | 10.68
Neigh | 0.017325 | 0.021917 | 0.026669 | 3.1 | 0.08
Comm | 4.7404 | 6.0917 | 7.4409 | 54.5 | 23.09
Output | 0.0043138 | 0.0065642 | 0.0087622 | 1.9 | 0.02
Modify | 13.258 | 14.716 | 16.132 | 35.6 | 55.77
Other | | 2.735 | | | 10.36
Nlocal: 250 ave 257 max 241 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 387.5 ave 477 max 299 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1233.5 ave 1523 max 917 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 4934
Ave neighs/atom = 4.934
Neighbor list builds = 168
Dangerous builds = 0
Total wall time: 0:00:40

482
examples/granregion/log.27Jun24.granregion.box.g++.1 Normal file
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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 48 every 566 steps, 100 by step 1133
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170772
1500 99 0.31486693 0.31486693 0.17429055 0.0064903432
1600 99 0.26369001 0.26369001 0.15095266 0.0045226847
1700 100 0.1925923 0.1925923 0.11308104 0.007362313
1800 100 0.13724978 0.13724978 0.083276845 0.0058136373
1900 100 0.077212636 0.077212636 0.053159386 0.0016509598
2000 100 0.065294031 0.065294031 0.04372752 0.0020346467
2100 100 0.057431398 0.057431398 0.037977068 0.0012681098
2200 100 0.059093045 0.059093045 0.037435193 0.00096610799
2300 100 0.03422338 0.03422338 0.025491304 0.00069886052
2400 100 0.020558284 0.020558284 0.016163009 0.0017260663
2500 100 0.015339709 0.015339709 0.012329236 0.00041308031
2600 100 0.012891354 0.012891354 0.009766054 0.00030356722
2700 100 0.0092634449 0.0092634449 0.0073580108 0.00077723051
2800 100 0.0073925841 0.0073925841 0.0059932218 0.00016466767
2900 100 0.0081228267 0.0081228267 0.006281761 0.00013828388
3000 100 0.0041833223 0.0041833223 0.0035147096 0.00013160599
3100 100 0.0035930775 0.0035930775 0.0030039922 0.00060639771
3200 100 0.0030824465 0.0030824465 0.0026541293 0.00047391014
3300 100 0.0035087522 0.0035087522 0.0027664508 0.00014080317
3400 100 0.0018537868 0.0018537868 0.0017099705 6.3326674e-05
3500 100 0.0015371228 0.0015371228 0.0014155433 0.00021612522
3600 100 0.001708556 0.001708556 0.0014369892 8.1034202e-05
3700 100 0.00095948652 0.00095948652 0.0009788528 3.4694023e-05
3800 100 0.00091875668 0.00091875668 0.00086805146 3.9373686e-05
3900 100 0.001557068 0.001557068 0.001159526 2.5178607e-05
4000 100 0.00062012451 0.00062012451 0.00066806922 5.6680551e-06
4100 100 0.00060940771 0.00060940771 0.00065614741 1.0137901e-05
4200 100 0.00059538437 0.00059538437 0.00064501521 7.3679744e-06
4300 100 0.00052946048 0.00052946048 0.00059353641 5.9225081e-06
4400 100 0.00051202281 0.00051202281 0.00057524772 3.6198435e-05
4500 100 0.00049986632 0.00049986632 0.00055754521 2.2275519e-05
4600 100 0.00048187334 0.00048187334 0.00053988815 2.2015243e-05
4700 100 0.00045261491 0.00045261491 0.00050298355 8.9681339e-05
4800 100 0.00034965427 0.00034965427 0.0004278781 1.0983535e-05
4900 100 0.00033555621 0.00033555621 0.00041435167 2.9266598e-05
5000 100 0.00031387148 0.00031387148 0.00039605781 2.5628425e-05
Loop time of 0.0497806 on 1 procs for 5000 steps with 100 atoms
Performance: 43390431.056 tau/day, 100440.813 timesteps/s, 10.044 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0052991 | 0.0052991 | 0.0052991 | 0.0 | 10.64
Neigh | 0.008529 | 0.008529 | 0.008529 | 0.0 | 17.13
Comm | 0.00050137 | 0.00050137 | 0.00050137 | 0.0 | 1.01
Output | 0.00028923 | 0.00028923 | 0.00028923 | 0.0 | 0.58
Modify | 0.033612 | 0.033612 | 0.033612 | 0.0 | 67.52
Other | | 0.00155 | | | 3.11
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 164 ave 164 max 164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 164
Ave neighs/atom = 1.64
Neighbor list builds = 281
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (../fix_wall_gran_region.cpp:96)
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00031387148 0.00031387148 0.00039605781 2.6174978e-05
5100 100 0.54537023 0.54537023 0.30042175 0.0087427352
5200 100 0.57210852 0.57210852 0.3192468 0.0098134067
5300 100 0.7168108 0.7168108 0.38577893 0.011004584
5400 100 0.78895524 0.78895524 0.41889428 0.013555713
5500 100 0.87797874 0.87797874 0.45689223 0.01565356
5600 100 0.95424379 0.95424379 0.48830429 0.014707858
5700 100 1.0046012 1.0046012 0.51054927 0.01469179
5800 100 1.0371453 1.0371453 0.5262568 0.015576788
5900 100 1.0545743 1.0545743 0.5361173 0.01589889
6000 100 1.0932949 1.0932949 0.55402214 0.017484573
6100 100 1.1148364 1.1148364 0.56241126 0.01721788
6200 100 1.1315267 1.1315267 0.57050887 0.017961246
6300 100 1.1506124 1.1506124 0.58009471 0.017159062
6400 100 1.1663328 1.1663328 0.5876586 0.017935311
6500 100 1.1821086 1.1821086 0.59595161 0.018005315
6600 100 1.2039397 1.2039397 0.60567524 0.021604662
6700 100 1.2269912 1.2269912 0.61770225 0.018907995
6800 100 1.2447035 1.2447035 0.6257652 0.020537656
6900 100 1.2625323 1.2625323 0.63486698 0.020106131
7000 100 1.2617127 1.2617127 0.63318163 0.019670429
7100 100 1.260715 1.260715 0.63311254 0.01981063
7200 100 1.2790404 1.2790404 0.64079 0.02021891
7300 100 1.2760228 1.2760228 0.6395331 0.021749943
7400 100 1.2799657 1.2799657 0.64139079 0.020472918
7500 100 1.2846472 1.2846472 0.64343078 0.02061003
7600 100 1.2883963 1.2883963 0.64491863 0.020748893
7700 100 1.2926891 1.2926891 0.6468454 0.02059959
7800 100 1.3033563 1.3033563 0.65126208 0.021822102
7900 100 1.3025795 1.3025795 0.65069464 0.021213858
8000 100 1.3052548 1.3052548 0.65209881 0.021398728
8100 100 1.3069801 1.3069801 0.6530457 0.021245966
8200 100 1.3092011 1.3092011 0.65438349 0.02122166
8300 100 1.3101277 1.3101277 0.65518546 0.021329292
8400 100 1.3117013 1.3117013 0.65550345 0.021460379
8500 100 1.3144455 1.3144455 0.65685825 0.021604641
8600 100 1.3164134 1.3164134 0.65789495 0.021563159
8700 100 1.3186879 1.3186879 0.6591421 0.021754259
8800 100 1.3216911 1.3216911 0.66041154 0.022161545
8900 100 1.3207611 1.3207611 0.65988391 0.021812278
9000 100 1.3213163 1.3213163 0.66021107 0.021890934
9100 100 1.3224957 1.3224957 0.66088572 0.021825725
9200 100 1.3240758 1.3240758 0.66183609 0.021785081
9300 100 1.3254189 1.3254189 0.66280087 0.021665121
9400 100 1.3325923 1.3325923 0.66627599 0.021935299
9500 100 1.3403779 1.3403779 0.66969078 0.022258389
9600 100 1.3360821 1.3360821 0.66729084 0.022125375
9700 100 1.3364048 1.3364048 0.66733374 0.022084635
9800 100 1.3348391 1.3348391 0.66653654 0.021957941
9900 100 1.3340902 1.3340902 0.66619851 0.022132442
10000 100 1.3341233 1.3341233 0.66625291 0.02242346
Loop time of 0.170031 on 1 procs for 5000 steps with 100 atoms
Performance: 12703591.746 tau/day, 29406.462 timesteps/s, 2.941 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02428 | 0.02428 | 0.02428 | 0.0 | 14.28
Neigh | 0.02016 | 0.02016 | 0.02016 | 0.0 | 11.86
Comm | 0.00063308 | 0.00063308 | 0.00063308 | 0.0 | 0.37
Output | 0.00026926 | 0.00026926 | 0.00026926 | 0.0 | 0.16
Modify | 0.12295 | 0.12295 | 0.12295 | 0.0 | 72.31
Other | | 0.001744 | | | 1.03
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 186 ave 186 max 186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 186
Ave neighs/atom = 1.86
Neighbor list builds = 626
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3341233 1.3341233 0.66625291 0.022389629
10100 100 0.29934208 0.29934208 0.17559716 0.0080511663
10200 100 0.15937333 0.15937333 0.10361049 0.0052770441
10300 100 0.083457844 0.083457844 0.067443759 0.0019700613
10400 100 0.065692832 0.065692832 0.055653291 0.0018339668
10500 100 0.052804438 0.052804438 0.045281034 0.0016027455
10600 100 0.04328663 0.04328663 0.037333736 0.0010520803
10700 100 0.034758594 0.034758594 0.030913039 0.00098209982
10800 100 0.031059386 0.031059386 0.027743119 0.00043771073
10900 100 0.025257043 0.025257043 0.023417455 0.00057319686
11000 100 0.020661736 0.020661736 0.019736355 0.00027957807
11100 100 0.017347891 0.017347891 0.017523904 0.00033806442
11200 100 0.013838843 0.013838843 0.013891648 0.0004814668
11300 100 0.010848849 0.010848849 0.011429994 0.00017218727
11400 100 0.0087243303 0.0087243303 0.0089442702 0.00075858277
11500 100 0.0073404505 0.0073404505 0.0074359014 0.00016419055
11600 100 0.005593778 0.005593778 0.0059169171 0.00067508582
11700 100 0.0051164194 0.0051164194 0.0053270943 8.4490639e-05
11800 100 0.00441161 0.00441161 0.0046984183 8.1750645e-05
11900 100 0.0040823871 0.0040823871 0.0044273607 0.00057274663
12000 100 0.0036457853 0.0036457853 0.0041171254 6.4466313e-05
12100 100 0.0034927566 0.0034927566 0.0039732335 0.00010435211
12200 100 0.0034030997 0.0034030997 0.0038913895 7.5846038e-05
12300 100 0.0032970662 0.0032970662 0.0036879396 8.4270392e-05
12400 100 0.0031107627 0.0031107627 0.0034222463 0.00010403492
12500 100 0.0029402407 0.0029402407 0.0033029532 3.6385479e-05
12600 100 0.0027926657 0.0027926657 0.0031897566 4.143403e-05
12700 100 0.0026584426 0.0026584426 0.0030863436 0.00017608636
12800 100 0.0020593472 0.0020593472 0.0024174548 2.5484422e-05
12900 100 0.0019445876 0.0019445876 0.0023331214 1.3291393e-05
13000 100 0.0019356798 0.0019356798 0.0023208275 3.7775631e-05
13100 100 0.001917674 0.001917674 0.0023067328 2.3731216e-05
13200 100 0.0018402122 0.0018402122 0.0022290175 2.3227838e-05
13300 100 0.0017947406 0.0017947406 0.0021839926 5.68555e-05
13400 100 0.0016930751 0.0016930751 0.0020981569 3.762312e-05
13500 100 0.0016591044 0.0016591044 0.0020636607 2.0531417e-05
13600 100 0.0015170608 0.0015170608 0.0019236349 2.87871e-05
13700 100 0.0014040099 0.0014040099 0.0017412115 3.7091497e-05
13800 100 0.0013892837 0.0013892837 0.0017134626 1.7192386e-05
13900 100 0.0013189709 0.0013189709 0.0016364794 0.00022920131
14000 100 0.0012610766 0.0012610766 0.0015926858 1.5605822e-05
14100 100 0.0010746324 0.0010746324 0.0014018754 1.8598362e-05
14200 100 0.0010259837 0.0010259837 0.0013546872 1.7918726e-05
14300 100 0.0008919653 0.0008919653 0.0011534101 0.00015490093
14400 100 0.00087001531 0.00087001531 0.0011016258 1.0766439e-05
14500 100 0.00083846397 0.00083846397 0.0010767041 1.0375992e-05
14600 100 0.0008155908 0.0008155908 0.00105642 1.2582086e-05
14700 100 0.00080868405 0.00080868405 0.00104978 7.027334e-05
14800 100 0.00073613153 0.00073613153 0.00098179118 3.236684e-05
14900 100 0.00071371931 0.00071371931 0.00095309072 8.6245124e-06
15000 100 0.00070031746 0.00070031746 0.0009423403 2.4693888e-05
Loop time of 0.0531531 on 1 procs for 5000 steps with 100 atoms
Performance: 40637346.357 tau/day, 94067.931 timesteps/s, 9.407 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0049693 | 0.0049693 | 0.0049693 | 0.0 | 9.35
Neigh | 0.0033529 | 0.0033529 | 0.0033529 | 0.0 | 6.31
Comm | 0.00045859 | 0.00045859 | 0.00045859 | 0.0 | 0.86
Output | 0.00031163 | 0.00031163 | 0.00031163 | 0.0 | 0.59
Modify | 0.042417 | 0.042417 | 0.042417 | 0.0 | 79.80
Other | | 0.001644 | | | 3.09
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 157 ave 157 max 157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 101
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00070031746 0.00070031746 0.0009423403 2.4820402e-05
15100 100 1.0378931 1.0378931 0.67940294 0.014665698
15200 100 1.0517533 1.0517533 0.69115597 0.01309217
15300 100 1.1062671 1.1062671 0.73515555 0.015692859
15400 100 1.385963 1.385963 0.89710836 0.022187064
15500 100 1.5008849 1.5008849 0.94689573 0.030001316
15600 100 1.6919387 1.6919387 1.0471028 0.026806301
15700 100 1.8311512 1.8311512 1.1071134 0.024492529
15800 100 1.8517819 1.8517819 1.1216762 0.028629961
15900 100 1.8895616 1.8895616 1.1177621 0.028934483
16000 100 2.0691195 2.0691195 1.1848851 0.032794489
16100 100 2.2520282 2.2520282 1.26292 0.030167679
16200 100 2.2879859 2.2879859 1.2866695 0.02974115
16300 100 2.3679798 2.3679798 1.3150501 0.032771704
16400 100 2.3846251 2.3846251 1.3122933 0.029948284
16500 100 2.528765 2.528765 1.3886857 0.032511301
16600 100 2.5465734 2.5465734 1.4009546 0.033614459
16700 100 2.6883939 2.6883939 1.457327 0.039494183
16800 100 2.8655546 2.8655546 1.5468292 0.036099395
16900 100 2.8919695 2.8919695 1.5768619 0.037384016
17000 100 3.0433407 3.0433407 1.6445056 0.037344364
17100 100 3.2283804 3.2283804 1.7335616 0.041395151
17200 100 3.3098823 3.3098823 1.7794605 0.04616548
17300 100 3.3890828 3.3890828 1.8289994 0.050512368
17400 100 3.278912 3.278912 1.7770308 0.04270684
17500 100 3.3373113 3.3373113 1.7927421 0.056764855
17600 100 3.3264731 3.3264731 1.8066541 0.045863538
17700 100 3.0707481 3.0707481 1.6881602 0.047285321
17800 100 3.0911023 3.0911023 1.7142589 0.040005715
17900 100 3.1368 3.1368 1.7314207 0.043475979
18000 100 3.1705064 3.1705064 1.7503598 0.042272578
18100 100 3.2348301 3.2348301 1.7599183 0.042974559
18200 100 3.4676237 3.4676237 1.8675014 0.051937094
18300 100 3.460493 3.460493 1.8710624 0.04615202
18400 100 3.4132328 3.4132328 1.8379148 0.048316249
18500 100 3.6046 3.6046 1.936101 0.046093227
18600 100 3.6898847 3.6898847 1.985425 0.048623681
18700 100 3.8073645 3.8073645 2.0517694 0.051139644
18800 100 3.9453683 3.9453683 2.121645 0.053091211
18900 100 3.891796 3.891796 2.1038949 0.047975378
19000 100 3.9805517 3.9805517 2.143216 0.052740909
19100 100 3.8032187 3.8032187 2.0535533 0.060896481
19200 100 3.8956813 3.8956813 2.1023053 0.055995941
19300 100 3.8441465 3.8441465 2.0783298 0.055586425
19400 100 3.6983054 3.6983054 1.9993476 0.051487825
19500 100 3.9082901 3.9082901 2.110386 0.055361137
19600 100 3.8183806 3.8183806 2.0521248 0.054637936
19700 100 3.9479599 3.9479599 2.123487 0.05654763
19800 100 3.7900356 3.7900356 2.0309629 0.055030689
19900 100 3.8526352 3.8526352 2.079537 0.052237722
20000 100 3.7004965 3.7004965 2.0054313 0.052260073
Loop time of 0.141466 on 1 procs for 5000 steps with 100 atoms
Performance: 15268708.811 tau/day, 35344.233 timesteps/s, 3.534 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0092801 | 0.0092801 | 0.0092801 | 0.0 | 6.56
Neigh | 0.030749 | 0.030749 | 0.030749 | 0.0 | 21.74
Comm | 0.00076276 | 0.00076276 | 0.00076276 | 0.0 | 0.54
Output | 0.00026657 | 0.00026657 | 0.00026657 | 0.0 | 0.19
Modify | 0.098434 | 0.098434 | 0.098434 | 0.0 | 69.58
Other | | 0.001973 | | | 1.39
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 144
Ave neighs/atom = 1.44
Neighbor list builds = 906
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.7004965 3.7004965 2.0054313 0.051978523
20100 100 1.0456682 1.0456682 0.65203589 0.01426764
20200 100 0.92132571 0.92132571 0.56692143 0.016160496
20300 100 0.9080139 0.9080139 0.54653258 0.011333456
20400 100 0.95504442 0.95504442 0.56626124 0.011989567
20500 100 0.85373295 0.85373295 0.5162143 0.011906206
20600 100 1.0224737 1.0224737 0.59801919 0.012676175
20700 100 0.98041767 0.98041767 0.57722359 0.015534239
20800 100 0.94580127 0.94580127 0.54452681 0.014648617
20900 100 0.92685337 0.92685337 0.52998999 0.012221026
21000 100 0.67355263 0.67355263 0.38349088 0.0096954349
21100 100 0.30344447 0.30344447 0.20123228 0.0065577613
21200 100 0.16818819 0.16818819 0.12097279 0.0042401405
21300 100 0.10742131 0.10742131 0.082910182 0.0032814832
21400 100 0.096764554 0.096764554 0.071534839 0.0029435039
21500 100 0.046970465 0.046970465 0.04129138 0.0017468115
21600 100 0.032766377 0.032766377 0.026265793 0.0016491276
21700 100 0.022152668 0.022152668 0.019394268 0.00050552315
21800 100 0.020778 0.020778 0.017776111 0.00098557239
21900 100 0.020778283 0.020778283 0.017641295 0.00074778783
22000 100 0.01698488 0.01698488 0.01429695 0.0005628648
22100 100 0.01418614 0.01418614 0.012102299 0.00051794337
22200 100 0.013346276 0.013346276 0.011394805 0.00032236098
22300 100 0.0079928433 0.0079928433 0.0077723623 0.00022112873
22400 100 0.0076254375 0.0076254375 0.0073027877 0.00031949798
22500 100 0.0069692597 0.0069692597 0.0069664447 0.00021312177
22600 100 0.006390305 0.006390305 0.0064208682 0.00041289648
22700 100 0.0056975941 0.0056975941 0.0057521988 0.00030399038
22800 100 0.0044357329 0.0044357329 0.0045549598 0.00017846882
22900 100 0.0036644546 0.0036644546 0.0038064043 0.00023078463
23000 100 0.002829538 0.002829538 0.0032135364 0.00022739562
23100 100 0.0027443908 0.0027443908 0.0030949164 0.00020554818
23200 100 0.0026840272 0.0026840272 0.00304758 0.00016936931
23300 100 0.0024070816 0.0024070816 0.0027285777 0.00016201789
23400 100 0.0021175586 0.0021175586 0.0023871632 0.00029731473
23500 100 0.0020591834 0.0020591834 0.0022740401 0.00015989214
23600 100 0.0020569788 0.0020569788 0.0022646534 0.00015753267
23700 100 0.0019823585 0.0019823585 0.0021969033 0.00015346211
23800 100 0.0021461846 0.0021461846 0.0022696006 0.00025075823
23900 100 0.001964677 0.001964677 0.0021583248 0.00014863082
24000 100 0.0019474488 0.0019474488 0.0021316684 0.00013004574
24100 100 0.0024970295 0.0024970295 0.0023832844 9.8929573e-05
24200 100 0.0017561148 0.0017561148 0.0019839926 7.1132622e-05
24300 100 0.0016986298 0.0016986298 0.001930582 7.1465912e-05
24400 100 0.001571577 0.001571577 0.0018168131 0.00015652173
24500 100 0.0015605078 0.0015605078 0.001789223 6.9843415e-05
24600 100 0.0018490208 0.0018490208 0.0019049916 5.2092258e-05
24700 100 0.0014134222 0.0014134222 0.0016814396 4.4173713e-05
24800 100 0.0013062268 0.0013062268 0.001520288 3.6497646e-05
24900 100 0.0012718438 0.0012718438 0.0014563564 3.8597512e-05
25000 100 0.0012686432 0.0012686432 0.0014211643 4.791856e-05
Loop time of 0.0562653 on 1 procs for 5000 steps with 100 atoms
Performance: 38389540.983 tau/day, 88864.678 timesteps/s, 8.886 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0068337 | 0.0068337 | 0.0068337 | 0.0 | 12.15
Neigh | 0.0087607 | 0.0087607 | 0.0087607 | 0.0 | 15.57
Comm | 0.00052045 | 0.00052045 | 0.00052045 | 0.0 | 0.92
Output | 0.00029698 | 0.00029698 | 0.00029698 | 0.0 | 0.53
Modify | 0.038112 | 0.038112 | 0.038112 | 0.0 | 67.74
Other | | 0.001742 | | | 3.10
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 150 ave 150 max 150 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 150
Ave neighs/atom = 1.5
Neighbor list builds = 267
Dangerous builds = 0
Total wall time: 0:00:00

482
examples/granregion/log.27Jun24.granregion.box.g++.4 Normal file
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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 2 by 2 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 48 every 566 steps, 100 by step 1133
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (../fix_pour.cpp:688)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170774
1500 99 0.31486691 0.31486691 0.17429054 0.0064903404
1600 99 0.26369 0.26369 0.15095263 0.0045226821
1700 100 0.19259352 0.19259352 0.11308184 0.0073603886
1800 100 0.1372448 0.1372448 0.083273652 0.0058163062
1900 100 0.077253038 0.077253038 0.053166156 0.0017440856
2000 100 0.065472093 0.065472093 0.04375349 0.0018416047
2100 100 0.057213469 0.057213469 0.037773954 0.001226231
2200 100 0.058857437 0.058857437 0.0372655 0.00090812381
2300 100 0.035066108 0.035066108 0.025934054 0.00072114554
2400 100 0.021272125 0.021272125 0.016635107 0.0018506654
2500 100 0.015530432 0.015530432 0.012533546 0.0013883971
2600 100 0.012603946 0.012603946 0.0096981459 0.00038648118
2700 100 0.0097347475 0.0097347475 0.0076016624 0.00057313888
2800 100 0.0067081771 0.0067081771 0.0056944431 0.00085080075
2900 100 0.0089177981 0.0089177981 0.0065036822 0.00028986539
3000 100 0.0057840287 0.0057840287 0.0044989265 0.00016111737
3100 100 0.0038909621 0.0038909621 0.0031511938 0.0001708892
3200 100 0.0029043214 0.0029043214 0.0025807767 9.2473673e-05
3300 100 0.0022769336 0.0022769336 0.0021487157 0.00022312666
3400 100 0.0015571397 0.0015571397 0.0016669068 0.0003381372
3500 100 0.0015978184 0.0015978184 0.001707772 4.9930818e-05
3600 100 0.0023358916 0.0023358916 0.0020709426 9.7687609e-05
3700 100 0.0011186736 0.0011186736 0.0012146914 9.3338234e-05
3800 100 0.0011657036 0.0011657036 0.0012313764 3.1931251e-05
3900 100 0.0014998387 0.0014998387 0.0014015491 2.4226798e-05
4000 100 0.0010858335 0.0010858335 0.0010623286 1.6359241e-05
4100 100 0.0010464314 0.0010464314 0.0010123557 1.2949588e-05
4200 100 0.0010022428 0.0010022428 0.00097338971 1.2402332e-05
4300 100 0.00080622372 0.00080622372 0.00084329652 0.00033857037
4400 100 0.00073613921 0.00073613921 0.00078373608 1.0103949e-05
4500 100 0.00071402196 0.00071402196 0.00076658004 8.8360218e-06
4600 100 0.00064851765 0.00064851765 0.00071533461 1.0736438e-05
4700 100 0.00061146699 0.00061146699 0.00068274687 4.1341755e-06
4800 100 0.00059511472 0.00059511472 0.0006625527 7.3645447e-06
4900 100 0.00057700347 0.00057700347 0.0006468562 1.5411897e-05
5000 100 0.00056205001 0.00056205001 0.00063592505 7.8813845e-06
Loop time of 0.0666388 on 4 procs for 5000 steps with 100 atoms
Performance: 32413524.665 tau/day, 75031.307 timesteps/s, 7.503 Matom-step/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001133 | 0.0024206 | 0.0039594 | 2.6 | 3.63
Neigh | 0.0040192 | 0.0046633 | 0.0052296 | 0.8 | 7.00
Comm | 0.015155 | 0.021785 | 0.029291 | 4.1 | 32.69
Output | 0.0012323 | 0.0014638 | 0.0016021 | 0.4 | 2.20
Modify | 0.0026785 | 0.011483 | 0.021199 | 8.2 | 17.23
Other | | 0.02482 | | | 37.25
Nlocal: 25 ave 53 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 4 ave 8 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 40.5 ave 92 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 162
Ave neighs/atom = 1.62
Neighbor list builds = 288
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (../fix_wall_gran_region.cpp:96)
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00056205001 0.00056205001 0.00063592505 7.871665e-06
5100 100 0.59585977 0.59585977 0.32464933 0.0141718
5200 100 0.67306764 0.67306764 0.35872096 0.013373672
5300 100 0.76065187 0.76065187 0.39925025 0.011460301
5400 100 0.87984446 0.87984446 0.45261417 0.013937042
5500 100 0.95548319 0.95548319 0.48706892 0.013601658
5600 100 0.9993278 0.9993278 0.50830306 0.015663766
5700 100 1.0449415 1.0449415 0.52967249 0.016797841
5800 100 1.0767598 1.0767598 0.54508699 0.016128855
5900 100 1.118688 1.118688 0.56530849 0.016830117
6000 100 1.1535698 1.1535698 0.58290663 0.01715335
6100 100 1.1753828 1.1753828 0.59419088 0.019273207
6200 100 1.1994171 1.1994171 0.60433264 0.018391566
6300 100 1.2244707 1.2244707 0.61626199 0.018842556
6400 100 1.2507994 1.2507994 0.62829386 0.019538413
6500 100 1.2684644 1.2684644 0.63747702 0.020794729
6600 100 1.2704726 1.2704726 0.63929889 0.020253985
6700 100 1.2737302 1.2737302 0.63970688 0.020858602
6800 100 1.287922 1.287922 0.64460894 0.021589773
6900 100 1.3028782 1.3028782 0.65197802 0.02135295
7000 100 1.306633 1.306633 0.65371741 0.021291182
7100 100 1.3161393 1.3161393 0.65785404 0.022554896
7200 100 1.3228158 1.3228158 0.6609031 0.021811977
7300 100 1.3245632 1.3245632 0.66161966 0.02206776
7400 100 1.3266822 1.3266822 0.662738 0.022070761
7500 100 1.3265138 1.3265138 0.6624472 0.021944768
7600 100 1.3286802 1.3286802 0.66338775 0.0219393
7700 100 1.332829 1.332829 0.66547051 0.022142398
7800 100 1.3323535 1.3323535 0.66534513 0.022787777
7900 100 1.3372424 1.3372424 0.66777556 0.02192759
8000 100 1.3396201 1.3396201 0.66910123 0.022439596
8100 100 1.3422271 1.3422271 0.67060566 0.023784952
8200 100 1.3468062 1.3468062 0.6728991 0.02243345
8300 100 1.3439408 1.3439408 0.6717529 0.022312339
8400 100 1.3484134 1.3484134 0.67346027 0.022770922
8500 100 1.3490032 1.3490032 0.67378177 0.022427863
8600 100 1.349789 1.349789 0.67398897 0.022494049
8700 100 1.3513512 1.3513512 0.67475613 0.022413559
8800 100 1.3535168 1.3535168 0.67589784 0.022356566
8900 100 1.3505765 1.3505765 0.67442168 0.022240615
9000 100 1.3499918 1.3499918 0.67419831 0.02226049
9100 100 1.3518103 1.3518103 0.67489482 0.022399038
9200 100 1.3526275 1.3526275 0.67529852 0.022395079
9300 100 1.353741 1.353741 0.67585205 0.022471008
9400 100 1.3538758 1.3538758 0.67589523 0.022461734
9500 100 1.3537199 1.3537199 0.67586527 0.022370169
9600 100 1.3539788 1.3539788 0.67602899 0.022400771
9700 100 1.3544874 1.3544874 0.67619552 0.022648464
9800 100 1.3555422 1.3555422 0.67666186 0.022367319
9900 100 1.3560106 1.3560106 0.6768751 0.02236585
10000 100 1.3563578 1.3563578 0.6770434 0.022359307
Loop time of 0.117825 on 4 procs for 5000 steps with 100 atoms
Performance: 18332213.198 tau/day, 42435.679 timesteps/s, 4.244 Matom-step/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00088578 | 0.0090104 | 0.017735 | 8.5 | 7.65
Neigh | 0.0078603 | 0.0087927 | 0.0097327 | 1.0 | 7.46
Comm | 0.006411 | 0.013582 | 0.022547 | 6.1 | 11.53
Output | 0.0011273 | 0.0015902 | 0.0019777 | 1.0 | 1.35
Modify | 0.0095221 | 0.034125 | 0.058989 | 13.2 | 28.96
Other | | 0.05073 | | | 43.05
Nlocal: 25 ave 52 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 3 ave 6 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 48.25 ave 109 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 193
Ave neighs/atom = 1.93
Neighbor list builds = 626
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3563578 1.3563578 0.6770434 0.022433108
10100 100 0.32881547 0.32881547 0.18968913 0.0063460187
10200 100 0.19880113 0.19880113 0.12812646 0.0074601538
10300 100 0.12614062 0.12614062 0.090121373 0.0028337336
10400 100 0.088358363 0.088358363 0.067236815 0.0020269846
10500 100 0.071199344 0.071199344 0.055567135 0.0016191769
10600 100 0.053909616 0.053909616 0.042301996 0.00098643468
10700 100 0.039560745 0.039560745 0.032482256 0.00089240864
10800 100 0.032130432 0.032130432 0.02705329 0.00058669881
10900 100 0.02462494 0.02462494 0.021121496 0.0017376127
11000 100 0.020941068 0.020941068 0.017866781 0.00031112553
11100 100 0.016775675 0.016775675 0.014620214 0.00026856842
11200 100 0.015005732 0.015005732 0.012803923 0.00067036626
11300 100 0.012099209 0.012099209 0.010308221 0.00032666902
11400 100 0.010559421 0.010559421 0.0090243729 0.00013645685
11500 100 0.0093738615 0.0093738615 0.0080176514 0.00098541099
11600 100 0.0081900702 0.0081900702 0.0070256953 0.00025935992
11700 100 0.0068100165 0.0068100165 0.0058703223 0.00014866816
11800 100 0.0060475708 0.0060475708 0.0052518105 0.00017895168
11900 100 0.0055607485 0.0055607485 0.0047184164 0.00011358846
12000 100 0.0053149064 0.0053149064 0.0045168418 0.00015222428
12100 100 0.0050909525 0.0050909525 0.0043196952 6.3000537e-05
12200 100 0.0041810842 0.0041810842 0.0036835522 4.6423956e-05
12300 100 0.0034305227 0.0034305227 0.0031222649 0.00020251115
12400 100 0.0031763077 0.0031763077 0.0028956456 0.00030307787
12500 100 0.0027440829 0.0027440829 0.0025087304 0.00010418607
12600 100 0.0024581964 0.0024581964 0.0022200229 3.042018e-05
12700 100 0.002259527 0.002259527 0.0020708869 4.192368e-05
12800 100 0.0019143448 0.0019143448 0.0018088032 4.6200439e-05
12900 100 0.0017935964 0.0017935964 0.0017028317 2.2195756e-05
13000 100 0.0017286429 0.0017286429 0.0016396753 2.3108871e-05
13100 100 0.0017055291 0.0017055291 0.0016122058 2.2444611e-05
13200 100 0.0016539275 0.0016539275 0.0015570166 2.0467353e-05
13300 100 0.0015777788 0.0015777788 0.0014852505 1.9525012e-05
13400 100 0.0015372199 0.0015372199 0.0014497102 2.3203566e-05
13500 100 0.0015066638 0.0015066638 0.0014097203 1.8644964e-05
13600 100 0.0012290618 0.0012290618 0.0012056216 1.3235643e-05
13700 100 0.0011781948 0.0011781948 0.0011685226 3.4312262e-05
13800 100 0.0011530136 0.0011530136 0.0011433171 2.8832126e-05
13900 100 0.0011085224 0.0011085224 0.0011052764 1.444139e-05
14000 100 0.0010656788 0.0010656788 0.0010702461 1.3187775e-05
14100 100 0.001029277 0.001029277 0.0010469537 1.2837267e-05
14200 100 0.0009750904 0.0009750904 0.0009915384 1.209089e-05
14300 100 0.00094893337 0.00094893337 0.00096909301 1.1743051e-05
14400 100 0.00087708427 0.00087708427 0.00087575318 1.9027338e-05
14500 100 0.00086229913 0.00086229913 0.0008643568 1.0670952e-05
14600 100 0.00084206808 0.00084206808 0.0008268172 3.2391722e-05
14700 100 0.00077682873 0.00077682873 0.00077186085 9.6132555e-06
14800 100 0.00074736908 0.00074736908 0.00074958372 9.2486924e-06
14900 100 0.00074456847 0.00074456847 0.00074779946 9.2140349e-06
15000 100 0.00073830282 0.00073830282 0.0007426924 9.1364974e-06
Loop time of 0.0608167 on 4 procs for 5000 steps with 100 atoms
Performance: 35516589.034 tau/day, 82214.326 timesteps/s, 8.221 Matom-step/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00059197 | 0.0022122 | 0.0043047 | 3.5 | 3.64
Neigh | 0.00087477 | 0.0012077 | 0.001588 | 1.0 | 1.99
Comm | 0.0017826 | 0.010005 | 0.018966 | 8.1 | 16.45
Output | 0.0010587 | 0.0013365 | 0.0015183 | 0.5 | 2.20
Modify | 0.00046958 | 0.012924 | 0.027298 | 11.0 | 21.25
Other | | 0.03313 | | | 54.48
Nlocal: 25 ave 53 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 3.75 ave 8 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 39.25 ave 82 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 100
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00073830282 0.00073830282 0.0007426924 9.1364974e-06
15100 100 1.1048281 1.1048281 0.7023727 0.018379275
15200 100 1.2022249 1.2022249 0.77748962 0.015662439
15300 100 1.2561351 1.2561351 0.82563065 0.01835048
15400 100 1.4372446 1.4372446 0.92907923 0.02087065
15500 100 1.6414713 1.6414713 1.0284489 0.025654324
15600 100 1.7844655 1.7844655 1.0861866 0.025170346
15700 100 2.034248 2.034248 1.2017171 0.040341642
15800 100 2.1253699 2.1253699 1.2228657 0.029297194
15900 100 2.1940232 2.1940232 1.2470589 0.033866758
16000 100 2.2624419 2.2624419 1.2828225 0.030063645
16100 100 2.3208536 2.3208536 1.3118956 0.0323489
16200 100 2.3564971 2.3564971 1.3261173 0.032882494
16300 100 2.3956066 2.3956066 1.3260307 0.03292972
16400 100 2.5025831 2.5025831 1.3817693 0.031132988
16500 100 2.5947914 2.5947914 1.4152657 0.036126782
16600 100 2.7688769 2.7688769 1.4975686 0.037497127
16700 100 2.812503 2.812503 1.5216659 0.039316167
16800 100 2.8977424 2.8977424 1.5599254 0.039996029
16900 100 3.045802 3.045802 1.6332888 0.041406156
17000 100 3.2195366 3.2195366 1.7247171 0.040023634
17100 100 3.2597294 3.2597294 1.7527958 0.04828292
17200 100 3.293587 3.293587 1.7693254 0.044001441
17300 100 3.1861836 3.1861836 1.7142076 0.049158822
17400 100 3.4593561 3.4593561 1.8426619 0.053469673
17500 100 3.3813767 3.3813767 1.8079958 0.058776299
17600 100 3.5834203 3.5834203 1.9094759 0.053256842
17700 100 3.2243306 3.2243306 1.7425111 0.064354789
17800 100 3.358228 3.358228 1.8202932 0.046798524
17900 100 3.2257908 3.2257908 1.7678964 0.043655204
18000 100 3.237732 3.237732 1.7598181 0.050850672
18100 100 3.2042441 3.2042441 1.751979 0.045582006
18200 100 3.1562775 3.1562775 1.7336068 0.042210739
18300 100 3.2630507 3.2630507 1.7925333 0.046412778
18400 100 3.4150588 3.4150588 1.8668408 0.044386435
18500 100 3.4913198 3.4913198 1.9125495 0.043329829
18600 100 3.5290036 3.5290036 1.9184098 0.048302721
18700 100 3.4852698 3.4852698 1.8865833 0.059566124
18800 100 3.7157551 3.7157551 2.0082235 0.051356305
18900 100 3.9504619 3.9504619 2.1377018 0.051553987
19000 100 3.9711274 3.9711274 2.1549121 0.051555312
19100 100 3.90954 3.90954 2.1135174 0.0548311
19200 100 4.0672819 4.0672819 2.1837089 0.064431553
19300 100 3.998355 3.998355 2.1572884 0.056830399
19400 100 3.9172127 3.9172127 2.1130164 0.051264041
19500 100 3.9120291 3.9120291 2.1088399 0.052545115
19600 100 3.8613614 3.8613614 2.0752883 0.055466569
19700 100 3.8428824 3.8428824 2.0787804 0.05129261
19800 100 3.5686751 3.5686751 1.9356553 0.059177256
19900 100 3.5573788 3.5573788 1.9430183 0.054618794
20000 100 3.5453022 3.5453022 1.9413343 0.047640543
Loop time of 0.120564 on 4 procs for 5000 steps with 100 atoms
Performance: 17915781.606 tau/day, 41471.717 timesteps/s, 4.147 Matom-step/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0022864 | 0.0035398 | 0.0056964 | 2.2 | 2.94
Neigh | 0.0095136 | 0.011233 | 0.012853 | 1.1 | 9.32
Comm | 0.043338 | 0.044586 | 0.046388 | 0.6 | 36.98
Output | 0.0011632 | 0.0012814 | 0.0013677 | 0.2 | 1.06
Modify | 0.01756 | 0.026391 | 0.03297 | 3.5 | 21.89
Other | | 0.03353 | | | 27.81
Nlocal: 25 ave 36 max 13 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 5 ave 9 max 2 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 37.5 ave 53 max 15 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 150
Ave neighs/atom = 1.5
Neighbor list builds = 913
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.5453022 3.5453022 1.9413343 0.047178052
20100 100 1.0878587 1.0878587 0.68666704 0.016139979
20200 100 1.0230655 1.0230655 0.63593494 0.014642345
20300 100 0.94958824 0.94958824 0.59306601 0.011745659
20400 100 0.93038108 0.93038108 0.57232527 0.01154829
20500 100 0.92183816 0.92183816 0.55466942 0.01212559
20600 100 1.0175846 1.0175846 0.59940035 0.013815361
20700 100 1.0564615 1.0564615 0.60726745 0.013073711
20800 100 0.99967869 0.99967869 0.57665019 0.012450813
20900 100 0.97051084 0.97051084 0.5574217 0.015686955
21000 100 0.639185 0.639185 0.37441942 0.017594616
21100 100 0.24979014 0.24979014 0.17121567 0.0084027295
21200 100 0.15147941 0.15147941 0.11124349 0.0030435746
21300 100 0.13117502 0.13117502 0.091432638 0.0029110318
21400 100 0.11158272 0.11158272 0.076264692 0.0021951204
21500 100 0.056660993 0.056660993 0.043503807 0.0010993096
21600 100 0.028640836 0.028640836 0.026000267 0.0010440792
21700 100 0.025816483 0.025816483 0.021922896 0.00081674646
21800 100 0.023929555 0.023929555 0.019936972 0.0010383614
21900 100 0.022271339 0.022271339 0.017947505 0.0014630387
22000 100 0.019277834 0.019277834 0.015483116 0.00058751407
22100 100 0.019997809 0.019997809 0.015919504 0.00064176101
22200 100 0.015870543 0.015870543 0.01244838 0.0004205505
22300 100 0.011797587 0.011797587 0.0096491363 0.00034907063
22400 100 0.010745212 0.010745212 0.008874218 0.00035427537
22500 100 0.0082372399 0.0082372399 0.0071217811 0.00028179943
22600 100 0.007942576 0.007942576 0.0067248822 0.001507115
22700 100 0.0061733667 0.0061733667 0.0053092324 0.00056018554
22800 100 0.0058287651 0.0058287651 0.004972189 0.00023807695
22900 100 0.0051352339 0.0051352339 0.004324157 0.00020849263
23000 100 0.0040107769 0.0040107769 0.0035769703 0.00022626101
23100 100 0.0040288854 0.0040288854 0.0034355474 0.00019107621
23200 100 0.003277858 0.003277858 0.0030013165 0.00016119888
23300 100 0.0033633749 0.0033633749 0.0030188927 0.00014459404
23400 100 0.003468042 0.003468042 0.0030079205 0.00013778427
23500 100 0.0027616702 0.0027616702 0.0024994596 0.00011834915
23600 100 0.0022531303 0.0022531303 0.0021182802 0.0002279623
23700 100 0.002067768 0.002067768 0.0019631752 0.00014341503
23800 100 0.0020069255 0.0020069255 0.0019209587 0.00010673435
23900 100 0.0019630617 0.0019630617 0.0018748221 0.00011856923
24000 100 0.0018800646 0.0018800646 0.0018190347 0.00010707562
24100 100 0.0018028137 0.0018028137 0.0017067233 0.00010884117
24200 100 0.0017278932 0.0017278932 0.0016251004 0.00013664683
24300 100 0.0016373288 0.0016373288 0.0015529481 0.00010025414
24400 100 0.0019876848 0.0019876848 0.0016912033 0.00011235942
24500 100 0.0013677345 0.0013677345 0.0012839488 7.8669645e-05
24600 100 0.0012852614 0.0012852614 0.0012065052 0.00010172361
24700 100 0.0011145002 0.0011145002 0.0010748344 7.5021689e-05
24800 100 0.0012860792 0.0012860792 0.0011429675 5.7939624e-05
24900 100 0.00097198499 0.00097198499 0.00096175911 5.443837e-05
25000 100 0.00096224466 0.00096224466 0.00095159089 5.4245409e-05
Loop time of 0.0658283 on 4 procs for 5000 steps with 100 atoms
Performance: 32812622.584 tau/day, 75955.145 timesteps/s, 7.596 Matom-step/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00079402 | 0.002735 | 0.0055522 | 3.9 | 4.15
Neigh | 0.0027088 | 0.003273 | 0.0038077 | 0.9 | 4.97
Comm | 0.010018 | 0.017119 | 0.024875 | 4.8 | 26.01
Output | 0.0010937 | 0.0013253 | 0.0015108 | 0.5 | 2.01
Modify | 0.0012967 | 0.011558 | 0.023237 | 9.5 | 17.56
Other | | 0.02982 | | | 45.30
Nlocal: 25 ave 56 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 5.5 ave 12 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 40 ave 101 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 160
Ave neighs/atom = 1.6
Neighbor list builds = 275
Dangerous builds = 0
Total wall time: 0:00:00

643
examples/granregion/log.27Jun24.granregion.funnel.g++.1 Normal file
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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/atomonly/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 3000 every 59965 steps, 2000 by step 1
Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.42422547 2000 -0
2000 0.61303447 2000 -0
3000 0.80093891 2000 -0
4000 0.9870726 2000 -0
5000 1.174735 2000 -0
6000 1.3615338 2000 -0
7000 1.5481574 2000 -0
8000 1.7332676 2000 -0
9000 1.9202086 2000 -0
10000 2.1067651 2000 -0
11000 2.2904529 2000 -0
12000 2.4750549 2000 -0
13000 2.6588335 2000 -0
14000 2.8432942 2000 -0
15000 3.0276634 2000 -0
16000 3.2143893 2000 -0
17000 3.3989855 2000 -0
18000 3.5835207 2000 -0
19000 3.7684773 2000 -0
20000 3.9550272 2000 -0
Loop time of 3.95505 on 1 procs for 20000 steps with 2000 atoms
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40709 | 0.40709 | 0.40709 | 0.0 | 10.29
Neigh | 0.065613 | 0.065613 | 0.065613 | 0.0 | 1.66
Comm | 0.0076015 | 0.0076015 | 0.0076015 | 0.0 | 0.19
Output | 0.00041671 | 0.00041671 | 0.00041671 | 0.0 | 0.01
Modify | 3.3895 | 3.3895 | 3.3895 | 0.0 | 85.70
Other | | 0.08486 | | | 2.15
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1607 ave 1607 max 1607 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1607
Ave neighs/atom = 0.8035
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.18540841 2000 6807.2201
22000 0.37080157 2000 6973.9359
23000 0.55573123 2000 7142.3648
24000 0.74112501 2000 7276.9717
25000 0.92686283 2000 7369.4191
26000 1.1145958 2000 7497.6526
27000 1.3033904 2000 7638.946
28000 1.4921406 2000 7780.0339
29000 1.6824098 2000 7881.8177
30000 1.8751801 2000 7967.2641
31000 2.0698118 2000 7994.9273
32000 2.2682778 2000 7937.0671
33000 2.4695819 2000 7774.0508
34000 2.675988 2000 7591.1491
35000 2.886376 2000 7357.5176
36000 3.102007 2000 7147.2024
37000 3.321435 2000 6979.1604
38000 3.5426417 2000 6813.2152
39000 3.7660203 2000 6660.2701
40000 3.998044 2000 6502.8957
41000 4.234151 2000 6324.3951
42000 4.4731702 2000 6132.7516
43000 4.7137403 2000 5913.1841
44000 4.9572451 2000 5732.2095
45000 5.2042391 2000 5508.8322
46000 5.462849 2000 5306.8932
47000 5.724072 2000 5152.0521
48000 5.987507 2000 5028.2274
49000 6.2495317 2000 4896.102
50000 6.5151951 2000 4723.5189
51000 6.7809368 2000 4583.7526
52000 7.0554059 2000 4447.0187
53000 7.5371151 2000 4303.2307
54000 7.8249388 2000 4168.5251
55000 8.1204418 2000 4036.9704
56000 8.4176628 2000 3901.1183
57000 8.7222873 2000 3716.7071
58000 9.0346411 2000 3473.5422
59000 9.3526758 2000 3245.1223
60000 9.6699173 2000 3039.7845
61000 9.9903491 2000 2780.0187
62000 10.318591 2000 2577.3345
63000 10.65279 2000 2346.2488
64000 10.993148 2000 2116.7298
65000 11.335466 2000 1903.7828
66000 11.686936 2000 1631.1676
67000 12.046515 2000 1431.0198
68000 12.413611 2000 1212.875
69000 12.783883 2000 995.45046
70000 13.156707 2000 811.54766
71000 13.532628 2000 624.08622
72000 13.91241 2000 471.00862
73000 14.296186 2000 358.33486
74000 14.680961 2000 284.39416
75000 15.06644 2000 234.26671
76000 15.447805 2000 185.61836
77000 15.825601 2000 152.95918
78000 16.205661 2000 122.49023
79000 16.582292 2000 102.29396
80000 16.96433 2000 86.284684
81000 17.347289 2000 73.984781
82000 17.739993 2000 63.042918
83000 18.142078 2000 53.338428
84000 18.547853 2000 45.89585
85000 18.95343 2000 40.412826
86000 19.35904 2000 34.183381
87000 19.765916 2000 29.671524
88000 20.18651 2000 26.90414
89000 20.598969 2000 24.362631
90000 21.016445 2000 21.887341
91000 21.437072 2000 19.985662
92000 21.86331 2000 18.728162
93000 22.291217 2000 16.99941
94000 22.724102 2000 15.71941
95000 23.155367 2000 14.744057
96000 23.590722 2000 14.214918
97000 24.028273 2000 13.450182
98000 24.47017 2000 12.79222
99000 24.913929 2000 12.10595
100000 25.361256 2000 11.281863
101000 25.807117 2000 10.025419
102000 26.257292 2000 9.9574468
103000 26.70767 2000 9.4078117
104000 27.161728 2000 8.9079161
105000 27.617856 2000 8.6269302
106000 28.069631 2000 8.5512649
107000 28.526606 2000 8.4703948
108000 28.982832 2000 8.2747542
109000 29.441422 2000 8.2895118
110000 29.906198 2000 8.1785613
111000 30.36715 2000 7.8443234
112000 30.829642 2000 7.7436124
113000 31.319634 2000 7.8118604
114000 31.791602 2000 7.3806177
115000 32.260138 2000 7.0857235
116000 32.725698 2000 7.1346752
117000 33.192963 2000 7.0653751
118000 33.661517 2000 6.6314104
119000 34.127108 2000 6.2169614
120000 34.597123 2000 5.8988829
121000 35.064919 2000 5.4197277
122000 35.535855 2000 4.6381303
123000 36.005284 2000 4.4949206
124000 36.47519 2000 4.4261118
125000 36.945117 2000 4.4223703
126000 37.417732 2000 4.4858898
127000 37.888171 2000 4.3312536
128000 38.360713 2000 3.7124973
129000 38.835798 2000 3.5467396
130000 39.311234 2000 3.5104139
131000 39.783409 2000 3.5725612
132000 40.255871 2000 3.669455
133000 40.728998 2000 3.6168912
134000 41.203148 2000 3.3598517
135000 41.677786 2000 3.3743407
136000 42.15241 2000 3.1109764
137000 42.627707 2000 3.0720146
138000 43.100904 2000 3.1303776
139000 43.574775 2000 3.2052806
140000 44.050804 2000 2.8958882
141000 44.525409 2000 2.9931572
142000 44.999822 2000 3.0967832
143000 45.476054 2000 3.0576365
144000 45.951361 2000 3.2016943
145000 46.429655 2000 3.3817709
146000 46.905577 2000 3.4527239
147000 47.38743 2000 3.5928733
148000 47.86409 2000 3.7784682
149000 48.342003 2000 3.6587944
150000 48.823792 2000 3.7945669
151000 49.30105 2000 3.5551557
152000 49.780315 2000 3.6248848
153000 50.257553 2000 3.7361463
154000 50.737624 2000 3.8534319
155000 51.218208 2000 4.0101408
156000 51.695675 2000 3.7670652
157000 52.176961 2000 3.1487676
158000 52.657466 2000 2.980076
159000 53.134109 2000 3.0350592
160000 53.615609 2000 3.125389
161000 54.093868 2000 2.7516115
162000 54.576681 2000 2.413911
163000 55.055496 2000 2.297713
164000 55.538174 2000 2.3190806
165000 56.020458 2000 2.2868879
166000 56.501206 2000 2.1658547
167000 56.983465 2000 1.7511071
168000 57.466833 2000 1.4112478
169000 57.949757 2000 1.3623558
170000 58.43349 2000 1.3701579
Loop time of 58.4335 on 1 procs for 150000 steps with 2000 atoms
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 29.221 | 29.221 | 29.221 | 0.0 | 50.01
Neigh | 0.57927 | 0.57927 | 0.57927 | 0.0 | 0.99
Comm | 0.060749 | 0.060749 | 0.060749 | 0.0 | 0.10
Output | 0.20563 | 0.20563 | 0.20563 | 0.0 | 0.35
Modify | 27.674 | 27.674 | 27.674 | 0.0 | 47.36
Other | | 0.6922 | | | 1.18
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15308 ave 15308 max 15308 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15308
Ave neighs/atom = 7.654
Neighbor list builds = 367
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
170000 0 2000 1.3701579
171000 0.48431316 2000 2.3724823
172000 0.96523693 2000 3.5881441
173000 1.4349569 2000 5.3771633
174000 1.902564 2000 7.5896471
175000 2.3637344 2000 10.77251
176000 2.817277 2000 14.806868
177000 3.2682365 2000 19.607624
178000 3.7215391 2000 25.426227
179000 4.1716711 2000 32.23584
180000 4.621872 2000 39.930468
181000 5.0676618 2000 47.686304
182000 5.5105545 2000 56.506806
183000 5.9489081 2000 66.514326
184000 6.3843739 2000 77.554644
185000 6.8189889 2000 89.224002
186000 7.2526358 2000 102.07846
187000 7.6807565 2000 116.08141
188000 8.1050895 2000 130.97964
189000 8.52413 2000 146.77806
190000 8.9479211 2000 162.79858
191000 9.3652194 2000 179.02052
192000 9.780893 2000 196.26683
193000 10.192876 2000 214.38928
194000 10.606655 2000 232.32068
195000 11.018129 2000 251.74644
196000 11.424821 2000 272.25231
197000 11.833891 2000 294.64075
198000 12.237613 2000 318.32895
199000 12.640094 2000 342.44005
200000 13.045535 2000 368.35469
201000 13.445497 2000 395.2465
202000 13.85102 2000 422.63599
203000 14.254213 2000 450.45248
204000 14.654729 2000 479.60812
205000 15.057527 2000 510.44155
206000 15.456223 2000 543.25751
207000 15.849932 2000 577.35928
208000 16.240706 2000 612.29718
209000 16.629756 2000 647.8951
210000 17.019318 2000 683.79409
211000 17.40949 2000 720.36556
212000 17.802521 2000 759.27331
213000 18.192311 2000 798.27302
214000 18.582347 2000 837.93849
215000 18.970586 2000 877.92945
216000 19.362316 2000 919.62532
217000 19.755364 2000 962.83509
218000 20.146845 2000 1008.5243
219000 20.530427 2000 1054.5769
220000 20.914645 2000 1103.1843
221000 21.296153 2000 1153.0349
222000 21.681747 2000 1204.5599
223000 22.06794 2000 1257.1367
224000 22.45394 2000 1308.6735
WARNING: Lost atoms: original 2000 current 1999 (../thermo.cpp:499)
225000 22.843026 1999 1360.1205
226000 23.221639 1998 1404.8405
227000 23.603256 1996 1448.4869
228000 23.985547 1992 1491.8112
229000 24.359685 1985 1518.7013
230000 24.733284 1971 1507.6699
231000 25.100372 1965 1533.5096
232000 25.470109 1948 1489.4128
233000 25.840892 1933 1477.4536
234000 26.207893 1915 1425.8398
235000 26.570401 1904 1410.1451
236000 26.931189 1892 1401.7595
237000 27.28796 1880 1368.893
238000 27.642985 1868 1341.8885
239000 27.998754 1850 1286.7968
240000 28.353974 1833 1219.5123
241000 28.709461 1820 1173.3608
242000 29.065121 1806 1106.0727
243000 29.418519 1788 1035.912
244000 29.770812 1779 1021.6147
245000 30.11704 1767 969.40032
246000 30.457702 1757 939.12022
247000 30.800392 1739 840.9396
248000 31.141047 1730 822.06575
249000 31.483192 1719 762.11057
250000 31.831879 1707 708.50308
251000 32.176299 1700 692.12647
252000 32.520059 1697 694.5812
253000 32.884872 1686 652.36951
254000 33.229261 1682 662.95256
255000 33.557987 1677 637.34619
256000 33.891681 1672 630.71277
257000 34.230081 1669 641.87365
258000 34.571663 1665 635.862
259000 34.913723 1664 658.5339
260000 35.253805 1662 669.95468
261000 35.587547 1660 676.93495
262000 35.920661 1657 681.72646
263000 36.25079 1655 687.4078
264000 36.5838 1651 681.61352
265000 36.914146 1647 673.20622
266000 37.245414 1644 677.30073
267000 37.571588 1641 671.05897
268000 37.896337 1639 689.55776
269000 38.22279 1637 711.98809
270000 38.550831 1633 705.29974
Loop time of 38.5508 on 1 procs for 100000 steps with 1633 atoms
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.145 | 20.145 | 20.145 | 0.0 | 52.25
Neigh | 0.42523 | 0.42523 | 0.42523 | 0.0 | 1.10
Comm | 0.042119 | 0.042119 | 0.042119 | 0.0 | 0.11
Output | 0.0022978 | 0.0022978 | 0.0022978 | 0.0 | 0.01
Modify | 17.495 | 17.495 | 17.495 | 0.0 | 45.38
Other | | 0.4416 | | | 1.15
Nlocal: 1633 ave 1633 max 1633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11358 ave 11358 max 11358 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11358
Ave neighs/atom = 6.955297
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:01:40

643
examples/granregion/log.27Jun24.granregion.funnel.g++.4 Normal file
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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 4 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/atomonly/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 3000 every 59965 steps, 2000 by step 1
Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.44807882 2000 -0
2000 0.63550417 2000 -0
3000 0.82082211 2000 -0
4000 1.0004254 2000 -0
5000 1.1738611 2000 -0
6000 1.3426033 2000 -0
7000 1.5076494 2000 -0
8000 1.6673766 2000 -0
9000 1.8244007 2000 -0
10000 1.9794011 2000 -0
11000 2.049584 2000 -0
12000 2.1210622 2000 -0
13000 2.1917604 2000 -0
14000 2.2631006 2000 -0
15000 2.3361511 2000 -0
16000 2.4131306 2000 -0
17000 2.4938482 2000 -0
18000 2.5771299 2000 -0
19000 2.6633207 2000 -0
20000 2.7541527 2000 -0
Loop time of 2.75417 on 4 procs for 20000 steps with 2000 atoms
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.028725 | 0.079701 | 0.18206 | 21.3 | 2.89
Neigh | 0.0072627 | 0.013673 | 0.023071 | 5.0 | 0.50
Comm | 0.084562 | 0.18785 | 0.28115 | 18.6 | 6.82
Output | 0.00088257 | 0.0016453 | 0.0021961 | 1.2 | 0.06
Modify | 0.66551 | 1.1062 | 1.9324 | 46.7 | 40.16
Other | | 1.365 | | | 49.57
Nlocal: 500 ave 510 max 493 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 154 ave 227 max 79 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 415.5 ave 610 max 258 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1662
Ave neighs/atom = 0.831
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.064679537 2000 6807.2201
22000 0.13180546 2000 6973.9359
23000 0.20116485 2000 7142.3648
24000 0.27404997 2000 7276.9717
25000 0.35093997 2000 7369.4191
26000 0.43258785 2000 7497.6526
27000 0.51758599 2000 7638.946
28000 0.60693744 2000 7780.0339
29000 0.7014587 2000 7881.8177
30000 0.80119592 2000 7967.2641
31000 0.87335402 2000 7994.9273
32000 0.95320537 2000 7937.0672
33000 1.0398918 2000 7774.0508
34000 1.1351184 2000 7591.1511
35000 1.2382665 2000 7357.5032
36000 1.3492928 2000 7147.3776
37000 1.467685 2000 6980.0719
38000 1.5926331 2000 6813.0872
39000 1.7265338 2000 6657.0693
40000 1.8700751 2000 6505.1155
41000 1.9833133 2000 6330.2864
42000 2.1004898 2000 6147.8022
43000 2.2208699 2000 5932.9244
44000 2.3442041 2000 5755.296
45000 2.4697527 2000 5511.622
46000 2.6055398 2000 5332.3171
47000 2.7455054 2000 5162.4926
48000 2.8851384 2000 5044.5764
49000 3.0239861 2000 4901.1141
50000 3.1614979 2000 4731.1949
51000 3.2810383 2000 4575.418
52000 3.4070575 2000 4428.9425
53000 3.5378444 2000 4291.7282
54000 3.6714875 2000 4154.1885
55000 3.8108149 2000 3994.9402
56000 3.9546982 2000 3855.5977
57000 4.0997167 2000 3672.9504
58000 4.2491708 2000 3435.3395
59000 4.408196 2000 3200.7379
60000 4.5700117 2000 2986.5411
61000 4.723306 2000 2747.3628
62000 4.878128 2000 2542.0805
63000 5.0341944 2000 2336.7687
64000 5.1923913 2000 2151.6388
65000 5.3556896 2000 1933.6773
66000 5.5238885 2000 1699.0747
67000 5.6948336 2000 1467.7209
68000 5.8690421 2000 1227.3577
69000 6.0509636 2000 1016.2766
70000 6.2387022 2000 812.90843
71000 6.4073364 2000 632.88108
72000 6.577617 2000 470.67731
73000 6.7470437 2000 360.47748
74000 6.9135965 2000 286.10584
75000 7.0795553 2000 229.70386
76000 7.2433614 2000 179.62654
77000 7.4108991 2000 142.40417
78000 7.5787629 2000 113.55745
79000 7.7455158 2000 93.787669
80000 7.9119881 2000 80.646319
81000 8.0788298 2000 70.944319
82000 8.2481597 2000 59.2275
83000 8.4164166 2000 49.633808
84000 8.5904585 2000 42.882698
85000 8.768017 2000 36.841824
86000 8.9516342 2000 31.776681
87000 9.1361653 2000 28.25076
88000 9.3230302 2000 25.228966
89000 9.5111334 2000 22.593627
90000 9.7013966 2000 21.15796
91000 9.8899455 2000 19.941629
92000 10.082329 2000 18.375654
93000 10.276769 2000 17.056701
94000 10.474742 2000 16.192511
95000 10.674727 2000 15.572922
96000 10.874807 2000 14.827788
97000 11.075291 2000 13.919613
98000 11.275072 2000 13.19525
99000 11.475537 2000 11.993376
100000 11.677999 2000 11.258787
101000 11.88024 2000 10.641688
102000 12.084353 2000 10.430435
103000 12.288658 2000 9.518069
104000 12.4935 2000 9.1332086
105000 12.70028 2000 9.2151611
106000 12.908347 2000 9.0035132
107000 13.116082 2000 8.7835861
108000 13.324126 2000 8.5124479
109000 13.53208 2000 8.2975453
110000 13.740687 2000 8.3483043
111000 13.948107 2000 8.4658572
112000 14.156079 2000 8.4771784
113000 14.364341 2000 7.8937975
114000 14.574123 2000 7.2472953
115000 14.783651 2000 6.5812074
116000 14.99421 2000 5.5651566
117000 15.204441 2000 5.3015807
118000 15.415336 2000 5.0133941
119000 15.625609 2000 4.8746036
120000 15.836675 2000 4.9133073
121000 16.047261 2000 4.3337392
122000 16.257951 2000 4.3374836
123000 16.468869 2000 4.3721818
124000 16.680533 2000 4.3894508
125000 16.890783 2000 4.1811774
126000 17.103698 2000 4.3011002
127000 17.315003 2000 4.442228
128000 17.526696 2000 4.6170394
129000 17.738415 2000 4.8184318
130000 17.952565 2000 4.8442096
131000 18.165389 2000 4.9668117
132000 18.378094 2000 4.8364562
133000 18.592482 2000 4.6658645
134000 18.804443 2000 4.5758487
135000 19.016578 2000 4.7251949
136000 19.230118 2000 4.5846492
137000 19.443202 2000 4.7565986
138000 19.656431 2000 4.8186623
139000 19.867627 2000 4.6571647
140000 20.080227 2000 4.0730143
141000 20.292696 2000 4.0605542
142000 20.503397 2000 4.1457179
143000 20.714516 2000 4.3418042
144000 20.925902 2000 4.0323813
145000 21.139161 2000 3.8064958
146000 21.352466 2000 3.1802044
147000 21.564201 2000 2.7947641
148000 21.772853 2000 2.7384164
149000 21.983847 2000 2.7428829
150000 22.196524 2000 2.7802186
151000 22.408229 2000 2.6703451
152000 22.619074 2000 2.3357647
153000 22.829739 2000 1.9855305
154000 23.039835 2000 1.9442713
155000 23.252204 2000 1.7348027
156000 23.464375 2000 1.5699942
157000 23.677869 2000 1.5224944
158000 23.888064 2000 1.4850914
159000 24.099703 2000 1.4461048
160000 24.312523 2000 1.3759525
161000 24.522295 2000 0.83754463
162000 24.733904 2000 0.7952922
163000 24.944962 2000 0.69670143
164000 25.155399 2000 0.66253723
165000 25.36618 2000 0.64602969
166000 25.576713 2000 0.60229858
167000 25.788559 2000 0.5757589
168000 25.998455 2000 0.5996023
169000 26.209944 2000 0.62130448
170000 26.420855 2000 0.63888277
Loop time of 26.4209 on 4 procs for 150000 steps with 2000 atoms
97.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6691 | 8.9481 | 11.368 | 85.5 | 33.87
Neigh | 0.087705 | 0.14369 | 0.18343 | 9.2 | 0.54
Comm | 1.9172 | 3.5612 | 4.2565 | 50.7 | 13.48
Output | 0.0045151 | 0.0090615 | 0.016477 | 4.7 | 0.03
Modify | 5.4247 | 7.6604 | 9.1464 | 49.8 | 28.99
Other | | 6.099 | | | 23.08
Nlocal: 500 ave 538 max 419 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 445.5 ave 688 max 200 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 4500.25 ave 5610 max 3443 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 18001
Ave neighs/atom = 9.0005
Neighbor list builds = 362
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
Step CPU Atoms KinEng
170000 0 2000 0.63888277
171000 0.21222344 2000 1.4139245
172000 0.42521156 2000 2.2400138
173000 0.63924412 2000 3.8034979
174000 0.85157975 2000 6.116727
175000 1.065247 2000 8.9536458
176000 1.2785495 2000 12.74348
177000 1.4916668 2000 17.410816
178000 1.7042214 2000 22.879174
179000 1.9186225 2000 28.966022
180000 2.1345716 2000 35.449239
181000 2.3486488 2000 42.694882
182000 2.5624316 2000 50.913279
183000 2.7760261 2000 60.098465
184000 2.9883219 2000 70.133474
185000 3.2007559 2000 80.950013
186000 3.4107595 2000 92.495525
187000 3.6204368 2000 104.83034
188000 3.8298085 2000 118.04659
189000 4.0383423 2000 132.7403
190000 4.2477798 2000 148.31955
191000 4.4421194 2000 164.26321
192000 4.6373112 2000 180.6933
193000 4.829991 2000 197.72012
194000 5.02323 2000 215.43637
195000 5.2162947 2000 234.29738
196000 5.4075928 2000 254.03407
197000 5.5974162 2000 274.58626
198000 5.7869821 2000 296.88915
199000 5.976701 2000 320.45001
200000 6.1650648 2000 344.75891
201000 6.3509022 2000 370.14016
202000 6.5363704 2000 395.72827
203000 6.7222457 2000 420.42026
204000 6.9107246 2000 446.08079
205000 7.0996055 2000 473.62963
206000 7.2878276 2000 501.05693
207000 7.4753237 2000 530.40427
208000 7.6643827 2000 560.62015
209000 7.8553563 2000 593.00113
210000 8.0454619 2000 626.36661
211000 8.2342734 2000 661.34861
212000 8.4248464 2000 697.41001
213000 8.6166264 2000 735.12299
214000 8.8061303 2000 773.89126
215000 8.9932827 2000 813.83268
216000 9.1797117 2000 854.63669
217000 9.3642361 2000 896.59089
218000 9.5486397 2000 938.70251
219000 9.7300675 2000 982.10773
220000 9.9142511 2000 1025.2953
221000 10.098593 2000 1069.8382
222000 10.284654 2000 1115.4449
223000 10.47145 2000 1161.6742
224000 10.656994 2000 1211.289
225000 10.839264 2000 1262.8074
226000 11.019273 2000 1316.6353
227000 11.198463 2000 1370.7434
WARNING: Lost atoms: original 2000 current 1991 (../thermo.cpp:499)
228000 11.377846 1991 1382.0924
229000 11.557302 1986 1407.1543
230000 11.737106 1975 1415.708
231000 11.915389 1968 1430.6498
232000 12.095672 1957 1421.0352
233000 12.275267 1939 1376.0322
234000 12.452526 1925 1350.1292
235000 12.629207 1912 1337.0529
236000 12.80204 1893 1273.2219
237000 12.975817 1879 1207.0473
238000 13.152228 1861 1132.0109
239000 13.331267 1846 1083.1042
240000 13.510046 1826 1004.3265
241000 13.67647 1819 989.36186
242000 13.842216 1812 983.26132
243000 14.006163 1805 985.79932
244000 14.168208 1794 936.34844
245000 14.331979 1784 889.17423
246000 14.495868 1770 846.65018
247000 14.662081 1753 751.16306
248000 14.830163 1740 709.23095
249000 14.999432 1732 687.61586
250000 15.166285 1721 638.82967
251000 15.331363 1714 618.71543
252000 15.493524 1709 611.25444
253000 15.651829 1705 606.6846
254000 15.809586 1702 601.7236
255000 15.966097 1697 575.97244
256000 16.12731 1695 577.1712
257000 16.292272 1691 576.93668
258000 16.460463 1688 586.63687
259000 16.628863 1686 581.52487
260000 16.797813 1682 566.49544
261000 16.95041 1681 586.18628
262000 17.101549 1678 582.11927
263000 17.251379 1675 589.96041
264000 17.403824 1672 577.55581
265000 17.556094 1669 570.45998
266000 17.710318 1666 574.0576
267000 17.865801 1662 578.07385
268000 18.019798 1660 587.65705
269000 18.177178 1657 584.43358
270000 18.332227 1654 591.22601
Loop time of 18.3323 on 4 procs for 100000 steps with 1654 atoms
96.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7775 | 6.3596 | 9.2369 | 92.3 | 34.69
Neigh | 0.088842 | 0.10453 | 0.12331 | 4.2 | 0.57
Comm | 1.1938 | 2.7006 | 3.3247 | 53.6 | 14.73
Output | 0.0013814 | 0.0063655 | 0.013334 | 5.5 | 0.03
Modify | 4.3454 | 4.8952 | 5.3813 | 20.7 | 26.70
Other | | 4.266 | | | 23.27
Nlocal: 413.5 ave 429 max 408 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 408.25 ave 653 max 182 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 3486.25 ave 4367 max 2213 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 13945
Ave neighs/atom = 8.4310762
Neighbor list builds = 227
Dangerous builds = 0
Total wall time: 0:00:47

642
examples/granregion/log.27Jun24.granregion.mixer.g++.1 Normal file
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@ -0,0 +1,642 @@
LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/atomonly/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 444 every 84653 steps, 1000 by step 169307
Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.081165379 444 -0 0.015707963
2000 0.15754332 444 -0 0.031415927
3000 0.23012784 444 -0 0.04712389
4000 0.30324079 444 -0 0.062831853
5000 0.37566627 444 -0 0.078539816
6000 0.4478183 444 -0 0.09424778
7000 0.52130598 444 -0 0.10995574
8000 0.59583276 444 -0 0.12566371
9000 0.67333641 444 -0 0.14137167
10000 0.75133989 444 -0 0.15707963
11000 0.88621821 444 -0 0.1727876
12000 0.96223543 444 -0 0.18849556
13000 1.0406719 444 -0 0.20420352
14000 1.1209824 444 -0 0.21991149
15000 1.2017612 444 -0 0.23561945
16000 1.2818653 444 -0 0.25132741
17000 1.36192 444 -0 0.26703538
18000 1.4377702 444 -0 0.28274334
19000 1.5144381 444 -0 0.2984513
20000 1.5913902 444 -0 0.31415927
21000 1.6673472 444 -0 0.32986723
22000 1.7434481 444 -0 0.34557519
23000 1.8190585 444 -0 0.36128316
24000 1.8962389 444 -0 0.37699112
25000 1.9736636 444 -0 0.39269908
26000 2.0534547 444 -0 0.40840704
27000 2.1298466 444 -0 0.42411501
28000 2.206882 444 -0 0.43982297
29000 2.2836177 444 -0 0.45553093
30000 2.4525793 444 -0 0.4712389
31000 2.528444 444 -0 0.48694686
32000 2.6062516 444 -0 0.50265482
33000 2.6838811 444 -0 0.51836279
34000 2.7618967 444 -0 0.53407075
35000 3.1234167 444 -0 0.54977871
36000 3.1992217 444 -0 0.56548668
37000 3.2744137 444 -0 0.58119464
38000 3.3504088 444 -0 0.5969026
39000 3.4259728 444 -0 0.61261057
40000 3.5020768 444 -0 0.62831853
41000 3.5794542 444 -0 0.64402649
42000 3.657433 444 -0 0.65973446
43000 3.7353763 444 -0 0.67544242
44000 3.8131676 444 -0 0.69115038
45000 3.8924163 444 -0 0.70685835
46000 3.973914 444 -0 0.72256631
47000 4.0525907 444 -0 0.73827427
48000 4.131257 444 -0 0.75398224
49000 4.2096226 444 -0 0.7696902
50000 4.2879179 444 -0 0.78539816
51000 4.3673368 444 -0 0.80110613
52000 4.4496186 444 -0 0.81681409
53000 4.5285675 444 -0 0.83252205
54000 4.6132205 444 -0 0.84823002
55000 4.6992461 444 -0 0.86393798
56000 4.7864008 444 -0 0.87964594
57000 4.8715403 444 -0 0.89535391
58000 4.9547161 444 -0 0.91106187
59000 5.0403186 444 -0 0.92676983
60000 5.123722 444 -0 0.9424778
61000 5.2068168 444 -0 0.95818576
62000 5.2899206 444 -0 0.97389372
63000 5.3725203 444 -0 0.98960169
64000 5.4561614 444 -0 1.0053096
65000 5.5399537 444 -0 1.0210176
66000 5.6233183 444 -0 1.0367256
67000 5.7075311 444 -0 1.0524335
68000 5.7921332 444 -0 1.0681415
69000 5.8772289 444 -0 1.0838495
70000 5.9626083 444 -0 1.0995574
71000 6.0468013 444 -0 1.1152654
72000 6.1325358 444 -0 1.1309734
73000 6.217391 444 -0 1.1466813
74000 6.3029286 444 -0 1.1623893
75000 6.3892387 444 -0 1.1780972
76000 6.4757637 444 -0 1.1938052
77000 6.5633899 444 -0 1.2095132
78000 6.6494516 444 -0 1.2252211
79000 6.7363426 444 -0 1.2409291
80000 6.8243808 444 -0 1.2566371
81000 6.9120999 444 -0 1.272345
82000 7.0004402 444 -0 1.288053
83000 7.0882632 444 -0 1.303761
84000 7.176153 444 -0 1.3194689
85000 7.2980017 888 -0 1.3351769
86000 7.4665034 888 -0 1.3508848
87000 7.634481 888 -0 1.3665928
88000 7.8021372 888 -0 1.3823008
89000 7.9705032 888 -0 1.3980087
90000 8.1395213 888 -0 1.4137167
91000 8.3093436 888 -0 1.4294247
92000 8.4791404 888 -0 1.4451326
93000 8.6448257 888 -0 1.4608406
94000 8.8096695 888 -0 1.4765485
95000 8.9806056 888 -0 1.4922565
96000 9.1479017 888 -0 1.5079645
97000 9.3159102 888 -0 1.5236724
98000 9.4817887 888 -0 1.5393804
99000 9.6484134 888 -0 1.5550884
100000 9.8145145 888 -0 1.5707963
101000 9.9833565 888 -0 1.5865043
102000 10.153126 888 -0 1.6022123
103000 10.32344 888 -0 1.6179202
104000 10.493544 888 -0 1.6336282
105000 10.663787 888 -0 1.6493361
106000 10.834335 888 -0 1.6650441
107000 11.004695 888 -0 1.6807521
108000 11.175239 888 -0 1.69646
109000 11.350053 888 -0 1.712168
110000 11.525953 888 -0 1.727876
111000 11.702706 888 -0 1.7435839
112000 11.880308 888 -0 1.7592919
113000 12.058561 888 -0 1.7749998
114000 12.236372 888 -0 1.7907078
115000 12.414617 888 -0 1.8064158
116000 12.592501 888 -0 1.8221237
117000 12.770926 888 -0 1.8378317
118000 12.949072 888 -0 1.8535397
119000 13.128801 888 -0 1.8692476
120000 13.311101 888 -0 1.8849556
121000 13.489781 888 -0 1.9006636
122000 13.669833 888 -0 1.9163715
123000 13.85109 888 -0 1.9320795
124000 14.032358 888 -0 1.9477874
125000 14.213661 888 -0 1.9634954
126000 14.393846 888 -0 1.9792034
127000 14.574645 888 -0 1.9949113
128000 14.755261 888 -0 2.0106193
129000 14.939145 888 -0 2.0263273
130000 15.123073 888 -0 2.0420352
131000 15.303459 888 -0 2.0577432
132000 15.484755 888 -0 2.0734512
133000 15.665288 888 -0 2.0891591
134000 15.845779 888 -0 2.1048671
135000 16.026283 888 -0 2.120575
136000 16.20857 888 -0 2.136283
137000 16.39054 888 -0 2.151991
138000 16.574105 888 -0 2.1676989
139000 16.758949 888 -0 2.1834069
140000 16.943594 888 -0 2.1991149
141000 17.127119 888 -0 2.2148228
142000 17.311688 888 -0 2.2305308
143000 17.498924 888 -0 2.2462387
144000 17.68621 888 -0 2.2619467
145000 17.873463 888 -0 2.2776547
146000 18.061679 888 -0 2.2933626
147000 18.248264 888 -0 2.3090706
148000 18.434172 888 -0 2.3247786
149000 18.620894 888 -0 2.3404865
150000 18.807222 888 -0 2.3561945
151000 18.993959 888 -0 2.3719025
152000 19.183597 888 -0 2.3876104
153000 19.372979 888 -0 2.4033184
154000 19.560741 888 -0 2.4190263
155000 19.760386 888 -0 2.4347343
156000 19.968774 888 -0 2.4504423
157000 20.179252 888 -0 2.4661502
158000 20.388599 888 -0 2.4818582
159000 20.598976 888 -0 2.4975662
160000 20.80891 888 -0 2.5132741
161000 21.026202 888 -0 2.5289821
162000 21.239367 888 -0 2.54469
163000 21.452486 888 -0 2.560398
164000 21.665343 888 -0 2.576106
165000 21.879421 888 -0 2.5918139
166000 22.093404 888 -0 2.6075219
167000 22.307097 888 -0 2.6232299
168000 22.521133 888 -0 2.6389378
169000 22.735535 888 -0 2.6546458
170000 22.968021 1000 -0 2.6703538
171000 23.205371 1000 -0 2.6860617
172000 23.44698 1000 -0 2.7017697
173000 23.689107 1000 -0 2.7174776
174000 23.930244 1000 -0 2.7331856
175000 24.168568 1000 -0 2.7488936
176000 24.405774 1000 -0 2.7646015
177000 24.645769 1000 -0 2.7803095
178000 24.886311 1000 -0 2.7960175
179000 25.129675 1000 -0 2.8117254
180000 25.375354 1000 -0 2.8274334
181000 25.620074 1000 -0 2.8431414
182000 25.867063 1000 -0 2.8588493
183000 26.111737 1000 -0 2.8745573
184000 26.356693 1000 -0 2.8902652
185000 26.601965 1000 -0 2.9059732
186000 26.847594 1000 -0 2.9216812
187000 27.09479 1000 -0 2.9373891
188000 27.343645 1000 -0 2.9530971
189000 27.593252 1000 -0 2.9688051
190000 27.84598 1000 -0 2.984513
191000 28.097785 1000 -0 3.000221
192000 28.347653 1000 -0 3.0159289
193000 28.588968 1000 -0 3.0316369
194000 28.82728 1000 -0 3.0473449
195000 29.066565 1000 -0 3.0630528
196000 29.309153 1000 -0 3.0787608
197000 29.894236 1000 -0 3.0944688
198000 30.138713 1000 -0 3.1101767
199000 30.381879 1000 -0 3.1258847
200000 30.627512 1000 -0 3.1415927
Loop time of 30.6275 on 1 procs for 200000 steps with 1000 atoms
Performance: 26659.225 tau/day, 6530.072 timesteps/s, 6.530 Matom-step/s
97.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4017 | 2.4017 | 2.4017 | 0.0 | 7.84
Neigh | 0.038916 | 0.038916 | 0.038916 | 0.0 | 0.13
Comm | 0.35872 | 0.35872 | 0.35872 | 0.0 | 1.17
Output | 0.78641 | 0.78641 | 0.78641 | 0.0 | 2.57
Modify | 26.719 | 26.719 | 26.719 | 0.0 | 87.24
Other | | 0.3225 | | | 1.05
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 186 ave 186 max 186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3782 ave 3782 max 3782 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3782
Ave neighs/atom = 3.782
Neighbor list builds = 200
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0680935 3.1415927
201000 0.23768219 1000 1.0599937 3.1573006
202000 0.47603693 1000 1.0366355 3.1730086
203000 0.71459797 1000 1.0189286 3.1887165
204000 0.95145301 1000 1.001478 3.2044245
205000 1.1869146 1000 0.99637635 3.2201325
206000 1.4249684 1000 0.99361197 3.2358404
207000 1.6635344 1000 0.99529657 3.2515484
208000 1.8992251 1000 0.98997171 3.2672564
209000 2.1484862 1000 0.97666133 3.2829643
210000 2.4012768 1000 0.97683679 3.2986723
211000 2.6554877 1000 0.98150752 3.3143802
212000 2.9093673 1000 0.97585316 3.3300882
213000 3.161481 1000 0.97389688 3.3457962
214000 3.4184197 1000 0.96426468 3.3615041
215000 3.6711643 1000 0.96552353 3.3772121
216000 3.9243061 1000 0.97713174 3.3929201
217000 4.1757021 1000 0.97062546 3.408628
218000 4.4291788 1000 0.97111212 3.424336
219000 4.6819445 1000 0.97645659 3.440044
220000 4.9376967 1000 0.98148797 3.4557519
221000 5.1883947 1000 0.97386268 3.4714599
222000 5.4387287 1000 0.97322415 3.4871678
223000 5.6878448 1000 0.95781163 3.5028758
224000 5.9358535 1000 0.93919542 3.5185838
225000 6.1822635 1000 0.9313702 3.5342917
226000 6.4302601 1000 0.92788207 3.5499997
227000 6.6795172 1000 0.91026919 3.5657077
228000 6.9286832 1000 0.89557479 3.5814156
229000 7.1797845 1000 0.89173643 3.5971236
230000 7.432965 1000 0.89292723 3.6128316
231000 7.6848123 1000 0.89944536 3.6285395
232000 7.9361745 1000 0.89319113 3.6442475
233000 8.1896078 1000 0.89273543 3.6599554
234000 8.4447838 1000 0.87360829 3.6756634
235000 8.7028153 1000 0.86841591 3.6913714
236000 8.9582068 1000 0.86559907 3.7070793
237000 9.2150326 1000 0.86231762 3.7227873
238000 9.4701361 1000 0.85170772 3.7384953
239000 9.7272256 1000 0.85616849 3.7542032
240000 9.985268 1000 0.86809668 3.7699112
241000 10.243685 1000 0.88066532 3.7856191
242000 10.50579 1000 0.89440189 3.8013271
243000 10.768046 1000 0.8939512 3.8170351
244000 11.030389 1000 0.8963829 3.832743
245000 11.29267 1000 0.88074176 3.848451
246000 11.553505 1000 0.8733699 3.864159
247000 11.81124 1000 0.86130993 3.8798669
248000 12.068927 1000 0.86035503 3.8955749
249000 12.326723 1000 0.84878437 3.9112829
250000 12.584681 1000 0.83989297 3.9269908
251000 12.841147 1000 0.82781463 3.9426988
252000 13.101351 1000 0.8142641 3.9584067
253000 13.361975 1000 0.80683745 3.9741147
254000 13.621901 1000 0.809379 3.9898227
255000 13.879382 1000 0.81147846 4.0055306
256000 14.136754 1000 0.79574281 4.0212386
257000 14.393097 1000 0.78339098 4.0369466
258000 14.65084 1000 0.7799887 4.0526545
259000 14.909563 1000 0.7848995 4.0683625
260000 15.171732 1000 0.78284201 4.0840704
261000 15.434923 1000 0.7776263 4.0997784
262000 15.699673 1000 0.77405185 4.1154864
263000 15.964731 1000 0.78130382 4.1311943
264000 16.231068 1000 0.81006815 4.1469023
265000 16.494447 1000 0.79467298 4.1626103
266000 16.757296 1000 0.78592963 4.1783182
267000 17.020773 1000 0.76857233 4.1940262
268000 17.281914 1000 0.76483523 4.2097342
269000 17.543254 1000 0.76549297 4.2254421
270000 17.807266 1000 0.75564385 4.2411501
271000 18.083451 1000 0.75445102 4.256858
272000 18.34927 1000 0.7514406 4.272566
273000 18.6133 1000 0.75170218 4.288274
274000 18.874318 1000 0.76454717 4.3039819
275000 19.137188 1000 0.75991671 4.3196899
276000 19.398218 1000 0.75817752 4.3353979
277000 19.65797 1000 0.7621338 4.3511058
278000 19.917364 1000 0.77239256 4.3668138
279000 20.178778 1000 0.7667469 4.3825218
280000 20.441559 1000 0.75761494 4.3982297
281000 20.704047 1000 0.74370218 4.4139377
282000 20.967325 1000 0.734955 4.4296456
283000 21.226371 1000 0.72783614 4.4453536
284000 21.485188 1000 0.72349874 4.4610616
285000 21.742828 1000 0.71585562 4.4767695
286000 22.002099 1000 0.70846101 4.4924775
287000 22.262387 1000 0.69307445 4.5081855
288000 22.523992 1000 0.68469722 4.5238934
289000 22.786885 1000 0.67892956 4.5396014
290000 23.050769 1000 0.67872999 4.5553093
291000 23.313704 1000 0.6820098 4.5710173
292000 23.576713 1000 0.67663229 4.5867253
293000 23.828165 1000 0.67477934 4.6024332
294000 24.081047 1000 0.67452515 4.6181412
295000 24.335392 1000 0.67341495 4.6338492
296000 24.590438 1000 0.67888865 4.6495571
297000 24.84277 1000 0.68373518 4.6652651
298000 25.097993 1000 0.68612329 4.6809731
299000 25.355621 1000 0.68169877 4.696681
300000 25.612938 1000 0.68602699 4.712389
301000 25.866694 1000 0.68485644 4.7280969
302000 26.120968 1000 0.68101185 4.7438049
303000 26.374411 1000 0.67663031 4.7595129
304000 26.628686 1000 0.67771638 4.7752208
305000 26.881546 1000 0.67525788 4.7909288
306000 27.163762 1000 0.6709689 4.8066368
307000 27.421347 1000 0.68328286 4.8223447
308000 27.674664 1000 0.70273998 4.8380527
309000 27.937573 1000 0.70461978 4.8537606
310000 28.206728 1000 0.70307737 4.8694686
311000 28.473159 1000 0.70087936 4.8851766
312000 28.739452 1000 0.70449303 4.9008845
313000 29.001716 1000 0.71030367 4.9165925
314000 29.267562 1000 0.71113177 4.9323005
315000 29.533541 1000 0.71089537 4.9480084
316000 29.798996 1000 0.70713116 4.9637164
317000 30.068605 1000 0.71002087 4.9794244
318000 30.339303 1000 0.71804737 4.9951323
319000 30.609227 1000 0.71925831 5.0108403
320000 30.879193 1000 0.72835371 5.0265482
321000 31.147328 1000 0.7236586 5.0422562
322000 31.413246 1000 0.71432128 5.0579642
323000 31.675418 1000 0.70905325 5.0736721
324000 31.938939 1000 0.71323674 5.0893801
325000 32.20437 1000 0.72466784 5.1050881
326000 32.471213 1000 0.72956158 5.120796
327000 32.739168 1000 0.74478918 5.136504
328000 33.005983 1000 0.74404284 5.152212
329000 33.273193 1000 0.74051597 5.1679199
330000 33.541489 1000 0.73438585 5.1836279
331000 33.805988 1000 0.73023911 5.1993358
332000 34.071435 1000 0.7373459 5.2150438
333000 34.337809 1000 0.73137848 5.2307518
334000 34.602061 1000 0.72917991 5.2464597
335000 34.87065 1000 0.72945658 5.2621677
336000 35.140112 1000 0.72046325 5.2778757
337000 35.411283 1000 0.72224629 5.2935836
338000 35.681774 1000 0.72177721 5.3092916
339000 35.952034 1000 0.72852277 5.3249995
340000 36.220116 1000 0.73244024 5.3407075
341000 36.484799 1000 0.74123436 5.3564155
342000 36.752429 1000 0.74117339 5.3721234
343000 37.019401 1000 0.74360263 5.3878314
344000 37.284441 1000 0.74998018 5.4035394
345000 37.548209 1000 0.75026985 5.4192473
346000 37.812297 1000 0.74415875 5.4349553
347000 38.078351 1000 0.73219169 5.4506633
348000 38.343692 1000 0.72316753 5.4663712
349000 38.60829 1000 0.71747804 5.4820792
350000 38.873334 1000 0.72055215 5.4977871
351000 39.135591 1000 0.71525775 5.5134951
352000 39.397948 1000 0.7157435 5.5292031
353000 39.65874 1000 0.71883293 5.544911
354000 39.921649 1000 0.72106381 5.560619
355000 40.184118 1000 0.7126019 5.576327
356000 40.44828 1000 0.70018005 5.5920349
357000 40.711808 1000 0.6948238 5.6077429
358000 40.974553 1000 0.70261087 5.6234508
359000 41.240667 1000 0.70651692 5.6391588
360000 41.508869 1000 0.71812614 5.6548668
361000 41.775889 1000 0.72247116 5.6705747
362000 42.044747 1000 0.73675936 5.6862827
363000 42.311154 1000 0.75136966 5.7019907
364000 42.577458 1000 0.75745313 5.7176986
365000 42.846131 1000 0.7541109 5.7334066
366000 43.113639 1000 0.75340643 5.7491146
367000 43.3804 1000 0.74817232 5.7648225
368000 43.644839 1000 0.73555712 5.7805305
369000 43.907875 1000 0.72911144 5.7962384
370000 44.173474 1000 0.72223387 5.8119464
371000 44.435762 1000 0.72012879 5.8276544
372000 44.698339 1000 0.72050435 5.8433623
373000 44.96325 1000 0.72789287 5.8590703
374000 45.228536 1000 0.74234609 5.8747783
375000 45.49447 1000 0.74808952 5.8904862
376000 45.76007 1000 0.74096035 5.9061942
377000 46.027203 1000 0.74052775 5.9219022
378000 46.294627 1000 0.74206885 5.9376101
379000 46.567974 1000 0.74385723 5.9533181
380000 46.837323 1000 0.74901717 5.969026
381000 47.104723 1000 0.760668 5.984734
382000 47.37249 1000 0.76622105 6.000442
383000 47.642871 1000 0.77784236 6.0161499
384000 47.913238 1000 0.78443266 6.0318579
385000 48.179637 1000 0.77604024 6.0475659
386000 48.444304 1000 0.76126822 6.0632738
387000 48.708424 1000 0.74932674 6.0789818
388000 48.972518 1000 0.7394025 6.0946897
389000 49.236663 1000 0.73446106 6.1103977
390000 49.502321 1000 0.73226431 6.1261057
391000 49.772781 1000 0.72676072 6.1418136
392000 50.047483 1000 0.7283395 6.1575216
393000 50.308297 1000 0.7289238 6.1732296
394000 50.564792 1000 0.72479408 6.1889375
395000 50.819957 1000 0.71014812 6.2046455
396000 51.078032 1000 0.70351995 6.2203535
397000 51.336319 1000 0.70221306 6.2360614
398000 51.593057 1000 0.70748482 6.2517694
399000 51.853527 1000 0.7046252 6.2674773
400000 52.1092 1000 0.70581734 6.2831853
Loop time of 52.1092 on 1 procs for 200000 steps with 1000 atoms
Performance: 15669.134 tau/day, 3838.093 timesteps/s, 3.838 Matom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7952 | 7.7952 | 7.7952 | 0.0 | 14.96
Neigh | 0.062504 | 0.062504 | 0.062504 | 0.0 | 0.12
Comm | 1.0937 | 1.0937 | 1.0937 | 0.0 | 2.10
Output | 0.0038447 | 0.0038447 | 0.0038447 | 0.0 | 0.01
Modify | 42.69 | 42.69 | 42.69 | 0.0 | 81.92
Other | | 0.4642 | | | 0.89
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 285 ave 285 max 285 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5094 ave 5094 max 5094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5094
Ave neighs/atom = 5.094
Neighbor list builds = 158
Dangerous builds = 0
Total wall time: 0:01:22

642
examples/granregion/log.27Jun24.granregion.mixer.g++.4 Normal file
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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 2 by 2 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/atomonly/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 444 every 84653 steps, 1000 by step 169307
Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.088111932 444 -0 0.015707963
2000 0.14514013 444 -0 0.031415927
3000 0.19901283 444 -0 0.04712389
4000 0.25271154 444 -0 0.062831853
5000 0.30627277 444 -0 0.078539816
6000 0.35966654 444 -0 0.09424778
7000 0.41280835 444 -0 0.10995574
8000 0.46584491 444 -0 0.12566371
9000 0.51843618 444 -0 0.14137167
10000 0.57151612 444 -0 0.15707963
11000 0.61192936 444 -0 0.1727876
12000 0.65265862 444 -0 0.18849556
13000 0.69377116 444 -0 0.20420352
14000 0.73526123 444 -0 0.21991149
15000 0.77783987 444 -0 0.23561945
16000 0.82128542 444 -0 0.25132741
17000 0.86603751 444 -0 0.26703538
18000 0.90981059 444 -0 0.28274334
19000 0.95383173 444 -0 0.2984513
20000 0.99782061 444 -0 0.31415927
21000 1.0370303 444 -0 0.32986723
22000 1.0764103 444 -0 0.34557519
23000 1.1154891 444 -0 0.36128316
24000 1.1549694 444 -0 0.37699112
25000 1.1953727 444 -0 0.39269908
26000 1.2364474 444 -0 0.40840704
27000 1.2777508 444 -0 0.42411501
28000 1.3195763 444 -0 0.43982297
29000 1.3618971 444 -0 0.45553093
30000 1.404607 444 -0 0.4712389
31000 1.4428952 444 -0 0.48694686
32000 1.4818254 444 -0 0.50265482
33000 1.5205701 444 -0 0.51836279
34000 1.559401 444 -0 0.53407075
35000 1.5987318 444 -0 0.54977871
36000 1.6379014 444 -0 0.56548668
37000 1.6781504 444 -0 0.58119464
38000 1.7190533 444 -0 0.5969026
39000 1.7604269 444 -0 0.61261057
40000 1.8019216 444 -0 0.62831853
41000 1.8402535 444 -0 0.64402649
42000 1.8791646 444 -0 0.65973446
43000 1.9188237 444 -0 0.67544242
44000 1.9584939 444 -0 0.69115038
45000 1.9992043 444 -0 0.70685835
46000 2.04024 444 -0 0.72256631
47000 2.0814641 444 -0 0.73827427
48000 2.123407 444 -0 0.75398224
49000 2.165223 444 -0 0.7696902
50000 2.2074047 444 -0 0.78539816
51000 2.2456301 444 -0 0.80110613
52000 2.2839661 444 -0 0.81681409
53000 2.3227369 444 -0 0.83252205
54000 2.3618801 444 -0 0.84823002
55000 2.401451 444 -0 0.86393798
56000 2.4414565 444 -0 0.87964594
57000 2.4813918 444 -0 0.89535391
58000 2.5221831 444 -0 0.91106187
59000 2.5637488 444 -0 0.92676983
60000 2.6055953 444 -0 0.9424778
61000 2.6456326 444 -0 0.95818576
62000 2.6857299 444 -0 0.97389372
63000 2.7259082 444 -0 0.98960169
64000 2.7665767 444 -0 1.0053096
65000 2.8082755 444 -0 1.0210176
66000 2.8503373 444 -0 1.0367256
67000 2.8938769 444 -0 1.0524335
68000 2.9373604 444 -0 1.0681415
69000 2.9810674 444 -0 1.0838495
70000 3.0246587 444 -0 1.0995574
71000 3.0655215 444 -0 1.1152654
72000 3.1075971 444 -0 1.1309734
73000 3.1497688 444 -0 1.1466813
74000 3.1915941 444 -0 1.1623893
75000 3.2352454 444 -0 1.1780972
76000 3.2799164 444 -0 1.1938052
77000 3.3245184 444 -0 1.2095132
78000 3.3693626 444 -0 1.2252211
79000 3.4144403 444 -0 1.2409291
80000 3.4609593 444 -0 1.2566371
81000 3.5037956 444 -0 1.272345
82000 3.5460391 444 -0 1.288053
83000 3.5890988 444 -0 1.303761
84000 3.6329781 444 -0 1.3194689
85000 3.6969324 888 -0 1.3351769
86000 3.7764618 888 -0 1.3508848
87000 3.855693 888 -0 1.3665928
88000 3.9341142 888 -0 1.3823008
89000 4.0125134 888 -0 1.3980087
90000 4.0915705 888 -0 1.4137167
91000 4.1526623 888 -0 1.4294247
92000 4.2142478 888 -0 1.4451326
93000 4.2776631 888 -0 1.4608406
94000 4.3413071 888 -0 1.4765485
95000 4.4047448 888 -0 1.4922565
96000 4.4682904 888 -0 1.5079645
97000 4.5328349 888 -0 1.5236724
98000 4.5968674 888 -0 1.5393804
99000 4.6612212 888 -0 1.5550884
100000 4.7263166 888 -0 1.5707963
101000 4.7899218 888 -0 1.5865043
102000 4.8548615 888 -0 1.6022123
103000 4.9201477 888 -0 1.6179202
104000 4.9848694 888 -0 1.6336282
105000 5.0511867 888 -0 1.6493361
106000 5.1167808 888 -0 1.6650441
107000 5.1831053 888 -0 1.6807521
108000 5.250398 888 -0 1.69646
109000 5.3169814 888 -0 1.712168
110000 5.3857277 888 -0 1.727876
111000 5.4527691 888 -0 1.7435839
112000 5.5214505 888 -0 1.7592919
113000 5.5892604 888 -0 1.7749998
114000 5.6579089 888 -0 1.7907078
115000 5.7279007 888 -0 1.8064158
116000 5.7971602 888 -0 1.8221237
117000 5.867895 888 -0 1.8378317
118000 5.9400645 888 -0 1.8535397
119000 6.0117635 888 -0 1.8692476
120000 6.0851132 888 -0 1.8849556
121000 6.1539323 888 -0 1.9006636
122000 6.2231605 888 -0 1.9163715
123000 6.2930557 888 -0 1.9320795
124000 6.3632912 888 -0 1.9477874
125000 6.4336358 888 -0 1.9634954
126000 6.5042786 888 -0 1.9792034
127000 6.5747889 888 -0 1.9949113
128000 6.6452984 888 -0 2.0106193
129000 6.7169482 888 -0 2.0263273
130000 6.7865487 888 -0 2.0420352
131000 6.8576956 888 -0 2.0577432
132000 6.9296299 888 -0 2.0734512
133000 7.0024987 888 -0 2.0891591
134000 7.0753126 888 -0 2.1048671
135000 7.1492322 888 -0 2.120575
136000 7.2243825 888 -0 2.136283
137000 7.3005224 888 -0 2.151991
138000 7.378849 888 -0 2.1676989
139000 7.4574391 888 -0 2.1834069
140000 7.5370788 888 -0 2.1991149
141000 7.6104683 888 -0 2.2148228
142000 7.6840599 888 -0 2.2305308
143000 7.7594508 888 -0 2.2462387
144000 7.8338839 888 -0 2.2619467
145000 7.9104471 888 -0 2.2776547
146000 7.9862744 888 -0 2.2933626
147000 8.0621903 888 -0 2.3090706
148000 8.1403104 888 -0 2.3247786
149000 8.2192751 888 -0 2.3404865
150000 8.2988877 888 -0 2.3561945
151000 8.3771585 888 -0 2.3719025
152000 8.4559615 888 -0 2.3876104
153000 8.5340116 888 -0 2.4033184
154000 8.612764 888 -0 2.4190263
155000 8.6925848 888 -0 2.4347343
156000 8.7739307 888 -0 2.4504423
157000 8.8541471 888 -0 2.4661502
158000 8.9371669 888 -0 2.4818582
159000 9.0204947 888 -0 2.4975662
160000 9.1037153 888 -0 2.5132741
161000 9.1860231 888 -0 2.5289821
162000 9.2695251 888 -0 2.54469
163000 9.3537318 888 -0 2.560398
164000 9.4396954 888 -0 2.576106
165000 9.5265215 888 -0 2.5918139
166000 9.6140047 888 -0 2.6075219
167000 9.7019854 888 -0 2.6232299
168000 9.7918781 888 -0 2.6389378
169000 9.8831043 888 -0 2.6546458
170000 9.9785874 1000 -0 2.6703538
171000 10.073548 1000 -0 2.6860617
172000 10.164183 1000 -0 2.7017697
173000 10.256327 1000 -0 2.7174776
174000 10.353455 1000 -0 2.7331856
175000 10.451392 1000 -0 2.7488936
176000 10.549792 1000 -0 2.7646015
177000 10.648615 1000 -0 2.7803095
178000 10.747357 1000 -0 2.7960175
179000 10.84476 1000 -0 2.8117254
180000 10.942242 1000 -0 2.8274334
181000 11.040635 1000 -0 2.8431414
182000 11.139273 1000 -0 2.8588493
183000 11.239382 1000 -0 2.8745573
184000 11.339673 1000 -0 2.8902652
185000 11.441311 1000 -0 2.9059732
186000 11.543812 1000 -0 2.9216812
187000 11.64542 1000 -0 2.9373891
188000 11.74731 1000 -0 2.9530971
189000 11.850149 1000 -0 2.9688051
190000 11.952154 1000 -0 2.984513
191000 12.055857 1000 -0 3.000221
192000 12.158418 1000 -0 3.0159289
193000 12.261926 1000 -0 3.0316369
194000 12.364315 1000 -0 3.0473449
195000 12.466776 1000 -0 3.0630528
196000 12.568419 1000 -0 3.0787608
197000 12.670258 1000 -0 3.0944688
198000 12.771091 1000 -0 3.1101767
199000 12.873654 1000 -0 3.1258847
200000 12.976411 1000 -0 3.1415927
Loop time of 12.9764 on 4 procs for 200000 steps with 1000 atoms
Performance: 62922.248 tau/day, 15412.556 timesteps/s, 15.413 Matom-step/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.35493 | 0.65797 | 0.98979 | 36.8 | 5.07
Neigh | 0.0084865 | 0.011137 | 0.013852 | 2.4 | 0.09
Comm | 3.7509 | 4.2375 | 4.7882 | 23.1 | 32.66
Output | 0.0027947 | 0.0036594 | 0.0042822 | 0.9 | 0.03
Modify | 5.6694 | 6.3746 | 7.0279 | 24.5 | 49.12
Other | | 1.692 | | | 13.04
Nlocal: 250 ave 260 max 242 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 279.25 ave 325 max 232 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 939.75 ave 1397 max 509 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3759
Ave neighs/atom = 3.759
Neighbor list builds = 201
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.88 | 11.89 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0071568 3.1415927
201000 0.093433184 1000 1.0036239 3.1573006
202000 0.18902203 1000 0.99846844 3.1730086
203000 0.28432792 1000 0.98236169 3.1887165
204000 0.38011419 1000 0.98625572 3.2044245
205000 0.47468558 1000 0.9893407 3.2201325
206000 0.56918796 1000 1.0012123 3.2358404
207000 0.66393867 1000 1.0231892 3.2515484
208000 0.75739212 1000 1.0265912 3.2672564
209000 0.85184147 1000 1.0190202 3.2829643
210000 0.94643219 1000 1.0267754 3.2986723
211000 1.0419472 1000 1.0186847 3.3143802
212000 1.1365263 1000 1.0159848 3.3300882
213000 1.232359 1000 0.99326329 3.3457962
214000 1.3262519 1000 0.97263135 3.3615041
215000 1.4200243 1000 0.97246409 3.3772121
216000 1.5161944 1000 0.96000626 3.3929201
217000 1.6118944 1000 0.95730432 3.408628
218000 1.7110719 1000 0.95605591 3.424336
219000 1.8103017 1000 0.94983 3.440044
220000 1.9104019 1000 0.95291888 3.4557519
221000 2.0104337 1000 0.93612997 3.4714599
222000 2.1116636 1000 0.93414081 3.4871678
223000 2.2119333 1000 0.93321246 3.5028758
224000 2.3141 1000 0.93026943 3.5185838
225000 2.4159209 1000 0.930478 3.5342917
226000 2.5183511 1000 0.92909096 3.5499997
227000 2.6187905 1000 0.92308495 3.5657077
228000 2.7162318 1000 0.91075986 3.5814156
229000 2.8156901 1000 0.9006662 3.5971236
230000 2.9175496 1000 0.88869212 3.6128316
231000 3.0178436 1000 0.8877611 3.6285395
232000 3.1199496 1000 0.89409636 3.6442475
233000 3.2221471 1000 0.90866091 3.6599554
234000 3.3254883 1000 0.90454601 3.6756634
235000 3.4290048 1000 0.89408327 3.6913714
236000 3.5311688 1000 0.8881044 3.7070793
237000 3.6334192 1000 0.89322168 3.7227873
238000 3.7368611 1000 0.89018045 3.7384953
239000 3.8423369 1000 0.88771268 3.7542032
240000 3.9476493 1000 0.88957717 3.7699112
241000 4.0539657 1000 0.89362036 3.7856191
242000 4.16111 1000 0.90967472 3.8013271
243000 4.2703542 1000 0.91366381 3.8170351
244000 4.3773387 1000 0.9150959 3.832743
245000 4.4845495 1000 0.92725789 3.848451
246000 4.5930315 1000 0.93024722 3.864159
247000 4.7046291 1000 0.93297974 3.8798669
248000 4.8170945 1000 0.94755869 3.8955749
249000 4.9268016 1000 0.94761679 3.9112829
250000 5.0368647 1000 0.92701064 3.9269908
251000 5.1471839 1000 0.91365252 3.9426988
252000 5.2579805 1000 0.90918381 3.9584067
253000 5.3685628 1000 0.90612685 3.9741147
254000 5.4809889 1000 0.90352142 3.9898227
255000 5.5948165 1000 0.90421567 4.0055306
256000 5.7098724 1000 0.90024688 4.0212386
257000 5.8267005 1000 0.88540341 4.0369466
258000 5.9410582 1000 0.87890423 4.0526545
259000 6.0566794 1000 0.86833748 4.0683625
260000 6.1707105 1000 0.85465694 4.0840704
261000 6.2863098 1000 0.83941242 4.0997784
262000 6.4015542 1000 0.81790404 4.1154864
263000 6.5166913 1000 0.82284562 4.1311943
264000 6.6306328 1000 0.80961447 4.1469023
265000 6.7436467 1000 0.80567073 4.1626103
266000 6.855163 1000 0.79577448 4.1783182
267000 6.9684761 1000 0.78489106 4.1940262
268000 7.0840143 1000 0.77348757 4.2097342
269000 7.1995596 1000 0.76606696 4.2254421
270000 7.3149459 1000 0.7649744 4.2411501
271000 7.4296104 1000 0.76050309 4.256858
272000 7.545919 1000 0.75378759 4.272566
273000 7.6616623 1000 0.75633811 4.288274
274000 7.7787912 1000 0.75703106 4.3039819
275000 7.8956703 1000 0.75227453 4.3196899
276000 8.0137649 1000 0.76003902 4.3353979
277000 8.1334933 1000 0.76274661 4.3511058
278000 8.2489616 1000 0.75888482 4.3668138
279000 8.3645369 1000 0.75071875 4.3825218
280000 8.4781847 1000 0.75454927 4.3982297
281000 8.5925071 1000 0.75617824 4.4139377
282000 8.7079255 1000 0.75230835 4.4296456
283000 8.8225434 1000 0.75417571 4.4453536
284000 8.9358224 1000 0.74559345 4.4610616
285000 9.0494588 1000 0.73274661 4.4767695
286000 9.1624226 1000 0.72385193 4.4924775
287000 9.2738683 1000 0.72398899 4.5081855
288000 9.3858476 1000 0.72009027 4.5238934
289000 9.496472 1000 0.72026686 4.5396014
290000 9.6064673 1000 0.72330145 4.5553093
291000 9.7157088 1000 0.71630656 4.5710173
292000 9.8251432 1000 0.71089192 4.5867253
293000 9.9340203 1000 0.70584923 4.6024332
294000 10.041427 1000 0.71350398 4.6181412
295000 10.150066 1000 0.72781836 4.6338492
296000 10.258912 1000 0.72285512 4.6495571
297000 10.368299 1000 0.71649517 4.6652651
298000 10.480058 1000 0.71132209 4.6809731
299000 10.592962 1000 0.73602072 4.696681
300000 10.706549 1000 0.74400837 4.712389
301000 10.818871 1000 0.76618562 4.7280969
302000 10.930873 1000 0.77476041 4.7438049
303000 11.040635 1000 0.77124283 4.7595129
304000 11.150729 1000 0.7625748 4.7752208
305000 11.260184 1000 0.74979361 4.7909288
306000 11.36913 1000 0.74515733 4.8066368
307000 11.477137 1000 0.74302741 4.8223447
308000 11.584107 1000 0.73732959 4.8380527
309000 11.692852 1000 0.73368237 4.8537606
310000 11.800777 1000 0.72374292 4.8694686
311000 11.906901 1000 0.72107784 4.8851766
312000 12.015001 1000 0.72944426 4.9008845
313000 12.122634 1000 0.73958637 4.9165925
314000 12.231473 1000 0.75160847 4.9323005
315000 12.343728 1000 0.74419683 4.9480084
316000 12.455114 1000 0.74652593 4.9637164
317000 12.564048 1000 0.74933482 4.9794244
318000 12.672355 1000 0.74200509 4.9951323
319000 12.778931 1000 0.7346024 5.0108403
320000 12.886067 1000 0.72806145 5.0265482
321000 12.993743 1000 0.72147888 5.0422562
322000 13.101955 1000 0.71460041 5.0579642
323000 13.212177 1000 0.70255075 5.0736721
324000 13.322528 1000 0.70640327 5.0893801
325000 13.435038 1000 0.70643428 5.1050881
326000 13.545443 1000 0.69751794 5.120796
327000 13.657538 1000 0.69035108 5.136504
328000 13.770475 1000 0.68068243 5.152212
329000 13.883136 1000 0.69123492 5.1679199
330000 13.995043 1000 0.70326515 5.1836279
331000 14.109604 1000 0.70551726 5.1993358
332000 14.222995 1000 0.70514444 5.2150438
333000 14.336604 1000 0.71102045 5.2307518
334000 14.44933 1000 0.71336747 5.2464597
335000 14.56056 1000 0.70816388 5.2621677
336000 14.67143 1000 0.69502472 5.2778757
337000 14.783295 1000 0.69314289 5.2935836
338000 14.893816 1000 0.68565794 5.3092916
339000 15.005631 1000 0.67268053 5.3249995
340000 15.119406 1000 0.68313196 5.3407075
341000 15.233786 1000 0.68782815 5.3564155
342000 15.349691 1000 0.6989326 5.3721234
343000 15.466599 1000 0.694926 5.3878314
344000 15.583585 1000 0.7006474 5.4035394
345000 15.702299 1000 0.70783177 5.4192473
346000 15.819367 1000 0.71334276 5.4349553
347000 15.935892 1000 0.72917419 5.4506633
348000 16.051074 1000 0.74315705 5.4663712
349000 16.165316 1000 0.76731311 5.4820792
350000 16.281794 1000 0.79761434 5.4977871
351000 16.397615 1000 0.80447724 5.5134951
352000 16.514271 1000 0.80118728 5.5292031
353000 16.632427 1000 0.77990459 5.544911
354000 16.750052 1000 0.76453299 5.560619
355000 16.868875 1000 0.76538392 5.576327
356000 16.985762 1000 0.76310698 5.5920349
357000 17.103471 1000 0.75897095 5.6077429
358000 17.223037 1000 0.75071115 5.6234508
359000 17.340073 1000 0.74034801 5.6391588
360000 17.457867 1000 0.72671924 5.6548668
361000 17.57503 1000 0.72111017 5.6705747
362000 17.69138 1000 0.71875181 5.6862827
363000 17.808661 1000 0.71469706 5.7019907
364000 17.925895 1000 0.70470493 5.7176986
365000 18.042976 1000 0.70863047 5.7334066
366000 18.162079 1000 0.70850561 5.7491146
367000 18.283911 1000 0.71413452 5.7648225
368000 18.407692 1000 0.71314184 5.7805305
369000 18.53068 1000 0.71309549 5.7962384
370000 18.652767 1000 0.71132937 5.8119464
371000 18.772131 1000 0.70788039 5.8276544
372000 18.892439 1000 0.71780071 5.8433623
373000 19.012886 1000 0.72352571 5.8590703
374000 19.132857 1000 0.71723739 5.8747783
375000 19.25312 1000 0.71556941 5.8904862
376000 19.372783 1000 0.70935312 5.9061942
377000 19.493215 1000 0.71551157 5.9219022
378000 19.614604 1000 0.7235163 5.9376101
379000 19.735704 1000 0.73896421 5.9533181
380000 19.856219 1000 0.74906169 5.969026
381000 19.974782 1000 0.75303336 5.984734
382000 20.093831 1000 0.75359492 6.000442
383000 20.213075 1000 0.75579354 6.0161499
384000 20.334366 1000 0.75178368 6.0318579
385000 20.455027 1000 0.74412159 6.0475659
386000 20.574847 1000 0.7360955 6.0632738
387000 20.691183 1000 0.73461103 6.0789818
388000 20.80664 1000 0.72496617 6.0946897
389000 20.92229 1000 0.7219047 6.1103977
390000 21.037387 1000 0.71837013 6.1261057
391000 21.152412 1000 0.71495923 6.1418136
392000 21.267451 1000 0.71436707 6.1575216
393000 21.382024 1000 0.71447834 6.1732296
394000 21.496952 1000 0.71334298 6.1889375
395000 21.611699 1000 0.71510229 6.2046455
396000 21.726328 1000 0.7121714 6.2203535
397000 21.840614 1000 0.70818894 6.2360614
398000 21.955122 1000 0.70059455 6.2517694
399000 22.068714 1000 0.69960089 6.2674773
400000 22.182962 1000 0.70261998 6.2831853
Loop time of 22.183 on 4 procs for 200000 steps with 1000 atoms
Performance: 36807.772 tau/day, 9015.918 timesteps/s, 9.016 Matom-step/s
95.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1609 | 2.0592 | 2.957 | 61.9 | 9.28
Neigh | 0.013526 | 0.018287 | 0.022861 | 3.3 | 0.08
Comm | 7.707 | 8.9501 | 10.214 | 41.1 | 40.35
Output | 0.0027437 | 0.0039021 | 0.0045769 | 1.1 | 0.02
Modify | 7.9431 | 9.4082 | 10.711 | 40.5 | 42.41
Other | | 1.743 | | | 7.86
Nlocal: 250 ave 258 max 241 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 412 ave 492 max 332 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1258.5 ave 1588 max 953 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 5034
Ave neighs/atom = 5.034
Neighbor list builds = 159
Dangerous builds = 0
Total wall time: 0:00:35

116
examples/granular/log.28Mar23.pour.drum.g++.1 → examples/granular/log.27Jun24.pour.drum.g++.1
View File

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

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