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Merge branch 'develop' into replicate_periodic_box

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This commit is contained in:
Jacob Gissinger
2024-02-13 18:52:43 -05:00
committed by GitHub
parent ad7b5e38ab 254a849a29
commit 0951e28a08
934 changed files with 16454 additions and 10453 deletions
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2
.github/workflows/coverity.yml vendored
View File

@ -25,7 +25,7 @@ jobs:
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

2
.github/workflows/unittest-macos.yml vendored
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@ -32,7 +32,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}

43
cmake/CMakeLists.txt
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@ -120,6 +120,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
set(CMAKE_TUNE_DEFAULT "-Minform=severe")
endif()
# this hack is required to compile fmt lib with CrayClang version 15.0.2
# CrayClang is only directly recognized by version 3.28 and later
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
endif()
endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@ -415,6 +428,7 @@ if(BUILD_OMP)
(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@ -971,14 +985,15 @@ if(PKG_KOKKOS)
endif()
endif()
if(PKG_KSPACE)
if (LMP_HEFFTE)
if (FFT_USE_HEFFTE)
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: heFFTe")
if (HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
if (FFT_HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${FFT_HEFFTE_BACKEND}")
else()
message(STATUS "heFFTe backend: stock (builtin FFT implementation, tested for corrected but not optimized for production)")
endif()
message(STATUS "Using distributed FFT algorithms from heFTTe")
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
@ -997,28 +1012,10 @@ if(PKG_KSPACE)
else()
message(STATUS "Using non-threaded FFTs")
endif()
if (FFT_HEFFTE)
message(STATUS "Using distributed algorithms from heFTTe")
else()
message(STATUS "Using builtin distributed algorithms")
message(STATUS "Using builtin distributed FFT algorithms")
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: cuFFT")
endif()
elseif(Kokkos_ENABLE_HIP)
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: hipFFT")
endif()
else()
message(STATUS "Kokkos FFT: ${FFT}")
endif()
endif()
message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
endif()
endif()
if(BUILD_DOC)

10
cmake/Modules/DetectHIPInstallation.cmake
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@ -1,11 +1,3 @@
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
"Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
@ -13,4 +5,4 @@ if(NOT DEFINED ROCM_PATH)
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

2
cmake/Modules/ExternalCMakeProject.cmake
View File

@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
"${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
endif()
add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
"${CMAKE_BINARY_DIR}/_deps/${target}-build")
"${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
endfunction(ExternalCMakeProject)

5
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)
@ -8,4 +8,3 @@ set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
include(ExternalCMakeProject)
ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
add_library(OpenCL::OpenCL ALIAS OpenCL)

7
cmake/Modules/Packages/GPU.cmake
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@ -1,3 +1,10 @@
# Silence CMake warnings about FindCUDA being obsolete.
# We may need to eventually rewrite this section to use enable_language(CUDA)
if(POLICY CMP0146)
cmake_policy(SET CMP0146 OLD)
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

29
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -16,11 +16,6 @@ endif()
if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
# NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
########################################################################
@ -131,16 +126,32 @@ if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(NOT (FFT STREQUAL "KISS"))
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
if(NOT (FFT STREQUAL "KISS"))
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "HIPFFT")
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
endif()

37
cmake/Modules/Packages/KSPACE.cmake
View File

@ -48,10 +48,15 @@ endif()
option(FFT_USE_HEFFTE "Use heFFTe as the distributed FFT engine, overrides the FFT option." OFF)
if(FFT_USE_HEFFTE)
# if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
# if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
# map standard FFT choices to available heFFTe backends: FFTW3 -> FFTW, KISS -> BUILTIN
set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL BUILTIN)
string(REPLACE FFTW3 FFTW FFT_HEFFTE_BACKEND_DEFAULT ${FFT})
string(REPLACE KISS BUILTIN FFT_HEFFTE_BACKEND_DEFAULT ${FFT_HEFFTE_BACKEND_DEFAULT})
set(FFT_HEFFTE_BACKEND "${FFT_HEFFTE_BACKEND_DEFAULT}" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
validate_option(FFT_HEFFTE_BACKEND FFT_HEFFTE_BACKEND_VALUES)
if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
set(HEFFTE_COMPONENTS "FFTW")
@ -60,24 +65,38 @@ if(FFT_USE_HEFFTE)
set(HEFFTE_COMPONENTS "MKL")
set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
else()
set(HEFFTE_COMPONENTS "BUILTIN")
message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
endif()
find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
if (NOT Heffte_FOUND) # download and build
if(BUILD_SHARED_LIBS)
set(BUILD_SHARED_LIBS_WAS_ON YES)
set(BUILD_SHARED_LIBS OFF)
endif()
if(CMAKE_REQUEST_PIC)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
set(Heffte_ENABLE_${FFT_HEFFTE_BACKEND} ON)
include(FetchContent)
FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
URL "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
)
FetchContent_Populate(HEFFTE_PROJECT)
add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
target_link_libraries(Heffte::Heffte INTERFACE Heffte)
endif()
# fixup git hash to show "(unknown)" to avoid compilation failures.
file(READ ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h HEFFTE_CFG_FILE_TEXT)
string(REPLACE "@Heffte_GIT_HASH@" "(unknown)" HEFFTE_CFG_FILE_TEXT "${HEFFTE_CFG_FILE_TEXT}")
file(WRITE ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h "${HEFFTE_CFG_FILE_TEXT}")
add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR} EXCLUDE_FROM_ALL)
add_library(Heffte::Heffte ALIAS Heffte)
if(BUILD_SHARED_LIBS_WAS_ON)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
target_link_libraries(lammps PRIVATE Heffte::Heffte)
endif()

4
cmake/Modules/Packages/MDI.cmake
View File

@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)

6
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -18,7 +18,9 @@ if(DOWNLOAD_QUIP)
set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
# quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
@ -56,7 +58,7 @@ if(DOWNLOAD_QUIP)
GIT_SUBMODULES "src/fox;src/GAP"
PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

4
cmake/Modules/Packages/PLUMED.cmake
View File

@ -21,9 +21,9 @@ else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

3
cmake/presets/kokkos-cuda.cmake
View File

@ -9,5 +9,8 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "CUFFT" CACHE STRING FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

3
cmake/presets/kokkos-hip.cmake
View File

@ -12,6 +12,9 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "HIPFFT" CACHE STRING FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

3
doc/Makefile
View File

@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -231,6 +233,7 @@ role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "21 November 2023" "2023-11-21"
.TH LAMMPS "1" "7 February 2024" "2024-02-07"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 21 November 2023
\- Molecular Dynamics Simulator. Version 7 February 2024
.SH SYNOPSIS
.B lmp

78
doc/src/Build_development.rst
View File

@ -122,32 +122,39 @@ Code Coverage and Unit Testing (CMake only)
-------------------------------------------
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
on various platforms and with a variety of settings), unit testing
(i.e. whether certain individual parts of the code produce the expected
results for given inputs), run testing (whether selected complete input
decks run without crashing for multiple configurations), and regression
testing (i.e. whether selected input examples reproduce the same
results over a given number of steps and operations within a given
error margin). The status of this automated testing can be viewed on
`https://ci.lammps.org <https://ci.lammps.org>`_.
during development:
- Integration testing (i.e. whether the code compiles
on various platforms and with a variety of compilers and settings),
- Unit testing (i.e. whether certain functions or classes of the code
produce the expected results for given inputs),
- Run testing (i.e. whether selected input decks can run to completion
without crashing for multiple configurations),
- Regression testing (i.e. whether selected input examples reproduce the
same results over a given number of steps and operations within a
given error margin).
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub.
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
It requires the `YAML <https://pyyaml.org/>`_ library and matching
development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
.. admonition:: Software version requirements for testing
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
The compiler and library version requirements for the testing
@ -155,7 +162,7 @@ for implementing the tests.
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect incompatible versions and either skip incompatible tests or
stop with an error. Also the number of tests will depend on
stop with an error. Also the number of available tests will depend on
installed LAMMPS packages, development environment, operating system,
and configuration settings.
@ -234,12 +241,31 @@ will be skipped if prerequisite features are not available in LAMMPS.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests for styles of the same kind of style (e.g. pair styles or bond
styles) are performed with the same test executable using different
input files in YAML format. So to add a test for another style of the
same kind it may be sufficient to add a suitable YAML file.
:doc:`Detailed instructions for adding tests <Developer_unittest>` are
provided in the Programmer Guide part of the manual.
Tests as shown by the ``ctest`` program are command lines defined in the
``CMakeLists.txt`` files in the ``unittest`` directory tree. A few
tests simply execute LAMMPS with specific command line flags and check
the output to the screen for expected content. A large number of unit
tests are special tests programs using the `GoogleTest framework
<https://github.com/google/googletest/>`_ and linked to the LAMMPS
library that test individual functions or create a LAMMPS class
instance, execute one or more commands and check data inside the LAMMPS
class hierarchy. There are also tests for the C-library, Fortran, and
Python module interfaces to LAMMPS. The Python tests use the Python
"unittest" module in a similar fashion than the others use `GoogleTest`.
These special test programs are structured to perform multiple
individual tests internally and each of those contains several checks
(aka assertions) for internal data being changed as expected.
Tests for force computing or modifying styles (e.g. styles for non-bonded
and bonded interactions and selected fixes) are run by using a more generic
test program that reads its input from files in YAML format. The YAML file
provides the information on how to customized the test program to test
a specific style and - if needed - with specific settings.
To add a test for another, similar style (e.g. a new pair style) it is
usually sufficient to add a suitable YAML file. :doc:`Detailed
instructions for adding tests <Developer_unittest>` are provided in the
Programmer Guide part of the manual. A description of what happens
during the tests is given below.
Unit tests for force styles
^^^^^^^^^^^^^^^^^^^^^^^^^^^

29
doc/src/Build_settings.rst
View File

@ -44,7 +44,7 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS, but other libraries can be faster.
LAMMPS can use them if they are available on your system.
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Alternatively, LAMMPS can use the `heFFTe
<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
@ -59,15 +59,19 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
.. note::
The values for the FFT variable must be in upper-case. This is
an exception to the rule that all CMake variables can be specified
with lower-case values.
When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos,
you must use either CUFFT or KISS.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
@ -106,6 +110,8 @@ libraries and better pipelining for packing and communication.
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
@ -116,6 +122,8 @@ libraries and better pipelining for packing and communication.
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
@ -178,6 +186,11 @@ The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
above).
The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
AMD's HIP installations, respectively. These FFT libraries require the
Kokkos acceleration package to be enabled and the Kokkos back end to be
GPU-resident (i.e., HIP or CUDA).
Performing 3d FFTs in parallel can be time-consuming due to data access
and required communication. This cost can be reduced by performing
single-precision FFTs instead of double precision. Single precision
@ -189,11 +202,11 @@ generally less than the difference in precision. Using the
``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
use and parallel communication costs for transposing 3d FFT data.
When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
library a second time with support for single-precision.
When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
the FFTW3 installation includes support for single-precision.
For FFTW3, do the following, which should produce the additional
library ``libfftw3f.a`` or ``libfftw3f.so``\ .
When compiler FFTW3 from source, you can do the following, which should
produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
.. code-block:: bash

2
doc/src/Commands_bond.rst
View File

@ -124,7 +124,7 @@ OPT.
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`

2
doc/src/Commands_pair.rst
View File

@ -146,7 +146,7 @@ OPT.
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

2
doc/src/Commands_removed.rst
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@ -129,7 +129,7 @@ USER-REAXC.
USER-REAXC package
------------------
.. deprecated:: TBD
.. deprecated:: 7Feb2024
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use

66
doc/src/Developer_updating.rst
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@ -20,6 +20,7 @@ Available topics in mostly chronological order are:
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
@ -196,6 +197,71 @@ New:
fp = utils::open_potential(filename, lmp);
Use symbolic Atom and AtomVec constants instead of numerical values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
Properties in LAMMPS that were represented by integer values (0, 1,
2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
classes derived from it) (and its derived classes) have been converted
to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
Old:
.. code-block:: c++
molecular = 0;
mass_type = 1;
if (atom->molecular == 2)
if (atom->map_style == 2)
atom->add_callback(0);
atom->delete_callback(id,1);
New:
.. code-block:: c++
molecular = Atom::ATOMIC;
mass_type = AtomVec::PER_TYPE;
if (atom->molecular == Atom::TEMPLATE)
if (atom->map_style == Atom::MAP_HASH)
atom->add_callback(Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

45
doc/src/Fortran.rst
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@ -315,6 +315,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_variable: function
:f set_variable: :f:subr:`set_variable`
:ftype set_variable: subroutine
:f set_string_variable: :f:subr:`set_set_string_variable`
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -1398,7 +1402,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Set the value of a string-style variable.
.. versionadded:: 3Nov2022
.. deprecated:: 7Feb2024
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
variable, an error is generated.
.. warning::
This subroutine is deprecated and :f:subr:`set_string_variable`
should be used instead.
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
--------
.. f:subroutine:: set_string_variable(name, str)
Set the value of a string-style variable.
.. versionadded:: 7Feb2024
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
@ -1406,7 +1431,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
:to: :cpp:func:`lammps_set_string_variable`
--------
.. f:subroutine:: set_internal_variable(name, val)
Set the value of a internal-style variable.
.. versionadded:: 7Feb2024
This function assigns a new value from the floating-point number *val* to
the internal-style variable *name*\ . If *name* does not exist or is not
an internal-style variable, an error is generated.
:p character(len=*) name: name of the variable
:p read(c_double) val: new value to assign to the variable
:to: :cpp:func:`lammps_set_internal_variable`
--------

2
doc/src/Howto_cmake.rst
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@ -349,6 +349,8 @@ Some common LAMMPS specific variables
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_KOKKOS``
- select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
* - ``FFT_SINGLE``
- select whether to use single precision FFTs (default: ``off``)
* - ``WITH_JPEG``

7
doc/src/Howto_structured_data.rst
View File

@ -52,8 +52,8 @@ JSON
"ke": 2.4962152903997174569
}
YAML format thermo_style output
===============================
YAML format thermo_style or dump_style output
=============================================
Extracting data from log file
-----------------------------
@ -112,6 +112,9 @@ of that run:
Number of runs: 2
TotEng = -4.62140097780047
Extracting data from dump file
------------------------------
.. versionadded:: 4May2022
YAML format output has been added to multiple commands in LAMMPS,

12
doc/src/Library_objects.rst
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@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
-----------------------
@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_set_string_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_set_internal_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_variable_info
:project: progguide

33
doc/src/Modify_style.rst
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@ -96,6 +96,39 @@ list all non-conforming lines. By adding the `-f` flag to the command
line, they will modify the flagged files to try to remove the detected
issues.
Constants (strongly preferred)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Global or per-file constants should be declared as `static constexpr`
variables rather than via the pre-processor with `#define`. The name of
constants should be all uppercase. This has multiple advantages:
- constants are easily identified as such by their all upper case name
- rather than a pure text substitution during pre-processing, `constexpr
variables` have a type associated with them and are processed later in
the parsing process where the syntax checks and type specific
processing (e.g. via overloads) can be applied to them.
- compilers can emit a warning if the constant is not used and thus can
be removed (we regularly check for and remove dead code like this)
- there are no unexpected substitutions and thus confusing syntax errors
when compiling leading to, for instance, conflicts so that LAMMPS
cannot be compiled with certain combinations of packages (this *has*
happened multiple times in the past).
Pre-processor defines should be limited to macros (but consider C++
templates) and conditional compilation. If a per-processor define must
be used, it should be defined at the top of the .cpp file after the
include statements and at all cost it should be avoided to put them into
header files.
Some sets of commonly used constants are provided in the ``MathConst``
and ``EwaldConst`` namespaces and implemented in the files
``math_const.h`` and ``ewald_const.h``, respectively.
There are always exceptions, special cases, and legacy code in LAMMPS,
so please contact the LAMMPS developers if you are not sure.
Placement of braces (strongly preferred)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

4
doc/src/angle_charmm.rst
View File

@ -70,7 +70,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

19
doc/src/angle_lepton.rst
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@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
angle_style lepton
angle_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
angle_style lepton
angle_style lepton no_offset
angle_coeff 1 120.0 "k*theta^2; k=250.0"
angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@ -41,6 +51,13 @@ angle coefficient. For example `"200.0*theta^2"` represents a
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
.. versionchanged:: 7Feb2024
By default the potential energy U is shifted so that the value U is 0.0
for $theta = theta_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an

614
doc/src/atom_style.rst
View File

@ -49,248 +49,221 @@ Examples
Description
"""""""""""
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
command.
The *atom_style* command selects which per-atom attributes are
associated with atoms in a LAMMPS simulation and thus stored and
communicated with those atoms as well as read from and stored in data
and restart files. Different models (e.g. :doc:`pair styles
<pair_style>`) require access to specific per-atom attributes and thus
require a specific atom style. For example, to compute Coulomb
interactions, the atom must have a "charge" (aka "q") attribute.
A number of distinct atom styles exist that combine attributes. Some
atom styles are a superset of other atom styles. Further attributes
may be added to atoms either via using a hybrid style which provides a
union of the attributes of the sub-styles, or via the :doc:`fix
property/atom <fix_property_atom>` command. The *atom_style* command
must be used before a simulation is setup via a :doc:`read_data
<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
<create_box>` command.
.. note::
Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Many of the atom styles discussed here are only enabled if LAMMPS was
built with a specific package, as listed below in the Restrictions
section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style *bond*, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
Once a style is selected and the simulation box defined, it cannot be
changed but only augmented with the :doc:`fix property/atom
<fix_property_atom>` command. So one should select an atom style
general enough to encompass all attributes required. E.g. with atom
style *bond*, it is not possible to define angles and use angle styles.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the :doc:`read_data <read_data>` command.
It is OK to use a style more general than needed, though it may be
slightly inefficient because it will allocate and communicate
additional unused data.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
Atom style attributes
"""""""""""""""""""""
The atom style *atomic* has the minimum subset of per-atom attributes
and is also the default setting. It encompasses the following per-atom
attributes (name of the vector or array in the :doc:`Atom class
<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
position (x), velocities (v), forces (f), image flags (image), group
membership (mask). Since all atom styles are a superset of atom style
*atomic*\ , they all include these attributes.
This table lists all the available atom styles, which attributes they
provide, which :doc:`package <Packages>` is required to use them, and
what the typical applications are that use them. See the
:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
:doc:`set <set>` commands for info on how to set these various
quantities.
:doc:`set <set>` commands for details on how to set these various
quantities. More information about many of the styles is provided in
the Additional Information section below.
+--------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+--------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+--------------+-----------------------------------------------------+--------------------------------------+
| *atomic* | only the default values | coarse-grain liquids, solids, metals |
+--------------+-----------------------------------------------------+--------------------------------------+
| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bond* | bonds | bead-spring polymers |
+--------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dpd* | internal temperature and internal energies | DPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *edpd* | temperature and heat capacity | eDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+--------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *full* | molecular + charge | bio-molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *line* | end points, angular velocity | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *peri* | mass, volume | mesoscopic Peridynamic models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sph* | rho, esph, cv | SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sphere* | diameter, mass, angular velocity | granular models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
+--------------+-----------------------------------------------------+--------------------------------------+
| *spin* | magnetic moment | system with magnetic particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tdpd* | chemical concentration | tDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *template* | template index, template atom | small molecules with fixed topology |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tri* | corner points, angular momentum | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
+--------------+-----------------------------------------------------+--------------------------------------+
.. list-table::
:header-rows: 1
:widths: auto
* - Atom style
- Attributes
- Required package
- Applications
* - *amoeba*
- *full* + "1-5 special neighbor data"
- :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA/HIPPO force fields
* - *angle*
- *bond* + "angle data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers with stiffness
* - *atomic*
- tag, type, x, v, f, image, mask
-
- atomic liquids, solids, metals
* - *body*
- *atomic* + radius, rmass, angmom, torque, body
- :ref:`BODY <PKG-BODY>`
- arbitrary bodies, see :doc:`body howto <Howto_body>`
* - *bond*
- *atomic* + molecule, nspecial, special + "bond data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers
* - *bpm/sphere*
- *bond* + radius, rmass, omega, torque, quat
- :ref:`BPM <PKG-BPM>`
- granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
* - *charge*
- *atomic* + q
-
- atomic systems with charges
* - *dielectric*
- *full* + mu, area, ed, em, epsilon, curvature, q_scaled
- :ref:`DIELECTRIC <PKG-DIELECTRIC>`
- systems with surface polarization
* - *dipole*
- *charge* + mu
- :ref:`DIPOLE <PKG-DIPOLE>`
- atomic systems with charges and point dipoles
* - *dpd*
- *atomic* + rho + "reactive DPD data"
- :ref:`DPD-REACT <PKG-DPD-REACT>`
- reactive DPD
* - *edpd*
- *atomic* + "eDPD data"
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Energy conservative DPD (eDPD)
* - *electron*
- *charge* + espin, eradius, ervel, erforce
- :ref:`EFF <PKG-EFF>`
- Electron force field systems
* - *ellipsoid*
- *atomic* + rmass, angmom, torque, ellipsoid
-
- aspherical particles
* - *full*
- *molecular* + q
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular force fields
* - *line*
- *atomic* + molecule, radius, rmass, omega, torque, line
-
- 2-d rigid body particles
* - *mdpd*
- *atomic* + rho, drho, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Many-body DPD (mDPD)
* - *molecular*
- *angle* + "dihedral and improper data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- apolar and uncharged molecules
* - *oxdna*
- *atomic* + id5p
- :ref:`CG-DNA <PKG-CG-DNA>`
- coarse-grained DNA and RNA models
* - *peri*
- *atomic* + rmass, vfrac, s0, x0
- :ref:`PERI <PKG-PERI>`
- mesoscopic Peridynamics models
* - *smd*
- *atomic* + molecule, radius, rmass + "smd data"
- :ref:`MACHDYN <PKG-MACHDYN>`
- Smooth Mach Dynamics models
* - *sph*
- *atomic* + "sph data"
- :ref:`SPH <PKG-SPH>`
- Smoothed particle hydrodynamics models
* - *sphere*
- *atomic* + radius, rmass, omega, torque
-
- finite size spherical particles, e.g. granular models
* - *spin*
- *atomic* + "magnetic moment data"
- :ref:`SPIN <PKG-SPIN>`
- magnetic particles
* - *tdpd*
- *atomic* + cc, cc_flux, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Transport DPD (tDPD)
* - *template*
- *atomic* + molecule, molindex, molatom
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular systems where attributes are taken from :doc:`molecule files <molecule>`
* - *tri*
- *sphere* + molecule, angmom, tri
-
- 3-d triangulated rigid body LJ particles
* - *wavepacket*
- *charge* + "wavepacket data"
- :ref:`AWPMD <PKG-AWPMD>`
- Antisymmetrized wave packet MD
.. note::
It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the :doc:`fix property/atom
<fix_property_atom>` command. This command also allows new custom
attributes consisting of extra integer or floating-point values to
be added to atoms. See the :doc:`fix property/atom
<fix_property_atom>` page for examples of cases where this is
useful and details on how to initialize, access, and output the
custom values.
It is possible to add some attributes, such as a molecule ID and
charge, to atom styles that do not have them built in using the
:doc:`fix property/atom <fix_property_atom>` command. This command
also allows new custom-named attributes consisting of extra integer
or floating-point values or vectors to be added to atoms. See the
:doc:`fix property/atom <fix_property_atom>` page for examples of
cases where this is useful and details on how to initialize,
access, and output these custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
*tri*, and *body* styles, which define finite-size particles. See the
:doc:`Howto spherical <Howto_spherical>` page for an overview of using
finite-size particle models with LAMMPS.
----------
All of the point-particle styles assign mass to particles on a
per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
Particle size and mass
""""""""""""""""""""""
For the *sphere* and *bpm/sphere* styles, the particles are spheres
and each stores a per-particle diameter and mass. If the diameter >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by use of the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
spheres can be effectively treated as 2d discs for a 2d simulation if
desired. See also the :doc:`set density/disc <set>` command. These
styles take an optional 0 or 1 argument. A value of 0 means the
radius of each sphere is constant for the duration of the simulation.
A value of 1 means the radii may vary dynamically during the simulation,
e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
All of the atom styles define point particles unless they (1) define
finite-size spherical particles via the *radius* attribute, or (2)
define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
*line*, and *tri* styles). Most of these styles can also be used with
mixtures of point and finite-size particles.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
Note that the *radius* property may need to be provided as a
*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
files <read_data>`). See the :doc:`Howto spherical <Howto_spherical>`
page for an overview of using finite-size spherical and aspherical
particle models with LAMMPS.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
Unless an atom style defines the per-atom *rmass* attribute, particle
masses are defined on a per-type basis, using the :doc:`mass <mass>`
command. This means each particle's mass is indexed by its atom
*type*.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use atom_style hybrid sphere dipole, which will assign both a
diameter and dipole moment to each particle.
A few styles define the per-atom *rmass* attribute which can also be
added using the :doc:`fix property/atom <fix_property_atom>` command.
In this case each particle stores its own mass. Atom styles that have
a per-atom rmass may define it indirectly through setting particle
diameter and density on a per-particle basis. If both per-type mass
and per-atom *rmass* are defined (e.g. in a hybrid style), the
per-atom mass will take precedence in any operation which which works
with both flavors of mass.
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
----------
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *bpm/sphere* style is part of the BPM package.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand. Note that this style is part of the CG-DNA package.
The *dpd* style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the DPD-REACT package, and is not for use with
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity(edpd_cv).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering
density-dependent many-body interactions.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The *sph* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (esph), and heat capacity
(cv).
The *smd* style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetrating each other.
For the *spin* style, a magnetic spin is associated to each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *wavepacket* style is similar to *electron*, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical *etag* values.
For the *line* style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the *tri* style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
*template* style instead of the *bond*, *angle*, *molecular* styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
Additional information about specific atom styles
"""""""""""""""""""""""""""""""""""""""""""""""""
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -309,6 +282,148 @@ Note that there may be additional arguments required along with the
*bstyle* specification, in the atom_style body command. These
arguments are described on the :doc:`Howto body <Howto_body>` doc page.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole vector mu is defined for each
point particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use the command `atom_style hybrid sphere dipole`, which will
assign both a diameter and dipole moment to each particle. This also
requires using an integrator with a "/sphere" suffix like :doc:`fix
nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
and the "update dipole" or "update dlm" parameters to the fix
commands.
The *dpd* style is for reactive dissipative particle dynamics (DPD)
particles. Note that it is part of the DPD-REACT package, and is not
required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
commands, which only require the attributes from atom_style *atomic*.
Atom_style *dpd* extends DPD particle properties with internal
temperature (dpdTheta), internal conductive energy (uCond), internal
mechanical energy (uMech), and internal chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity (edpd_cv).
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the *ellipsoid* style, particles can be ellipsoids which each
stores a shape vector with the 3 diameters of the ellipsoid and a
quaternion 4-vector with its orientation. Each particle stores a flag
in the ellipsoid vector which indicates whether it is an ellipsoid (1)
or a point particle (0).
For the *line* style, particles can be are idealized line segments
which store a per-particle mass and length and orientation (i.e. the
end points of the line segment). Each particle stores a flag in the
line vector which indicates whether it is a line segment (1) or a
point particle (0).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering density-dependent
many-body interactions.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *smd* style is for Smooth Particle Mach dynamics. Both fluids and
solids can be modeled. Particles store the mass and volume of an
integration point, a kernel diameter used for calculating the field
variables (e.g. stress and deformation) and a contact radius for
calculating repulsive forces which prevent individual physical bodies
from penetrating each other.
The *sph* style is for smoothed particle hydrodynamics (SPH) particles
which store a density (rho), energy (esph), and heat capacity (cv).
For the *spin* style, a magnetic spin is associated with each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The *wavepacket* style is similar to the *electron* style, but the
electrons may consist of several Gaussian wave packets, summed up with
coefficients cs= (cs_re,cs_im). Each of the wave packets is treated
as a separate particle in LAMMPS, wave packets belonging to the same
electron must have identical *etag* values.
The *sphere* and *bpm/sphere* styles allow particles to be either point
particles or finite-size particles. If the *radius* attribute is >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by using the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. These styles also
take an optional 0 or 1 argument. A value of 0 means the radius of
each sphere is constant for the duration of the simulation (this is
the default). A value of 1 means the radii may vary dynamically
during the simulation, e.g. due to use of the :doc:`fix adapt
<fix_adapt>` command.
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms only
store a template index and template atom to identify which molecule and
which atom-within-the-molecule they represent. Using the *template*
style instead of the *bond*, *angle*, *molecular* styles can save memory
for systems comprised of a large number of small molecules, all of a
single type (or small number of types). See the paper by Grime and
Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
advantageous for large-scale coarse-grained systems. The
``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
For the *tri* style, particles can be planar triangles which each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle). Each particle stores a flag in the tri
vector which indicates whether it is a triangle (1) or a point
particle (0).
----------
Typically, simulations require only a single (non-hybrid) atom style.
@ -326,11 +441,12 @@ dipole". When a hybrid style is used, atoms store and communicate the
union of all quantities implied by the individual styles.
When using the *hybrid* style, you cannot combine the *template* style
with another molecular style that stores bond,angle,etc info on a
with another molecular style that stores bond, angle, etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see the :doc:`Modify <Modify>` doc page.
LAMMPS can be extended with new atom styles as well as new body styles;
see the corresponding manual page on :doc:`modifying & extending LAMMPS
<Modify_atom>`.
----------
@ -346,54 +462,20 @@ This command cannot be used after the simulation box is defined by a
Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :doc:`Build package
<Build_package>` page for more info.
The *amoeba* style is part of the AMOEBA package.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
The *line* and *tri* styles are part of the ASPHERE package.
The *body* style is part of the BODY package.
The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *oxdna* style is part of the CG-DNA package for coarse-grained
simulation of DNA and RNA.
The *electron* style is part of the EFF package for :doc:`electronic
force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
<Build_package>` page for more info. The table above lists which package
is required for individual atom styles.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
Default
"""""""
The default atom style is atomic. If atom_style sphere is used its
default argument is 0.
The default atom style is *atomic*. If atom_style *sphere* or
*bpm/sphere* is used, its default argument is 0.
----------

4
doc/src/bond_bpm_rotational.rst
View File

@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

4
doc/src/bond_bpm_spring.rst
View File

@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

19
doc/src/bond_lepton.rst
View File

@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
bond_style lepton
bond_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
bond_style lepton
bond_style lepton no_offset
bond_coeff 1 1.5 "k*r^2; k=250.0"
bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@ -40,6 +50,13 @@ constant *K* of 200.0 energy units:
U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
.. versionchanged:: 7Feb2024
By default the potential energy U is shifted so that he value U is 0.0
for $r = r_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical

2
doc/src/compute_pace.rst
View File

@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
This compute calculates a set of quantities related to the atomic
cluster expansion (ACE) descriptors of the atoms in a group. ACE

2
doc/src/compute_rattlers_atom.rst
View File

@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a compute that identifies rattlers in a system. Rattlers are often
identified in granular or glassy packings as under-coordinated atoms that

2
doc/src/compute_reaxff_atom.rst
View File

@ -40,7 +40,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a computation that extracts bond information computed by the ReaxFF
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.

2
doc/src/compute_slcsa_atom.rst
View File

@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Define a computation that performs the Supervised Learning Crystal
Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`

5
doc/src/create_atoms.rst
View File

@ -536,6 +536,11 @@ command.
A rotation vector specified for a single molecule must be in
the z-direction for a 2d model.
For :doc:`molecule templates <molecule>` that are created from multiple
files, i.e. contain multiple molecule *sets*, only the first set is
used. To create multiple molecules the files currently need to be
merged and different molecule IDs assigned with a Molecules section.
Related commands
""""""""""""""""

7
doc/src/dihedral_charmm.rst
View File

@ -3,6 +3,7 @@
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
.. index:: dihedral_style charmmfsw/kk
dihedral_style charmm command
=============================
@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
dihedral_style charmmfsw command
================================
Accelerator Variants: *charmmfsw/kk*
Syntax
""""""
@ -144,7 +147,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

96
doc/src/fix_neb.rst
View File

@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
force/distance units.
With a value of *ideal*, the spring force is computed as suggested in
ref`(WeinanE) <WeinanE>`
:ref:`(WeinanE) <WeinanE>`
.. math::
@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
equally spaced. I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
climbing replica is off, where *i* is the replica number). The
*meanDist* is the average distance between replicas. Note that in this
case the specified *Kspring* is in force units. When the climbing replica
is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
each side of the climbing image. Note that the *ideal* form of nudging
can often be more effective at keeping the replicas equally spaced before
climbing, then equally spaced either side of the climbing image whilst
climbing.
case the specified *Kspring* is in force units. When the climbing
replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
separately each side of the climbing image. Note that the *ideal* form
of nudging can often be more effective at keeping the replicas equally
spaced before climbing, then equally spaced either side of the climbing
image whilst climbing.
With a value of *equal* the spring force is computed as for *ideal*
when the climbing replica is off, promoting equidistance. When the climbing
With a value of *equal* the spring force is computed as for *ideal* when
the climbing replica is off, promoting equidistance. When the climbing
replica is on, the spring force is computed to promote equidistant
absolute differences in energy, rather than distance, each side of
the climbing image:
absolute differences in energy, rather than distance, each side of the
climbing image:
.. math::
@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
*meanEdist* is the average absolute energy difference between
replicas up to the climbing image or from the climbing image
to the final image, for images before or after the climbing
image respectively. :math:`ED_{ideal}` is the corresponding
cumulative sum of average absolute energy differences in
each case, in close analogy to *ideal*. This form of nudging
is to aid schemes which integrate forces along, or near to,
NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
*meanEdist* is the average absolute energy difference between replicas
up to the climbing image or from the climbing image to the final image,
for images before or after the climbing image
respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
average absolute energy differences in each case, in close analogy to
*ideal*. This form of nudging is to aid schemes which integrate forces
along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
----------
The keyword *perp* specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too strongly kinked. It can
The keyword *perp* specifies if and how a perpendicular nudging force is
computed. It adds a spring force perpendicular to the path in order to
prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
:ref:`(Maras) <Maras1>` for details.
resolution is poor. I.e. when few replicas are used; see :ref:`(Maras)
<Maras1>` for details.
The perpendicular spring force is given by
@ -181,10 +180,10 @@ force is added.
By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word *end*, additional
forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy E to the
target energy ETarget.
respective local minima. By using the key word *end*, additional forces
can be applied to the first and/or last replicas, to enable them to
relax toward a MEP while constraining their energy E to the target
energy ETarget.
If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
specified replica becomes:
@ -197,33 +196,33 @@ specified replica becomes:
The "spring" constant on the difference in energies is the specified
*Kspring3* value.
When *estyle* is specified as *first*, the force is applied to the
first replica. When *estyle* is specified as *last*, the force is
applied to the last replica. Note that the *end* keyword can be used
twice to add forces to both the first and last replicas.
When *estyle* is specified as *first*, the force is applied to the first
replica. When *estyle* is specified as *last*, the force is applied to
the last replica. Note that the *end* keyword can be used twice to add
forces to both the first and last replicas.
For both these *estyle* settings, the target energy *ETarget* is set
to the initial energy of the replica (at the start of the NEB
calculation).
If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
force is applied to the last replica, but the target energy *ETarget*
is continuously set to the energy of the first replica, as it evolves
force is applied to the last replica, but the target energy *ETarget* is
continuously set to the energy of the first replica, as it evolves
during the NEB relaxation.
The difference between these two *estyle* options is as follows. When
*estyle* is specified as *last/efirst*, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying *estyle* as *last/efirst/middle* which will alter the
inter-replica force applied to intermediate replicas by removing the
contribution of the gradient to the inter-replica force. This will
only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
inter-replica force applied to the intermediate replicas (neither first
or last). If the initial path is too far from the MEP, an intermediate
replica may relax "faster" and reach a lower energy than the last
replica. In this case the intermediate replica will be relaxing toward
its own local minima. This behavior can be prevented by specifying
*estyle* as *last/efirst/middle* which will alter the inter-replica
force applied to intermediate replicas by removing the contribution of
the gradient to the inter-replica force. This will only be done if a
particular intermediate replica has a lower energy than the first
replica. This should effectively prevent the intermediate replicas from
over-relaxing.
After converging a NEB calculation using an *estyle* of
*last/efirst/middle*, you should check that all intermediate replicas
@ -237,9 +236,10 @@ target energy.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

2
doc/src/fix_nonaffine_displacement.rst
View File

@ -44,7 +44,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 7Feb2024
This fix computes different metrics of the nonaffine displacement of
particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`

2
doc/src/fix_qeq.rst
View File

@ -232,8 +232,6 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These qeq fixes are not compatible with the GPU and USER-INTEL packages.
These qeq fixes will ignore electric field contributions from
:doc:`fix efield <fix_efield>`.

9
doc/src/info.rst
View File

@ -10,7 +10,7 @@ Syntax
info args
* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, or *configuration*
* args = one or more of the following keywords: *out*, *all*, *system*, *memory*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *coeffs*, *styles*, *time*, *accelerator*, *fft* or *configuration*
* *out* values = *screen*, *log*, *append* filename, *overwrite* filename
* *styles* values = *all*, *angle*, *atom*, *bond*, *compute*, *command*, *dump*, *dihedral*, *fix*, *improper*, *integrate*, *kspace*, *minimize*, *pair*, *region*
@ -92,6 +92,13 @@ The *accelerator* category prints out information about compile time
settings of included accelerator support for the GPU, KOKKOS, INTEL,
and OPENMP packages.
.. versionadded:: 7Feb2024
The *fft* category prints out information about the included 3d-FFT
support. This lists the 3d-FFT engine, FFT precision, FFT library
used by the FFT engine. If the KOKKOS package is included, the settings
used for the KOKKOS package are displayed as well.
The *styles* category prints the list of styles available in the
current LAMMPS binary. It supports one of the following options
to control which category of styles is printed out:

5
doc/src/kspace_style.rst
View File

@ -450,7 +450,10 @@ relative RMS error.
For the KOKKOS package, the *pppm/kk* style performs charge
assignment and force interpolation calculations, along with the FFTs
themselves, on the GPU or (optionally) threaded on the CPU when
using OpenMP and FFTW3.
using OpenMP and FFTW3. The specific FFT library is selected using
the FFT_KOKKOS CMake parameter. See the
:doc:`Build settings <Build_settings>` doc page for how to select a
3rd-party FFT library.
----------

138
doc/src/molecule.rst
View File

@ -126,14 +126,50 @@ molecule (header keyword = inertia).
Format of a molecule file
"""""""""""""""""""""""""
The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
.. code-block::
# Water molecule. TIP3P geometry
# header section:
3 atoms
2 bonds
1 angles
# body section:
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
first line of the header and thus of the molecule file is *always*
skipped; it typically contains a description of the file or a comment
from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values
in body particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
.. list-table::
:header-rows: 1
:widths: auto
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
* - Number(s)
- Keyword
- Meaning
- Default Value
* - N
- atoms
- # of atoms N in molecule
- 0
* - Nb
- bonds
- # of bonds Nb in molecule
- 0
* - Na
- angles
- # of angles Na in molecule
- 0
* - Nd
- dihedrals
- # of dihedrals Nd in molecule
- 0
* - Ni
- impropers
- # of impropers Ni in molecule
- 0
* - Nf
- fragments
- # of fragments Nf in molecule
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
* - Mtotal
- mass
- total mass of molecule
- computed
* - Xc Yc Zc
- com
- coordinates of center-of-mass of molecule
- computed
* - Ixx Iyy Izz Ixy Ixz Iyz
- inertia
- 6 components of inertia tensor of molecule
- computed
For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
this quantity itself if needed, assuming the molecules consist of a set
of point particles or finite-size particles (with a non-zero diameter)
that do **not** overlap. If finite-size particles in the molecule
**do** overlap, LAMMPS will not account for the overlap effects when
calculating any of these 3 quantities, so you should pre-compute them
yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@ -188,7 +261,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
----------
.. versionadded:: 7Feb2024
*Dipoles* section:
* one line per atom
* line syntax: ID mux muy muz
* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
This section is only allowed for :doc:`atom styles <atom_style>` that
support particles with point dipoles, e.g. atom_style dipole. If not
listed, the default dipole component of each atom in the molecule is set
to 0.0.
----------
*Masses* section:
* one line per atom

13
doc/src/neb.rst
View File

@ -10,7 +10,7 @@ Syntax
neb etol ftol N1 N2 Nevery file-style arg keyword values
* etol = stopping tolerance for energy (energy units)
* etol = stopping tolerance for energy (dimensionless)
* ftol = stopping tolerance for force (force units)
* N1 = max # of iterations (timesteps) to run initial NEB
* N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@ -89,10 +89,11 @@ potentials, and the starting configuration when the neb command is
issued should be the same for every replica.
In a NEB calculation each replica is connected to other replicas by
inter-replica nudging forces. These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
neb command. The group used to define the fix neb command defines the
NEB atoms which are the only ones that inter-replica springs are
applied to. If the group does not include all atoms, then non-NEB
inter-replica nudging forces. These forces are imposed by the
:doc:`fix neb <fix_neb>` command, which must be used in conjunction
with the neb command. The group used to define the fix neb command
defines the NEB atoms which are the only ones that inter-replica springs
are applied to. If the group does not include all atoms, then non-NEB
atoms have no inter-replica springs and the forces they feel and their
motion is computed in the usual way due only to other atoms within
their replica. Conceptually, the non-NEB atoms provide a background
@ -445,7 +446,7 @@ Related commands
""""""""""""""""
:doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix viscous <fix_viscous>`
:doc:`fix viscous <fix_viscous>`, :doc:`fix neb <fix_neb>`
Default
"""""""

7
doc/src/pair_charmm.rst
View File

@ -16,6 +16,7 @@
.. index:: pair_style lj/charmm/coul/msm/omp
.. index:: pair_style lj/charmmfsw/coul/charmmfsh
.. index:: pair_style lj/charmmfsw/coul/long
.. index:: pair_style lj/charmmfsw/coul/long/kk
pair_style lj/charmm/coul/charmm command
========================================
@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
pair_style lj/charmmfsw/coul/long command
=========================================
Accelerator Variants: *lj/charmmfsw/coul/long/kk*
Syntax
""""""
@ -281,7 +284,9 @@ page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

6
doc/src/pair_lepton.rst
View File

@ -72,7 +72,7 @@ interactions between particles which depend on the distance and have a
cutoff. The potential function must be provided as an expression string
using "r" as the distance variable. With pair style *lepton/coul* one
may additionally reference the charges of the two atoms of the pair with
"qi" and "qj", respectively. With pair style *lepton/coul* one may
"qi" and "qj", respectively. With pair style *lepton/sphere* one may
instead reference the radii of the two atoms of the pair with "radi" and
"radj", respectively; this is half of the diameter that can be set in
:doc:`data files <read_data>` or the :doc:`set command <set>`.
@ -166,8 +166,8 @@ mixing. Thus, expressions for *all* I,J pairs must be specified
explicitly.
Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
option for shifting the energy of the pair interaction so that it is
0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
option for shifting the potential energy of the pair interaction so that
it is 0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
The :doc:`pair_modify table <pair_modify>` options are not relevant for
the these pair styles.

4
doc/src/variable.rst
View File

@ -706,7 +706,7 @@ library. Ceil() is the smallest integer not less than its argument.
Floor() if the largest integer not greater than its argument. Round()
is the nearest integer to its argument.
.. versionadded:: TBD
.. versionadded:: 7Feb2024
The ternary(x,y,z) function is the equivalent of the ternary operator
(? and :) in C or C++. It takes 3 arguments. The first argument is a
@ -1155,7 +1155,7 @@ variable by using the :doc:`compute property/atom
Custom atom properties
----------------------
.. versionadded:: TBD
.. versionadded:: 7Feb2024
Custom atom properties refer to per-atom integer and floating point
vectors or arrays that have been added via the :doc:`fix property/atom

9
doc/utils/sphinx-config/false_positives.txt
View File

@ -125,6 +125,7 @@ antisymmetry
anton
Antonelli
api
apolar
Apoorva
Appl
Appshaw
@ -151,6 +152,7 @@ asphericity
Asq
assignee
assively
associativity
Asta
Astart
Astop
@ -798,6 +800,7 @@ dlabel
dlambda
DLAMMPS
dll
dlm
dlopen
dm
dmax
@ -1015,6 +1018,7 @@ Ercolessi
Erdmann
erf
erfc
erforce
Erhart
erorate
erose
@ -2235,8 +2239,10 @@ Mohd
Mohles
mol
Mol
molatom
molfile
Molfile
molindex
MolPairStyle
moltemplate
momb
@ -2569,6 +2575,7 @@ ns
Ns
Nsample
Nskip
nspecial
Nspecies
nsq
Nstart
@ -3790,6 +3797,7 @@ unimodal
uninstall
unitarg
unitless
unittest
Universite
unix
unmaintained
@ -3877,6 +3885,7 @@ versa
Verstraelen
ves
vflag
vfrac
vhi
vibrational
Vij

4
examples/ASPHERE/dimer/in.dimer
View File

@ -7,7 +7,7 @@ dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
set type 1 mass 1.0
@ -101,4 +101,4 @@ thermo 1000
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

4
examples/ASPHERE/dimer/in.dimer.mp
View File

@ -7,7 +7,7 @@ dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
set type 1 mass 1.0
@ -102,4 +102,4 @@ thermo 1000
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
run 25000

286
examples/ASPHERE/dimer/log.1Feb14.dimer.g++.8
View File

@ -1,286 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD diffusion demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.dimer fix molprop NULL Molecules
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
set type 1 mass 1.0
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Memory usage per processor = 3.1029 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.584346 5.5141254 0 9.0872901 4.4231056
500 15.331515 6.6554832 0 10.411704 4.847642
600 16.953755 7.4794317 0 11.633102 5.2020696
700 16.503256 8.8572339 0 12.900532 5.6694613
800 17.006131 9.877343 0 14.043845 5.5483363
900 17.305927 11.081594 0 15.321546 6.2908201
1000 18.122491 12.126462 0 16.566472 5.7536055
Loop time of 0.185949 on 8 procs for 1000 steps with 200 atoms
Pair time (%) = 0.00187448 (1.00806)
Neigh time (%) = 0.000561714 (0.30208)
Comm time (%) = 0.0652371 (35.0833)
Outpt time (%) = 0.00209856 (1.12857)
Other time (%) = 0.116177 (62.4779)
Nlocal: 25 ave 30 max 20 min
Histogram: 1 0 1 1 0 0 3 1 0 1
Nghost: 28.375 ave 36 max 22 min
Histogram: 1 0 1 2 1 0 2 0 0 1
Neighs: 33.125 ave 45 max 22 min
Histogram: 1 0 2 1 0 1 1 0 1 1
Total # of neighbors = 265
Ave neighs/atom = 1.325
Neighbor list builds = 99
Dangerous builds = 96
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 29929 atoms
set type 2 mass 0.1
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 12759 atoms, new total = 17370
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.dimer
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 17170 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
SRD per actual grid cell = 5.5499
SRD viscosity = 0.235551
big/SRD mass density ratio = 0.142367
# of rescaled SRD velocities = 0
ave/max small velocity = 4.20347 7.72323
ave/max big velocity = 2.64047 6.60911
Memory usage per processor = 7.0395 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.1941672 3369 0.24718395 20.578272 21.467926 9.8944086 13658 56 56 2 664 40320 5625 3369 1.1358997 0 4 0
2000 1.3247909 3390 0.24717547 20.48022 21.467189 6.5341926 13389 48 48 3 1988 40320 5625 3390 1.1814916 0 144 0
3000 1.386904 3355 0.24769415 20.478993 21.512237 6.1207029 13507 45 45 0 2871 40320 5625 3355 1.1657697 0 144 0
4000 1.1567347 3376 0.24573733 20.48052 21.342287 3.5540965 13475 46 46 0 3731 40320 5625 3376 1.1485984 0 144 0
5000 1.2565155 3376 0.24620928 20.447172 21.383276 2.5808161 13267 55 55 0 4559 40320 5625 3376 1.1778096 0 144 0
6000 1.1489985 3375 0.24520477 20.440031 21.296035 7.8204262 13362 59 59 0 5354 40320 5625 3375 1.1530517 0 144 0
7000 1.1608248 3399 0.24587989 20.489854 21.354669 7.9622779 13333 59 59 2 6254 40320 5625 3399 1.1809325 0 144 0
8000 1.1749441 3374 0.24700359 20.576929 21.452262 6.7498405 13495 64 64 0 7134 40320 5625 3374 1.1445035 0 144 0
9000 1.1285085 3405 0.24536183 20.468936 21.309675 5.8959937 13333 60 60 0 8008 40320 5625 3405 1.162836 0 144 0
10000 1.1462675 3425 0.24564758 20.480523 21.334492 7.0047543 13487 45 45 0 8967 40320 5625 3425 1.1881074 0 144 0
11000 1.2854766 3388 0.246088 20.415062 21.372742 7.8508136 13491 60 60 1 9833 40320 5625 3388 1.1698514 0 144 0
12000 1.2926536 3360 0.24602616 20.404345 21.367372 7.9286141 13142 64 64 1 11029 40320 5625 3360 1.1658039 0 161 0
13000 1.2289767 3412 0.24595657 20.44574 21.361328 2.2809592 13162 56 56 1 12018 40320 5625 3412 1.1665531 0 161 0
14000 1.3518235 3380 0.24629055 20.383226 21.390334 8.0062608 13310 59 59 7 13146 40320 5625 3380 1.1733296 0 161 0
15000 1.2971143 3355 0.24671134 20.46053 21.42688 9.7871945 12967 60 60 3 14084 40320 5625 3355 1.1703643 0 161 0
16000 1.4160948 3384 0.2478594 20.471598 21.526589 7.3141215 13123 56 56 1 14929 40320 5625 3384 1.1666782 0 161 0
17000 1.3172038 3391 0.247377 20.503375 21.484692 6.1541908 12957 54 54 0 15778 40320 5625 3391 1.1639931 0 161 0
18000 0.98748293 3369 0.2443499 20.486114 21.221789 4.0981146 13355 50 50 1 17031 40320 5625 3369 1.2083414 0 192 0
19000 1.4619261 3367 0.24867817 20.508564 21.597699 11.68547 13519 58 58 0 18334 40320 5625 3367 1.1667505 0 192 0
20000 1.44087 3391 0.24747923 20.420123 21.493571 4.0409936 13594 67 67 0 19303 40320 5625 3391 1.1869387 0 192 0
21000 1.1155365 3377 0.24474418 20.424957 21.256032 8.4985692 13423 52 52 0 20245 40320 5625 3377 1.1726608 0 192 0
22000 1.2045785 3382 0.24466159 20.351448 21.248859 7.0518674 13271 62 62 0 21128 40320 5625 3382 1.1658557 0 192 0
23000 1.2634616 3378 0.24571326 20.398918 21.340197 6.8382109 13246 61 61 1 22067 40320 5625 3378 1.170196 0 192 0
24000 1.365723 3375 0.24749053 20.477089 21.494552 5.9584152 13017 46 46 1 23017 40320 5625 3375 1.1841192 0 192 0
25000 1.1421045 3367 0.24497142 20.4249 21.275768 10.381661 13049 66 66 1 23907 40320 5625 3367 1.1856767 0 192 0
26000 1.4008939 3340 0.24678624 20.389719 21.433385 7.3799658 12971 53 53 5 24850 40320 5625 3340 1.1713233 0 192 0
27000 1.1835022 3379 0.24522732 20.416284 21.297993 7.2251705 12717 46 46 1 25723 40320 5625 3379 1.1798333 0 192 0
28000 1.0496668 3398 0.24461816 20.463086 21.245087 6.5485338 13385 60 60 0 26990 40320 5625 3398 1.1765205 0 192 0
29000 1.1779927 3453 0.24501083 20.401586 21.27919 4.8540048 13157 77 77 2 28023 40320 5625 3453 1.1741595 0 192 0
30000 1.2277637 3375 0.24554215 20.410652 21.325336 10.087705 12939 72 72 1 28855 40320 5625 3375 1.1627414 0 192 0
31000 1.1575066 3397 0.24504213 20.419566 21.281909 6.4849648 12977 66 66 0 29745 40320 5625 3397 1.1575018 0 192 0
32000 1.1752733 3381 0.2451073 20.41199 21.287569 7.2784509 12971 48 48 0 30561 40320 5625 3381 1.1790395 0 192 0
33000 1.1743895 3370 0.24485514 20.390748 21.265669 9.084299 12810 64 64 0 31342 40320 5625 3370 1.1429061 0 192 0
34000 1.2975876 3377 0.24608262 20.405573 21.372276 10.624304 12610 60 60 1 32140 40320 5625 3377 1.1685718 0 192 0
35000 1.7701252 3356 0.2497356 20.370794 21.689537 7.107766 12983 45 45 8 33862 40320 5625 3356 1.1720964 0 242 0
36000 1.2711521 3393 0.24675748 20.483878 21.430887 8.7087273 13175 60 60 0 34920 40320 5625 3393 1.1796212 0 242 0
37000 1.1140649 3373 0.24450996 20.405711 21.23569 8.0025138 12964 50 50 1 35770 40320 5625 3373 1.1772234 0 242 0
38000 1.3128798 3379 0.24583813 20.372946 21.351041 5.0554655 12939 56 56 1 36679 40320 5625 3379 1.1702949 0 242 0
39000 1.2093703 3365 0.24536578 20.409037 21.310018 5.6243735 12873 62 62 3 37511 40320 5625 3365 1.1751064 0 242 0
40000 1.2095402 3365 0.24485106 20.364207 21.265315 3.9565189 12876 54 54 1 38503 40320 5625 3365 1.1637516 0 242 0
41000 1.1146238 3350 0.24476111 20.427107 21.257502 6.5033046 12656 53 53 0 39313 40320 5625 3350 1.1553197 0 242 0
42000 1.2302245 3370 0.24452048 20.320087 21.236604 10.7363 12676 52 52 1 40108 40320 5625 3370 1.1492163 0 242 0
43000 1.2749689 3404 0.24511103 20.338041 21.287893 9.18604 13057 72 72 1 41014 40320 5625 3404 1.1572511 0 242 0
44000 1.1989211 3385 0.24450633 20.342179 21.235375 7.6714085 13086 52 53 1 41840 40320 5625 3385 1.1530041 0 242 0
45000 1.6465972 3370 0.249994 20.485264 21.711979 7.4908607 12894 58 58 7 43545 40320 5625 3370 1.1978571 0 361 0
46000 1.3082316 3412 0.24665637 20.447473 21.422106 8.9900563 13136 53 53 4 44510 40320 5625 3412 1.1686573 0 361 0
47000 1.2163258 3355 0.24493724 20.366636 21.272799 6.9309438 13020 56 56 0 45414 40320 5625 3355 1.1620943 0 361 0
48000 1.349966 3362 0.24683156 20.431596 21.437321 8.8527164 13044 64 64 1 46260 40320 5625 3362 1.1683452 0 361 0
49000 1.3903769 3347 0.24726403 20.439051 21.474881 5.9250552 13103 58 59 2 49229 40320 5625 3347 1.1924538 0 578 0
50000 1.2737918 3349 0.24563843 20.384723 21.333698 7.2419874 12892 41 41 1 50225 40320 5625 3349 1.1803233 0 578 0
51000 1.2229799 3355 0.24504936 20.371417 21.282537 8.5556146 12912 63 63 0 51096 40320 5625 3355 1.1333843 0 578 0
52000 1.2326547 3386 0.24596384 20.443632 21.361959 6.1757404 12790 66 66 1 52114 40320 5625 3386 1.1685608 0 578 0
53000 1.3695441 3389 0.24696147 20.428294 21.448604 8.7464732 12997 60 60 1 53115 40320 5625 3389 1.1631228 0 578 0
54000 1.0711204 3400 0.24322154 20.325806 21.12379 8.7228921 13005 56 56 0 53913 40320 5625 3400 1.1250986 0 578 0
55000 1.3412565 3360 0.24617922 20.381429 21.380665 6.9489559 12960 46 46 0 55249 40320 5625 3360 1.176467 0 578 0
56000 1.3910761 3355 0.2467942 20.397725 21.434077 6.6762734 12966 65 65 2 56653 40320 5625 3355 1.1715559 0 578 0
57000 1.1177307 3388 0.24424738 20.380176 21.212885 5.5073089 13153 62 62 1 57550 40320 5625 3388 1.1576307 0 578 0
58000 1.3136279 3365 0.24661231 20.439627 21.418279 9.1390284 12799 52 52 1 58366 40320 5625 3365 1.159026 0 578 0
59000 1.2667621 3374 0.24556104 20.383238 21.326976 3.4246418 13127 54 54 1 59170 40320 5625 3374 1.1461442 0 578 0
60000 1.1903121 3326 0.24492127 20.384629 21.271412 6.9439977 13078 47 47 2 60105 40320 5625 3326 1.1665886 0 578 0
61000 1.209313 3362 0.2455341 20.423699 21.324637 9.1212002 13225 61 61 4 61358 40320 5625 3362 1.1725894 0 578 0
62000 1.1720074 3366 0.24476301 20.384522 21.257667 7.7592884 13187 53 54 2 62257 40320 5625 3366 1.1599665 0 578 0
63000 1.2155508 3386 0.24486685 20.361101 21.266686 5.7864126 13090 42 42 0 63137 40320 5625 3386 1.1724234 0 578 0
64000 1.1967326 3379 0.2451834 20.402613 21.294179 4.8815049 13033 48 48 4 64152 40320 5625 3379 1.1818756 0 578 0
65000 1.1732378 3386 0.24500733 20.404824 21.278887 11.381026 12998 59 59 0 65071 40320 5625 3386 1.1625543 0 578 0
66000 1.1960739 3385 0.24407516 20.306852 21.197927 12.17249 12994 61 61 0 65941 40320 5625 3385 1.1826516 0 578 0
67000 1.3468331 3366 0.24657491 20.41164 21.415031 7.8115623 12894 62 62 1 66788 40320 5625 3366 1.1750424 0 578 0
68000 1.0742924 3369 0.24347736 20.345661 21.146009 9.5240252 13065 68 68 2 67665 40320 5625 3369 1.1561575 0 578 0
69000 1.1411254 3380 0.2450544 20.432836 21.282975 8.0392218 13134 49 49 1 68471 40320 5625 3380 1.1405485 0 578 0
70000 1.1585312 3388 0.24435206 20.358871 21.221977 7.5303626 13113 59 59 0 69320 40320 5625 3388 1.1726416 0 578 0
71000 1.3418857 3382 0.24598802 20.364355 21.36406 9.2840877 13265 68 68 0 70522 40320 5625 3382 1.1696767 0 578 0
72000 1.1547857 3388 0.24328952 20.26938 21.129695 7.9643121 13270 50 50 1 71384 40320 5625 3388 1.1647353 0 578 0
73000 1.1114283 3385 0.24397276 20.36102 21.189034 13.168935 13110 62 62 0 72335 40320 5625 3385 1.1625358 0 578 0
74000 1.6120075 3370 0.25009739 20.520013 21.720959 12.065782 12902 51 51 9 73743 40320 5625 3370 1.1873738 0 578 0
75000 1.3271087 3353 0.24600453 20.376798 21.365493 7.5902315 13076 51 51 1 74746 40320 5625 3353 1.1706259 0 578 0
76000 1.1908626 3386 0.2451628 20.405197 21.292389 6.8084086 13124 58 58 1 75702 40320 5625 3386 1.1765809 0 578 0
77000 1.042536 3391 0.24320847 20.345966 21.122655 6.4883579 12846 57 57 0 76930 40320 5625 3391 1.1769829 0 578 0
78000 1.3791243 3355 0.24628683 20.362563 21.390011 9.2397346 12897 56 56 12 78068 40320 5625 3355 1.1905167 0 578 0
79000 1.2058397 3391 0.2453076 20.406614 21.304965 9.7949819 13020 51 51 1 79065 40320 5625 3391 1.1777257 0 578 0
80000 1.0634737 3383 0.24440921 20.434652 21.22694 7.5296946 12973 61 61 2 80029 40320 5625 3383 1.1648017 0 578 0
81000 1.3768966 3373 0.24730623 20.452758 21.478546 7.1508584 13297 56 56 1 81172 40320 5625 3373 1.1740603 0 578 0
82000 1.3348382 3375 0.24680945 20.440946 21.4354 9.3251946 12822 56 56 2 82447 40320 5625 3375 1.1573749 0 578 0
83000 1.2042501 3393 0.24484972 20.368032 21.265198 7.5283729 12990 51 51 0 83344 40320 5625 3393 1.1833162 0 578 0
84000 1.1985223 3405 0.24537841 20.418216 21.311115 7.848856 13189 60 60 0 84147 40320 5625 3405 1.173911 0 578 0
85000 1.1811593 3391 0.24418657 20.32764 21.207604 8.3169438 13303 51 51 0 85022 40320 5625 3391 1.1586027 0 578 0
86000 1.2595689 3385 0.24556774 20.389179 21.327558 8.3808674 12966 56 56 1 85962 40320 5625 3385 1.1617838 0 578 0
87000 1.1419322 3356 0.24399697 20.340397 21.191137 6.8911116 13166 63 63 0 86753 40320 5625 3356 1.1729274 0 578 0
88000 1.275219 3380 0.24586129 20.403015 21.353053 6.838563 12963 56 56 0 87729 40320 5625 3380 1.1511968 0 578 0
89000 1.2794858 3366 0.24507826 20.33183 21.285047 9.3370019 12889 64 64 1 88575 40320 5625 3366 1.1660311 0 578 0
90000 1.0549593 3402 0.24289618 20.309589 21.095533 4.9944605 13076 59 59 1 89560 40320 5625 3402 1.1744335 0 578 0
91000 1.214812 3402 0.24442304 20.323106 21.228141 7.5681019 13229 44 44 1 90440 40320 5625 3402 1.1696689 0 578 0
92000 1.2019714 3374 0.24469176 20.356011 21.25148 7.6728432 13331 64 64 2 91243 40320 5625 3374 1.1678246 0 578 0
93000 1.0964004 3364 0.24364709 20.343931 21.16075 5.9650235 13086 55 55 0 92088 40320 5625 3364 1.1570838 0 578 0
94000 1.1722133 3393 0.24332541 20.259513 21.132812 7.1743779 13206 66 66 0 92858 40320 5625 3393 1.154328 0 578 0
95000 1.2413711 3373 0.24549874 20.396744 21.321566 8.131371 12967 61 61 1 93789 40320 5625 3373 1.1635681 0 578 0
96000 1.1702409 3363 0.24528289 20.430989 21.302819 11.399295 12776 63 63 0 94571 40320 5625 3363 1.1367365 0 578 0
97000 1.0696537 3368 0.242673 20.279258 21.07615 8.537175 13054 55 55 0 95403 40320 5625 3368 1.1648141 0 578 0
98000 1.1635952 3369 0.24486659 20.399785 21.266664 8.6714443 12750 70 70 0 96296 40320 5625 3369 1.1686272 0 578 0
99000 1.1286255 3397 0.24343772 20.30174 21.142566 6.7153212 12810 44 45 1 97021 40320 5625 3397 1.137818 0 578 0
100000 1.2847818 3367 0.24509282 20.329149 21.286312 8.7486629 13260 64 64 0 97855 40320 5625 3367 1.1597138 0 578 0
Loop time of 20.8136 on 8 procs for 100000 steps with 17370 atoms
Pair time (%) = 0.322913 (1.55145)
Neigh time (%) = 1.11753 (5.36921)
Comm time (%) = 1.72335 (8.27991)
Outpt time (%) = 0.00594518 (0.0285638)
Other time (%) = 17.6439 (84.7709)
Nlocal: 2171.25 ave 2428 max 1747 min
Histogram: 1 0 0 0 1 1 2 1 0 2
Nghost: 61.25 ave 69 max 54 min
Histogram: 1 1 0 1 1 1 0 2 0 1
Neighs: 175.625 ave 225 max 132 min
Histogram: 1 1 1 1 1 0 1 0 0 2
Total # of neighbors = 1405
Ave neighs/atom = 0.0808866
Neighbor list builds = 5156
Dangerous builds = 1
Please see the log.cite file for references relevant to this simulation

237
examples/ASPHERE/dimer/log.1Feb14.dimer.mp.g++.8
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@ -1,237 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD viscosity demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.dimer fix molprop NULL Molecules
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
set type 1 mass 1.0
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Memory usage per processor = 3.1029 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.584346 5.5141254 0 9.0872901 4.4231056
500 15.331515 6.6554832 0 10.411704 4.847642
600 16.953755 7.4794317 0 11.633102 5.2020696
700 16.503256 8.8572339 0 12.900532 5.6694613
800 17.006131 9.877343 0 14.043845 5.5483363
900 17.305927 11.081594 0 15.321546 6.2908201
1000 18.122491 12.126462 0 16.566472 5.7536055
Loop time of 0.0603173 on 8 procs for 1000 steps with 200 atoms
Pair time (%) = 0.00182396 (3.02395)
Neigh time (%) = 0.000557959 (0.92504)
Comm time (%) = 0.0127766 (21.1823)
Outpt time (%) = 0.000280827 (0.465583)
Other time (%) = 0.0448779 (74.4031)
Nlocal: 25 ave 30 max 20 min
Histogram: 1 0 1 1 0 0 3 1 0 1
Nghost: 28.375 ave 36 max 22 min
Histogram: 1 0 1 2 1 0 2 0 0 1
Neighs: 33.125 ave 45 max 22 min
Histogram: 1 0 2 1 0 1 1 0 1 1
Total # of neighbors = 265
Ave neighs/atom = 1.325
Neighbor list builds = 99
Dangerous builds = 96
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 29929 atoms
set type 2 mass 0.1
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 12759 atoms, new total = 17370
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 500 dump.dimer.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
SRD info:
SRD/big particles = 17170 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
SRD per actual grid cell = 5.5499
SRD viscosity = 0.235551
big/SRD mass density ratio = 0.142367
# of rescaled SRD velocities = 0
ave/max small velocity = 4.20347 7.72323
ave/max big velocity = 2.64047 6.60911
Memory usage per processor = 7.0395 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.906187 3319 0.25279446 20.53509 21.955199 9.3471734 14560 77 77 9 6051 40320 5625 3319 1.2073941 0 1062 0
2000 1.6009081 3420 0.25060769 20.572601 21.765278 12.835365 13521 63 63 1 7515 40320 5625 3420 1.1621445 0 1062 0
3000 1.8288965 3342 0.25195284 20.519576 21.882104 7.1720562 13550 62 62 1 8561 40320 5625 3342 1.1411375 0 1062 0
4000 1.8940522 3383 0.25185767 20.462769 21.873838 7.3011842 13210 55 55 0 9536 40320 5625 3383 1.1541274 0 1062 0
5000 1.7848964 3377 0.25063675 20.438054 21.767801 5.7235852 13258 60 60 1 10628 40320 5625 3377 1.1401366 0 1062 0
6000 2.0436442 3393 0.2528503 20.437534 21.960048 4.3266887 13369 65 65 1 11693 40320 5625 3393 1.1363335 0 1062 0
7000 2.0248598 3377 0.25304247 20.468218 21.976738 9.1535003 13126 69 69 2 12819 40320 5625 3377 1.1556137 0 1062 0
8000 1.9627172 3397 0.25201977 20.425693 21.887917 7.9563872 13216 58 58 3 14113 40320 5625 3397 1.144738 0 1062 0
9000 2.4805409 3385 0.25688024 20.462046 22.310049 6.0178529 13031 42 42 1 15329 40320 5625 3385 1.1667813 0 1062 0
10000 2.534712 3377 0.25802283 20.520922 22.409283 5.8494568 12804 49 50 1 16835 40320 5625 3377 1.1559636 0 1062 0
11000 2.4295377 3368 0.25671703 20.485869 22.295874 7.0797587 13097 56 56 2 18180 40320 5625 3368 1.1634145 0 1062 0
12000 2.5699389 3377 0.25784825 20.479516 22.39412 10.440503 13263 63 63 5 19848 40320 5625 3377 1.1714081 0 1062 0
13000 2.5416625 3359 0.25893582 20.595038 22.488576 6.823793 12926 57 57 1 21307 40320 5625 3359 1.1478982 0 1062 0
14000 2.9400702 3353 0.26140738 20.512878 22.703231 10.592709 12848 67 67 0 22782 40320 5625 3353 1.1642018 0 1062 0
15000 2.7315042 3364 0.26050572 20.589951 22.624922 7.6633608 12640 49 49 0 24273 40320 5625 3364 1.1532394 0 1062 0
16000 2.7176527 3389 0.25840703 20.418 22.442651 8.0150175 13019 59 59 1 25970 40320 5625 3389 1.1555937 0 1062 0
17000 2.883266 3355 0.26040537 20.468173 22.616206 6.053208 12916 54 54 1 27532 40320 5625 3355 1.1363169 0 1062 0
18000 2.8072496 3369 0.26013039 20.500924 22.592325 5.7179969 12989 45 45 0 29011 40320 5625 3369 1.1341799 0 1062 0
19000 2.8007066 3372 0.2602809 20.51887 22.605396 8.9063895 12817 59 59 1 30504 40320 5625 3372 1.1253001 0 1062 0
20000 3.0147455 3352 0.26233709 20.537991 22.783977 10.01786 13099 63 63 2 32100 40320 5625 3352 1.1263738 0 1062 0
21000 2.5502874 3354 0.25762968 20.475174 22.375138 7.4525361 12917 55 55 3 33904 40320 5625 3354 1.1432482 0 1062 0
22000 2.5643661 3357 0.25754499 20.45733 22.367782 9.5567227 12893 58 58 0 35500 40320 5625 3357 1.1309581 0 1062 0
23000 2.8451307 3387 0.26090715 20.540164 22.659786 7.8308779 12735 65 65 2 37080 40320 5625 3387 1.1666359 0 1062 0
24000 2.6241046 3341 0.25916876 20.553849 22.508807 9.7905794 12815 54 54 1 38864 40320 5625 3341 1.1422596 0 1062 0
25000 2.6054468 3374 0.25897446 20.550874 22.491932 9.4099539 13094 59 59 4 40505 40320 5625 3374 1.1887482 0 1062 0
26000 3.1370949 3356 0.26301193 20.50545 22.842586 9.930938 12785 59 59 0 42126 40320 5625 3356 1.1539158 0 1062 0
27000 2.757373 3361 0.26029623 20.552484 22.606727 7.4336931 12687 59 59 2 43728 40320 5625 3361 1.1408006 0 1062 0
28000 2.9939441 3393 0.26250984 20.568491 22.79898 9.201853 12802 66 66 0 45174 40320 5625 3393 1.1429688 0 1062 0
29000 3.1611971 3376 0.26252235 20.444974 22.800066 8.2146139 13042 48 48 0 46696 40320 5625 3376 1.1370708 0 1062 0
30000 2.2624796 3374 0.25475303 20.439753 22.125301 9.3304907 13249 53 53 1 48164 40320 5625 3374 1.1062325 0 1062 0
31000 2.6864602 3393 0.2607928 20.648442 22.649855 7.6108593 13028 58 58 0 49556 40320 5625 3393 1.1154125 0 1062 0
32000 2.8404087 3377 0.26037369 20.497351 22.613455 6.9017135 13055 63 63 1 51004 40320 5625 3377 1.1320087 0 1062 0
33000 2.8467378 3365 0.26095982 20.543541 22.664361 7.194747 13306 58 58 0 52481 40320 5625 3365 1.1312548 0 1062 0
34000 3.0833296 3382 0.26259198 20.509033 22.806114 7.44833 12988 59 60 1 54049 40320 5625 3382 1.1447344 0 1062 0
35000 3.1068536 3382 0.26441995 20.650266 22.964872 9.3804156 13139 54 54 0 55749 40320 5625 3382 1.1272861 0 1062 0
36000 2.6998442 3369 0.25864735 20.452138 22.463522 6.3327985 13317 52 52 0 57348 40320 5625 3369 1.1312386 0 1062 0
37000 2.600171 3376 0.25882039 20.541424 22.478551 9.3909788 12841 57 57 0 58880 40320 5625 3376 1.1319429 0 1062 0
38000 2.3962821 3367 0.25728672 20.560122 22.345352 7.4364329 13039 66 66 0 60627 40320 5625 3367 1.1468141 0 1062 0
39000 2.8548804 3422 0.26044489 20.492753 22.619638 6.0832552 13249 50 50 0 62327 40320 5625 3422 1.1442726 0 1062 0
40000 2.7721124 3375 0.25927374 20.452701 22.517924 10.368128 13197 55 55 1 63903 40320 5625 3375 1.140807 0 1062 0
41000 3.0463159 3378 0.26123216 20.418508 22.688013 10.179554 13030 64 64 0 65629 40320 5625 3378 1.1277894 0 1062 0
42000 2.9625288 3388 0.26205988 20.552817 22.759901 8.8326646 12958 64 64 0 67242 40320 5625 3388 1.159201 0 1062 0
43000 2.7524867 3347 0.2592403 20.464417 22.51502 10.30221 12815 65 65 2 68734 40320 5625 3347 1.1444123 0 1062 0
44000 2.8779981 3354 0.26009923 20.44551 22.589618 12.127509 12743 67 67 3 70309 40320 5625 3354 1.1467915 0 1062 0
45000 2.7833999 3365 0.25968205 20.479753 22.553386 8.6942365 12909 46 47 0 71846 40320 5625 3365 1.1480348 0 1062 0
46000 2.6564678 3370 0.25935897 20.546258 22.525327 9.2618375 12923 61 61 1 73491 40320 5625 3370 1.1528284 0 1062 0
47000 2.821625 3414 0.25999655 20.47859 22.5807 7.5359036 12861 55 55 2 75201 40320 5625 3414 1.1395745 0 1062 0
48000 2.9301623 3351 0.26139433 20.519127 22.702098 9.5177842 13037 49 49 2 76819 40320 5625 3351 1.1472505 0 1062 0
49000 2.528824 3390 0.25834586 20.553364 22.437338 8.953785 13127 49 49 0 78450 40320 5625 3390 1.1495903 0 1062 0
50000 3.0054471 3375 0.261046 20.432787 22.671845 7.9749959 13089 56 56 2 80717 40320 5625 3375 1.1574724 0 1062 0
Loop time of 10.5055 on 8 procs for 50000 steps with 17370 atoms
Pair time (%) = 0.156617 (1.49081)
Neigh time (%) = 0.556925 (5.30126)
Comm time (%) = 0.902042 (8.58637)
Outpt time (%) = 0.00305247 (0.0290559)
Other time (%) = 8.88688 (84.5925)
Nlocal: 2171.25 ave 2567 max 1849 min
Histogram: 2 0 0 1 1 2 1 0 0 1
Nghost: 62.625 ave 71 max 57 min
Histogram: 2 0 1 0 2 2 0 0 0 1
Neighs: 168.25 ave 232 max 120 min
Histogram: 1 0 1 2 2 1 0 0 0 1
Total # of neighbors = 1346
Ave neighs/atom = 0.0774899
Neighbor list builds = 2599
Dangerous builds = 17
Please see the log.cite file for references relevant to this simulation

312
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 27 27 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.576837 5.5141059 0 9.0854309 4.422762
500 15.227825 6.6472106 0 10.378028 4.8598912
600 16.93219 7.454865 0 11.603251 5.2908894
700 16.573769 8.7323442 0 12.792918 5.3544684
800 17.482599 9.7221047 0 14.005341 5.6200973
900 18.548144 10.739353 0 15.283649 4.7817995
1000 18.068079 12.058417 0 16.485096 6.5773091
Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms
Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0095507 | 0.0095507 | 0.0095507 | 0.0 | 18.69
Neigh | 0.0042239 | 0.0042239 | 0.0042239 | 0.0 | 8.26
Comm | 0.002203 | 0.002203 | 0.002203 | 0.0 | 4.31
Output | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 | 0.0 | 0.17
Modify | 0.03336 | 0.03336 | 0.03336 | 0.0 | 65.27
Other | | 0.001685 | | | 3.30
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 275 ave 275 max 275 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 29929 atoms
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
create_atoms CPU = 0.007 seconds
set type 2 mass 0.1
Setting atom values ...
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.dimer
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 17153 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
SRD per actual grid cell = 5.544404
SRD viscosity = 0.23553122
big/SRD mass density ratio = 0.14250828
# of rescaled SRD velocities = 0
ave/max small velocity = 4.191188 7.6900178
ave/max big velocity = 2.6813242 7.1846104
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 18.683304, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.2285566 3375 0.24673495 20.492683 21.407958 5.237464 13477 54 54 1 652 16900 5625 3375 1.1653557 0 15 0
2000 1.3561011 3395 0.24763991 20.476182 21.486477 9.2878509 13435 67 67 0 1504 16900 5625 3395 1.1651182 0 15 0
3000 1.2445369 3352 0.24713723 20.515681 21.442861 8.0289529 13186 62 63 2 2379 16900 5625 3352 1.1746721 0 15 0
4000 1.1058201 3389 0.24596239 20.51709 21.340926 10.003266 13466 66 66 0 3264 16900 5625 3389 1.1671415 0 15 0
5000 1.0584198 3407 0.24539623 20.503281 21.291804 9.1119405 13254 64 64 0 4189 16900 5625 3407 1.1687685 0 15 0
6000 1.3335611 3360 0.24737788 20.470239 21.463742 8.6885126 13281 62 62 1 5031 16900 5625 3360 1.1568996 0 15 0
7000 1.1384759 3401 0.24570869 20.47075 21.318914 9.1801119 13059 47 47 1 5878 16900 5625 3401 1.182474 0 15 0
8000 1.2982334 3397 0.24667224 20.435333 21.402517 6.5904007 13405 56 56 0 6729 16900 5625 3397 1.169017 0 24 0
9000 1.0456752 3381 0.24504517 20.482316 21.261344 10.497413 13205 81 81 2 7706 16900 5625 3381 1.1694675 0 24 0
10000 1.2222547 3394 0.24653264 20.479825 21.390405 8.7495888 13296 68 68 1 8581 16900 5625 3394 1.1613437 0 24 0
Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms
Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14497 | 0.14497 | 0.14497 | 0.0 | 2.02
Neigh | 0.031835 | 0.031835 | 0.031835 | 0.0 | 0.44
Comm | 0.094201 | 0.094201 | 0.094201 | 0.0 | 1.31
Output | 0.00082765 | 0.00082765 | 0.00082765 | 0.0 | 0.01
Modify | 6.8507 | 6.8507 | 6.8507 | 0.0 | 95.35
Other | | 0.06259 | | | 0.87
Nlocal: 17353 ave 17353 max 17353 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1334 ave 1334 max 1334 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1334
Ave neighs/atom = 0.076874316
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:07

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 27 27 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.576837 5.5141059 0 9.0854309 4.422762
500 15.227825 6.6472106 0 10.378028 4.8598912
600 16.93219 7.454865 0 11.603251 5.2908894
700 16.573769 8.7323442 0 12.792918 5.3544684
800 17.482599 9.7221047 0 14.005341 5.6200973
900 18.548144 10.739353 0 15.283649 4.7817995
1000 18.068079 12.058417 0 16.485096 6.5773093
Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms
Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0022758 | 0.0023448 | 0.002442 | 0.1 | 5.52
Neigh | 0.0011082 | 0.0011236 | 0.0011582 | 0.1 | 2.64
Comm | 0.0099484 | 0.010092 | 0.010247 | 0.1 | 23.76
Output | 9.551e-05 | 0.00010604 | 0.00013381 | 0.0 | 0.25
Modify | 0.026025 | 0.026222 | 0.026405 | 0.1 | 61.73
Other | | 0.00259 | | | 6.10
Nlocal: 50 ave 55 max 47 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 33.75 ave 38 max 32 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 68.75 ave 77 max 64 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 29929 atoms
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
create_atoms CPU = 0.002 seconds
set type 2 mass 0.1
Setting atom values ...
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.dimer
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 17153 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
SRD per actual grid cell = 5.544404
SRD viscosity = 0.23553122
big/SRD mass density ratio = 0.14250828
# of rescaled SRD velocities = 0
ave/max small velocity = 4.191188 7.6900178
ave/max big velocity = 2.6813242 7.1846103
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 18.683304, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.1648085 3389 0.24643931 20.514525 21.382307 5.5927686 13390 59 59 0 1015 28224 5625 3389 1.1513276 0 111 0
2000 1.1870311 3385 0.24701637 20.548037 21.432375 5.9269821 13271 57 57 2 1878 28224 5625 3385 1.1619099 0 111 0
3000 1.1362839 3365 0.24577276 20.477942 21.324474 5.1621045 13244 59 60 1 2778 28224 5625 3365 1.1807679 0 111 0
4000 1.3023748 3390 0.24679509 20.442907 21.413176 5.6127077 13413 65 65 1 3705 28224 5625 3390 1.1726946 0 111 0
5000 1.195496 3387 0.2458055 20.43667 21.327314 6.1843476 13248 51 51 1 4638 28224 5625 3387 1.1730279 0 111 0
6000 1.2389419 3387 0.24546635 20.374876 21.297888 5.5909826 13184 54 54 1 5494 28224 5625 3387 1.1859134 0 111 0
7000 1.2068912 3378 0.24564722 20.414447 21.313581 8.5604547 13188 57 57 1 6428 28224 5625 3378 1.1499181 0 111 0
8000 1.1014154 3374 0.24514746 20.449665 21.270219 7.3483529 13179 63 63 0 7591 28224 5625 3374 1.1769322 0 121 0
9000 1.356464 3388 0.24749513 20.463349 21.473915 7.6809833 13138 50 50 2 8485 28224 5625 3388 1.1448659 0 121 0
10000 1.1632951 3402 0.24560819 20.44354 21.310195 9.5738599 13323 64 67 0 9304 28224 5625 3402 1.1550136 0 121 0
Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms
Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037524 | 0.039903 | 0.042215 | 1.1 | 1.61
Neigh | 0.01053 | 0.010805 | 0.011068 | 0.2 | 0.44
Comm | 0.14536 | 0.14822 | 0.15102 | 0.6 | 6.00
Output | 0.00051847 | 0.00054674 | 0.0006272 | 0.0 | 0.02
Modify | 2.2276 | 2.2334 | 2.2381 | 0.3 | 90.35
Other | | 0.03895 | | | 1.58
Nlocal: 4338.25 ave 4488 max 4277 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 76.75 ave 85 max 69 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 331.25 ave 355 max 306 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1325
Ave neighs/atom = 0.076355673
Neighbor list builds = 507
Dangerous builds = 0
Total wall time: 0:00:02

328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.1 Normal file
View File

@ -0,0 +1,328 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 27 27 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.576837 5.5141059 0 9.0854309 4.422762
500 15.227825 6.6472106 0 10.378028 4.8598912
600 16.93219 7.454865 0 11.603251 5.2908894
700 16.573769 8.7323442 0 12.792918 5.3544684
800 17.482599 9.7221047 0 14.005341 5.6200973
900 18.548144 10.739353 0 15.283649 4.7817995
1000 18.068079 12.058417 0 16.485096 6.5773091
Loop time of 0.0502552 on 1 procs for 1000 steps with 200 atoms
Performance: 8596132.389 tau/day, 19898.455 timesteps/s, 3.980 Matom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0095071 | 0.0095071 | 0.0095071 | 0.0 | 18.92
Neigh | 0.0042809 | 0.0042809 | 0.0042809 | 0.0 | 8.52
Comm | 0.0022049 | 0.0022049 | 0.0022049 | 0.0 | 4.39
Output | 0.0001259 | 0.0001259 | 0.0001259 | 0.0 | 0.25
Modify | 0.032467 | 0.032467 | 0.032467 | 0.0 | 64.60
Other | | 0.00167 | | | 3.32
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 275 ave 275 max 275 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 29929 atoms
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
create_atoms CPU = 0.006 seconds
set type 2 mass 0.1
Setting atom values ...
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 500 dump.dimer.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 25000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 17153 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
SRD per actual grid cell = 5.544404
SRD viscosity = 0.23553122
big/SRD mass density ratio = 0.14250828
# of rescaled SRD velocities = 0
ave/max small velocity = 4.191188 7.6900178
ave/max big velocity = 2.6813242 7.1846104
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 18.683304, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.3421139 3394 0.24797209 20.515424 21.515299 5.9986227 13474 52 52 1 704 16900 5625 3394 1.1328453 0 14 0
2000 1.3372296 3366 0.24694513 20.429958 21.426194 9.640193 13302 74 74 0 1516 16900 5625 3366 1.1634167 0 14 0
3000 1.4022742 3360 0.24799552 20.472637 21.517331 5.9446731 13483 47 47 0 2989 16900 5625 3360 1.1774442 0 217 0
4000 1.6325677 3376 0.25066282 20.532497 21.74876 6.9698781 13206 61 61 2 4198 16900 5625 3376 1.1749717 0 217 0
5000 2.0992887 3391 0.25484065 20.547279 22.111249 10.648531 13414 62 69 1 6389 16900 5625 3391 1.1862903 0 412 0
6000 1.7584548 3388 0.25126127 20.490636 21.800684 8.68036 13456 58 58 0 7672 16900 5625 3388 1.1553986 0 412 0
7000 2.2384486 3343 0.25650382 20.58791 22.255554 12.008146 13187 59 59 0 8879 16900 5625 3343 1.1728994 0 412 0
8000 2.4981644 3380 0.25734806 20.467672 22.328804 6.7156077 13383 51 51 0 10085 16900 5625 3380 1.156205 0 412 0
9000 2.4321991 3384 0.25838085 20.606426 22.418415 9.9820399 12847 55 55 0 11445 16900 5625 3384 1.156145 0 412 0
10000 2.2560205 3387 0.25541566 20.480404 22.161139 10.87418 13022 66 66 0 12863 16900 5625 3387 1.1559136 0 412 0
11000 2.2321955 3378 0.25533735 20.491359 22.154345 8.510825 13175 70 70 1 14273 16900 5625 3378 1.1470284 0 412 0
12000 2.2715125 3377 0.25469529 20.40636 22.098637 9.0604601 13146 68 68 0 15742 16900 5625 3377 1.171755 0 412 0
13000 2.3766974 3364 0.25667348 20.499635 22.270275 10.766786 12829 60 60 1 17214 16900 5625 3364 1.130354 0 412 0
14000 2.5659704 3347 0.25802994 20.47632 22.387967 8.2568074 13090 66 66 1 18767 16900 5625 3347 1.1609852 0 412 0
15000 2.3235671 3400 0.25603152 20.483517 22.214574 5.4785711 13389 50 50 0 20173 16900 5625 3400 1.149754 0 412 0
16000 2.6335413 3373 0.25956137 20.558854 22.520843 4.7121947 13027 58 58 1 21668 16900 5625 3373 1.1308267 0 412 0
17000 2.5603168 3410 0.25744829 20.430065 22.337501 6.1898616 13218 51 51 1 23170 16900 5625 3410 1.1285699 0 412 0
18000 2.7801428 3362 0.26002524 20.489884 22.56109 8.9919312 13002 57 57 3 24829 16900 5625 3362 1.1610153 0 412 0
19000 2.7869738 3364 0.26033026 20.51126 22.587555 9.6539159 13085 46 46 0 26476 16900 5625 3364 1.1431913 0 412 0
20000 2.678182 3383 0.2586317 20.444934 22.44018 7.3468277 12939 42 42 0 27992 16900 5625 3383 1.143534 0 412 0
21000 2.8094503 3375 0.26088069 20.542272 22.635313 8.2257869 13449 52 52 0 29570 16900 5625 3375 1.1375499 0 412 0
22000 3.2220363 3377 0.26464914 20.561866 22.962283 6.6329375 13178 65 65 6 31203 16900 5625 3377 1.1683184 0 412 0
23000 3.2268368 3339 0.26414495 20.514543 22.918536 4.6879815 12589 51 51 0 32929 16900 5625 3339 1.1378613 0 412 0
24000 2.6062461 3380 0.25967238 20.588821 22.530474 10.036449 12745 53 54 0 34460 16900 5625 3380 1.1396017 0 412 0
25000 3.2519674 3373 0.26376614 20.462953 22.885669 7.7592712 12856 52 52 1 36172 16900 5625 3373 1.1858891 0 412 0
Loop time of 20.7208 on 1 procs for 25000 steps with 17353 atoms
Performance: 104243.242 tau/day, 1206.519 timesteps/s, 20.937 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39343 | 0.39343 | 0.39343 | 0.0 | 1.90
Neigh | 0.09039 | 0.09039 | 0.09039 | 0.0 | 0.44
Comm | 0.26483 | 0.26483 | 0.26483 | 0.0 | 1.28
Output | 0.0021023 | 0.0021023 | 0.0021023 | 0.0 | 0.01
Modify | 19.785 | 19.785 | 19.785 | 0.0 | 95.49
Other | | 0.1847 | | | 0.89
Nlocal: 17353 ave 17353 max 17353 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 146 ave 146 max 146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1326 ave 1326 max 1326 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1326
Ave neighs/atom = 0.0764133
Neighbor list builds = 1290
Dangerous builds = 0
Total wall time: 0:00:21

328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.4 Normal file
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@ -0,0 +1,328 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - dimer particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.dimer fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
200 settings made for mass
group big type 1
200 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 27 27 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.576837 5.5141059 0 9.0854309 4.422762
500 15.227825 6.6472106 0 10.378028 4.8598912
600 16.93219 7.454865 0 11.603251 5.2908894
700 16.573769 8.7323442 0 12.792918 5.3544684
800 17.482599 9.7221047 0 14.005341 5.6200973
900 18.548144 10.739353 0 15.283649 4.7817995
1000 18.068079 12.058417 0 16.485096 6.5773093
Loop time of 0.0421376 on 4 procs for 1000 steps with 200 atoms
Performance: 10252121.014 tau/day, 23731.762 timesteps/s, 4.746 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.002222 | 0.0023177 | 0.0024199 | 0.2 | 5.50
Neigh | 0.0010943 | 0.0011428 | 0.001174 | 0.1 | 2.71
Comm | 0.0097533 | 0.009878 | 0.010001 | 0.1 | 23.44
Output | 9.4323e-05 | 0.0001028 | 0.00012783 | 0.0 | 0.24
Modify | 0.02557 | 0.026225 | 0.026638 | 0.3 | 62.24
Other | | 0.002471 | | | 5.86
Nlocal: 50 ave 55 max 47 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 33.75 ave 38 max 32 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 68.75 ave 77 max 64 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 29929 atoms
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
create_atoms CPU = 0.002 seconds
set type 2 mass 0.1
Setting atom values ...
29929 settings made for mass
group small type 2
29929 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 500 dump.dimer.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 25000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 17153 200
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
SRD per actual grid cell = 5.544404
SRD viscosity = 0.23553122
big/SRD mass density ratio = 0.14250828
# of rescaled SRD velocities = 0
ave/max small velocity = 4.191188 7.6900178
ave/max big velocity = 2.6813242 7.1846103
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 18.683304, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.2739082 3360 0.24704957 20.486195 21.435256 3.6693454 13497 46 46 2 816 28224 5625 3360 1.1564821 0 54 0
2000 1.3843858 3380 0.24759985 20.451634 21.483001 5.2299666 13363 70 70 0 1671 28224 5625 3380 1.170199 0 54 0
3000 1.3942166 3373 0.24823326 20.499268 21.537959 7.7943821 13214 59 59 2 2600 28224 5625 3373 1.1539593 0 54 0
4000 1.6387342 3366 0.24966206 20.441071 21.661928 4.3859226 13280 49 49 2 3568 28224 5625 3366 1.176006 0 54 0
5000 1.8677297 3388 0.25278915 20.541792 21.933251 5.9053775 13238 68 68 2 4553 28224 5625 3388 1.1728833 0 54 0
6000 1.8884914 3372 0.25216944 20.472555 21.879481 7.5864922 13142 62 62 1 5645 28224 5625 3372 1.1733967 0 54 0
7000 2.0575519 3387 0.25374609 20.483403 22.016279 6.9842803 13101 41 41 0 6805 28224 5625 3387 1.1503024 0 54 0
8000 1.9800593 3373 0.252975 20.474232 21.949376 8.3493951 13176 63 64 1 8166 28224 5625 3373 1.1621339 0 67 0
9000 2.2288114 3403 0.25526729 20.487802 22.148267 6.7676677 12866 61 61 1 9360 28224 5625 3403 1.1446891 0 67 0
10000 2.4854456 3339 0.25713924 20.45903 22.310687 9.3781009 12692 65 65 1 10680 28224 5625 3339 1.1417733 0 67 0
11000 2.5850677 3335 0.25820147 20.476975 22.402851 9.9421534 12954 70 70 2 11964 28224 5625 3335 1.1497985 0 67 0
12000 2.5087529 3358 0.25746572 20.469992 22.339013 9.9566718 12959 58 58 0 13462 28224 5625 3358 1.1365643 0 98 0
13000 2.5480838 3371 0.25761214 20.453395 22.351717 8.6628089 13142 54 54 3 14985 28224 5625 3371 1.1510123 0 98 0
14000 2.946645 3384 0.26176446 20.516743 22.711994 8.5668798 12579 53 53 0 16336 28224 5625 3384 1.1546089 0 98 0
15000 4.025292 3338 0.27188564 20.591315 23.590157 9.8722859 12824 50 50 15 18115 28224 5625 3338 1.164518 0 122 0
16000 2.2744945 3376 0.25598709 20.516221 22.21072 9.1890215 13020 52 52 0 19689 28224 5625 3376 1.1439385 0 122 0
17000 2.3857021 3353 0.25662954 20.489114 22.266462 10.24809 12776 51 51 0 21158 28224 5625 3353 1.1435041 0 122 0
18000 2.9678193 3330 0.26255063 20.56918 22.780206 8.6799225 12810 49 49 2 23066 28224 5625 3330 1.1567395 0 133 0
19000 2.7464034 3368 0.2613984 20.634162 22.680232 9.5420188 12746 47 47 3 24675 28224 5625 3368 1.1426658 0 133 0
20000 2.8228684 3367 0.26137363 20.575046 22.678083 8.0865322 12886 51 51 0 26119 28224 5625 3367 1.1484398 0 133 0
21000 2.8903033 3389 0.26173565 20.556218 22.709494 11.038294 13152 41 41 1 27685 28224 5625 3389 1.1398936 0 133 0
22000 2.8279828 3331 0.26058759 20.503035 22.609882 8.3647396 12895 57 57 1 29333 28224 5625 3331 1.1551348 0 133 0
23000 2.9320035 3376 0.26178899 20.529779 22.714121 7.1841698 13077 54 54 1 30908 28224 5625 3376 1.1453809 0 133 0
24000 2.8508425 3366 0.26104722 20.525884 22.649762 10.680819 13019 58 58 4 32831 28224 5625 3366 1.1391852 0 154 0
25000 2.7878254 3333 0.25961 20.448132 22.525062 11.149479 12960 57 57 1 34494 28224 5625 3333 1.172964 0 154 0
Loop time of 6.5335 on 4 procs for 25000 steps with 17353 atoms
Performance: 330603.792 tau/day, 3826.433 timesteps/s, 66.400 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.097519 | 0.10401 | 0.10744 | 1.2 | 1.59
Neigh | 0.027038 | 0.028067 | 0.028678 | 0.4 | 0.43
Comm | 0.39354 | 0.39697 | 0.40246 | 0.6 | 6.08
Output | 0.0013442 | 0.0014045 | 0.0015827 | 0.3 | 0.02
Modify | 5.8667 | 5.8905 | 5.9143 | 0.8 | 90.16
Other | | 0.1126 | | | 1.72
Nlocal: 4338.25 ave 4476 max 4199 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 78.5 ave 83 max 75 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 328 ave 352 max 309 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 1312
Ave neighs/atom = 0.075606523
Neighbor list builds = 1274
Dangerous builds = 0
Total wall time: 0:00:06

2
examples/ASPHERE/ellipsoid/in.ellipsoid
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@ -116,4 +116,4 @@ thermo 1000
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

2
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
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@ -117,4 +117,4 @@ thermo 1000
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
run 10000

190
examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.g++.8
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@ -1,190 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD diffusion demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
4 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
Memory usage per processor = 3.31932 Mbytes
Step Temp rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051714 2.5292571 1.1630889
800 2.7632971 2.9060854 -0.52075339 2.2149107 0.77106814
900 2.9905601 2.8869672 -0.49099457 2.4696599 0.69616725
1000 2.8470146 2.9004954 -0.51281252 2.305732 0.68820531
Loop time of 0.0485955 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.0201517 (41.4682)
Neigh time (%) = 0.000492364 (1.01319)
Comm time (%) = 0.0191883 (39.4858)
Outpt time (%) = 0.000273198 (0.562188)
Other time (%) = 0.00848994 (17.4706)
Nlocal: 12.5 ave 16 max 8 min
Histogram: 1 1 0 0 0 3 0 0 1 2
Nghost: 34.125 ave 42 max 28 min
Histogram: 1 0 2 2 0 1 0 1 0 1
Neighs: 46.125 ave 65 max 20 min
Histogram: 1 0 1 0 1 2 0 0 1 2
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
create_atoms 2 region plane
Created 85849 atoms
set type 2 mass 0.01
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z # quatw quati quatj quatk
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
SRD per actual grid cell = 1.92757
SRD viscosity = 0.688101
big/SRD mass density ratio = 1.37367
# of rescaled SRD velocities = 0
ave/max small velocity = 13.3093 24.3359
ave/max big velocity = 2.08028 5.05671
Memory usage per processor = 10.9077 Mbytes
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 2.9004954 2.9004954 0 0.025582146 -0.51281252 3.8089257 0.89865242 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.3106106 3.3106106 1.0635866 0.029956176 -0.47263474 4.4601751 1.8111247 14000 35 160 0 224946 98040 11449 4182 1.0635866 1047 50 0
2000 2.2814487 2.2814487 1.2237286 0.017972589 -0.72341981 2.6759388 1.3454977 15318 47 276 0 528340 98040 11449 4136 1.2237286 2383 50 0
3000 4.2476485 4.2476485 1.2992612 0.038526442 -0.59279435 5.7362019 1.6896403 16506 63 410 0 830594 98040 11449 4172 1.2992612 3834 50 0
4000 2.4798681 2.4798681 1.3453264 0.022837826 -0.29467953 3.4003239 2.0765724 17201 51 403 0 1185573 98040 11449 4233 1.3453264 5456 50 0
5000 3.0852629 3.0852629 1.3915904 0.02760985 -0.48621111 4.1108305 1.2676357 17540 61 591 0 1594856 98040 11449 4306 1.3915904 7419 50 0
6000 6.7201122 6.7201122 1.3649223 0.064627842 -0.39052776 9.6224394 2.5524159 17997 59 564 0 2010250 98040 11449 4213 1.3649223 9280 50 0
7000 2.720343 2.720343 1.3909677 0.024282471 -0.43789405 3.6154171 1.5288376 17922 64 342 0 2392388 98040 11449 4228 1.3909677 10947 50 0
8000 1.9181626 1.9181626 1.3514483 0.014305579 -0.72810462 2.1299577 0.89423917 18188 42 260 0 2751626 98040 11449 4236 1.3514483 12556 50 0
9000 2.9090186 2.9090186 1.3688847 0.02558926 -0.52445278 3.8099849 1.1756318 18536 63 440 0 3112508 98040 11449 4227 1.3688847 14164 50 0
10000 1.9647403 1.9647403 1.3979066 0.015375037 -0.63827389 2.2891892 0.65597214 18817 60 466 0 3501352 98040 11449 4257 1.3979066 16016 50 0
11000 1.9989051 1.9989051 1.3872043 0.016191243 -0.56765443 2.4107142 0.80582429 18756 58 767 0 3856028 98040 11449 4254 1.3872043 17611 50 0
12000 1.7538755 1.7538755 1.4594883 0.013930543 -0.53915598 2.0741185 1.0563875 18602 58 335 0 4248666 98040 11449 4251 1.4594883 19350 50 0
13000 13.730871 13.730871 1.4864545 0.13447802 -0.43656501 20.022433 3.6701166 19144 74 681 0 4708523 98040 11449 4104 1.4864545 21589 50 0
14000 5.1078782 5.1078782 1.3637807 0.049721182 -0.20775172 7.4029868 2.559935 18494 65 713 0 5139143 98040 11449 4167 1.3637807 23555 50 0
15000 2.5843962 2.5843962 1.3450247 0.022294373 -0.53134114 3.3194092 1.1069147 18489 52 260 0 5489252 98040 11449 4262 1.3450247 25209 50 0
ERROR: Lost atoms: original 14889 current 14819 (../thermo.cpp:392)

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LAMMPS (1 Feb 2014)
# SRD viscosity demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
4 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
Memory usage per processor = 3.31932 Mbytes
Step Temp rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051714 2.5292571 1.1630889
800 2.7632971 2.9060854 -0.52075339 2.2149107 0.77106814
900 2.9905601 2.8869672 -0.49099457 2.4696599 0.69616725
1000 2.8470146 2.9004954 -0.51281252 2.305732 0.68820531
Loop time of 0.0581853 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.0202803 (34.8546)
Neigh time (%) = 0.000480682 (0.826122)
Comm time (%) = 0.0264942 (45.5342)
Outpt time (%) = 0.000326395 (0.560958)
Other time (%) = 0.0106037 (18.2241)
Nlocal: 12.5 ave 16 max 8 min
Histogram: 1 1 0 0 0 3 0 0 1 2
Nghost: 34.125 ave 42 max 28 min
Histogram: 1 0 2 2 0 1 0 1 0 1
Neighs: 46.125 ave 65 max 20 min
Histogram: 1 0 1 0 1 2 0 0 1 2
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
create_atoms 2 region plane
Created 85849 atoms
set type 2 mass 0.01
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z # quatw quati quatj quatk
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
SRD per actual grid cell = 1.92757
SRD viscosity = 0.688101
big/SRD mass density ratio = 1.37367
# of rescaled SRD velocities = 0
ave/max small velocity = 13.3093 24.3359
ave/max big velocity = 2.08028 5.05671
Memory usage per processor = 10.9077 Mbytes
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 2.9004954 2.9004954 0 0.025582146 -0.51281252 3.8089257 0.89865242 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.1663129 3.1663129 1.0612788 0.028825811 -0.42593131 4.291875 1.8917479 14347 45 319 0 247730 98040 11449 4128 1.0612788 1160 50 0
2000 2.3854865 2.3854865 1.2711805 0.019550917 -0.6434388 2.910936 1.4342405 15199 41 151 0 526468 98040 11449 4191 1.2711805 2321 50 0
3000 2.6796789 2.6796789 1.2494843 0.023573743 -0.48282696 3.5098946 1.6090734 16441 52 230 0 827117 98040 11449 4203 1.2494843 3659 50 0
4000 2.7945661 2.7945661 1.3021617 0.024256529 -0.5523488 3.6115547 1.2702377 16935 52 474 0 1127934 98040 11449 4215 1.3021617 4966 50 0
5000 2.7061959 2.7061959 1.338483 0.023736966 -0.498035 3.5341969 1.2801942 17578 49 277 0 1435089 98040 11449 4261 1.338483 6351 50 0
6000 3.2698703 3.2698703 1.3285507 0.029840303 -0.42918398 4.4429227 1.4528039 17882 63 228 0 1776449 98040 11449 4252 1.3285507 7935 50 0
7000 3.9340641 3.9340641 1.3823898 0.035368008 -0.59581277 5.2659427 1.1321242 18069 49 462 0 2090062 98040 11449 4265 1.3823898 9343 50 0
8000 3.6037728 3.6037728 1.4150583 0.032400676 -0.54548483 4.8241367 1.2091317 18275 56 369 0 2486575 98040 11449 4229 1.4150583 11121 50 0
9000 105.15275 105.15275 1.3630934 1.0504642 -0.27397996 156.40361 23.278069 18139 107 732 0 2861341 98040 11449 4217 1.3630934 12781 50 0
10000 3.5224307 3.5224307 1.3897056 0.0324883 -0.4112387 4.837183 1.6093705 19100 61 347 0 3248400 98040 11449 4204 1.3897056 14424 50 0
11000 4.1949959 4.1949959 1.421272 0.03853305 -0.51335814 5.7371858 1.3586332 18670 52 590 0 3722041 98040 11449 4263 1.421272 16373 50 0
12000 3.1692742 3.1692742 1.3999982 0.028463927 -0.48422456 4.237994 1.1713046 18787 61 323 0 4117517 98040 11449 4202 1.3999982 18125 50 0
13000 3.5868757 3.5868757 1.3193021 0.032298734 -0.53548629 4.8089585 1.0664078 18572 67 224 0 4417636 98040 11449 4277 1.3193021 19546 50 0
14000 3.708681 3.708681 1.317797 0.033355183 -0.55968141 4.9662533 1.3959088 18284 67 207 0 4675359 98040 11449 4253 1.317797 20631 50 0
15000 3.7410393 3.7410393 1.4017441 0.033377852 -0.60452027 4.9696283 1.2506767 18385 51 189 0 4956150 98040 11449 4275 1.4017441 21763 50 0
16000 5.3298522 5.3298522 1.3456075 0.049673767 -0.54555257 7.3959272 1.841432 18693 63 549 0 5301393 98040 11449 4196 1.3456075 23216 50 0
17000 3.7425275 3.7425275 1.321554 0.036608704 -0.12569607 5.4506699 2.3767421 18377 68 526 0 5637038 98040 11449 4261 1.321554 24829 50 0
18000 6.1904009 6.1904009 1.3905006 0.05857936 -0.50181651 8.7218809 1.7936734 18422 63 522 0 6049781 98040 11449 4280 1.3905006 26646 50 0
19000 3.1770374 3.1770374 1.3694174 0.028096405 -0.55051202 4.1832737 0.98036773 18342 54 343 0 6383253 98040 11449 4239 1.3694174 28038 50 0
20000 3.5793112 3.5793112 1.3160294 0.031413769 -0.65597761 4.677196 1.0713128 18739 60 272 0 6692090 98040 11449 4262 1.3160294 29389 50 0
21000 3.2300481 3.2300481 1.3407923 0.027955254 -0.65051393 4.1622578 0.89783071 18582 55 456 0 6999361 98040 11449 4237 1.3407923 30653 50 0
22000 3.5879886 3.5879886 1.3790201 0.031692391 -0.6274228 4.7186802 0.97752405 18768 63 552 0 7350833 98040 11449 4308 1.3790201 32120 50 0
23000 3.5666316 3.5666316 1.4123826 0.031275136 -0.6577261 4.656555 0.99950405 18864 49 231 0 7741276 98040 11449 4265 1.4123826 33939 50 0
24000 3.7306353 3.7306353 1.3854831 0.032426295 -0.7306956 4.827951 0.93575015 18488 63 552 0 8096740 98040 11449 4238 1.3854831 35503 50 0
25000 4.2971901 4.2971901 1.4207289 0.038358698 -0.69158669 5.7112265 1.0308127 18922 58 430 0 8518804 98040 11449 4254 1.4207289 37429 50 0
26000 9.514164 9.514164 1.4209186 0.09200552 -0.47740255 13.698702 2.4102159 18934 63 570 0 8931705 98040 11449 4233 1.4209186 39132 50 0
27000 3.9153535 3.9153535 1.3814961 0.036650525 -0.37698007 5.4568967 1.4531475 19153 65 553 0 9277922 98040 11449 4299 1.3814961 40660 50 0
28000 3.6560048 3.6560048 1.3520603 0.033100525 -0.51910991 4.9283372 1.3474705 19529 59 447 0 9642607 98040 11449 4278 1.3520603 42335 50 0
29000 14.835118 14.835118 1.3981622 0.14535835 -0.4619207 21.642405 3.6917556 19265 52 102 0 9937354 98040 11449 4224 1.3981622 43664 50 0
30000 5.3595251 5.3595251 1.3636194 0.050893845 -0.40810785 7.5775845 1.7023989 19065 43 131 0 10261222 98040 11449 4170 1.3636194 45193 50 0
31000 5.1821698 5.1821698 1.3180039 0.049074014 -0.41480304 7.30663 1.6943582 19142 58 282 0 10584027 98040 11449 4228 1.3180039 46636 50 0
32000 4.3056534 4.3056534 1.3508467 0.040670309 -0.36002116 6.0554024 1.7875405 19065 36 284 0 10933981 98040 11449 4286 1.3508467 48240 50 0
33000 3.8277999 3.8277999 1.3770405 0.034411971 -0.57982354 5.1235984 1.1046562 18838 71 729 0 11329901 98040 11449 4257 1.3770405 50046 50 0
34000 4.6562056 4.6562056 1.3938501 0.043777831 -0.41966518 6.5180812 1.3815841 18914 61 269 0 11758952 98040 11449 4221 1.3938501 51773 50 0
35000 3.4251492 3.4251492 1.3813031 0.031876928 -0.35731644 4.7461558 1.4152845 18838 60 283 0 12159425 98040 11449 4238 1.3813031 53477 50 0
36000 4.2565688 4.2565688 1.3474871 0.039214915 -0.5035788 5.8387088 1.1222014 18765 56 240 0 12568711 98040 11449 4249 1.3474871 55170 50 0
37000 5.3745505 5.3745505 1.4215553 0.053606226 -0.02664916 7.981431 2.8011643 19103 58 504 0 12941065 98040 11449 4270 1.4215553 56743 50 0
38000 4.0346121 4.0346121 1.4354472 0.036753623 -0.53932498 5.472247 1.1475792 18829 62 623 0 13351480 98040 11449 4226 1.4354472 58443 50 0
39000 4.0471971 4.0471971 1.417888 0.037884509 -0.3896991 5.6406246 1.3824278 19047 70 579 0 13752101 98040 11449 4219 1.417888 60208 50 0
40000 4.1611575 4.1611575 1.3712048 0.039505792 -0.31810741 5.8820173 1.6615204 18811 65 378 0 14143802 98040 11449 4313 1.3712048 61793 50 0
41000 4.852673 4.852673 1.3719985 0.044831688 -0.5554927 6.67499 1.2744313 18899 53 414 0 14505662 98040 11449 4274 1.3719985 63358 50 0
42000 4.8338875 4.8338875 1.3595624 0.045465888 -0.43307636 6.7694161 1.6297026 18708 46 360 0 14839866 98040 11449 4224 1.3595624 64895 50 0
43000 5.0243115 5.0243115 1.4371431 0.047111836 -0.47174292 7.0144813 1.5899963 18704 55 291 0 15195383 98040 11449 4209 1.4371431 66440 50 0
44000 7.2748224 7.2748224 1.3693754 0.069498669 -0.49182853 10.347657 1.9007074 18751 73 423 0 15572639 98040 11449 4253 1.3693754 68148 50 0
45000 5.4888002 5.4888002 1.3501677 0.050885254 -0.60200685 7.5763055 1.2841374 18662 51 314 0 15972088 98040 11449 4227 1.3501677 69998 50 0
46000 3.2144774 3.2144774 1.3342547 0.028194354 -0.59171403 4.1978573 0.9459541 18948 50 534 0 16308430 98040 11449 4253 1.3342547 71549 50 0
47000 4.0640905 4.0640905 1.3473081 0.036715084 -0.58898597 5.4665088 1.2043249 19188 57 236 0 16670321 98040 11449 4239 1.3473081 73216 50 0
48000 3.7843815 3.7843815 1.3413467 0.034360184 -0.52284075 5.1158877 1.1195984 19477 57 283 0 17000588 98040 11449 4307 1.3413467 74662 50 0
49000 4.3042567 4.3042567 1.354248 0.039635615 -0.51199566 5.9013468 1.410884 19628 68 456 0 17319627 98040 11449 4277 1.354248 75983 50 0
50000 4.015575 4.015575 1.3058373 0.036258162 -0.58472888 5.3984778 0.84500807 19257 63 416 0 17675269 98040 11449 4254 1.3058373 77468 50 0
Loop time of 11.9502 on 8 procs for 50000 steps with 14889 atoms
Pair time (%) = 1.09132 (9.13222)
Neigh time (%) = 0.959464 (8.02883)
Comm time (%) = 1.19057 (9.96277)
Outpt time (%) = 0.00310364 (0.0259714)
Other time (%) = 8.70577 (72.8502)
Nlocal: 1861.12 ave 1979 max 1606 min
Histogram: 1 0 0 0 1 1 1 0 0 4
Nghost: 35 ave 39 max 32 min
Histogram: 1 0 2 0 3 1 0 0 0 1
Neighs: 46 ave 61 max 31 min
Histogram: 1 1 0 1 1 0 2 0 1 1
Total # of neighbors = 368
Ave neighs/atom = 0.0247162
Neighbor list builds = 2624
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.000 seconds
set type 1 mass 1.0
Setting atom values ...
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
Setting atom values ...
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
Setting atom values ...
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair gayberne command: doi:10.1063/1.3058435
@Article{Brown09,
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
title = {Liquid Crystal Nanodroplets in Solution},
journal = {J.~Chem.\ Phys.},
year = 2009,
volume = 130,
number = 4,
pages = {044901}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
Step Temp c_rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678
900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841
1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567
Loop time of 0.192737 on 1 procs for 1000 steps with 100 atoms
Performance: 2241395.423 tau/day, 5188.415 timesteps/s, 518.842 katom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.37
Neigh | 0.0025287 | 0.0025287 | 0.0025287 | 0.0 | 1.31
Comm | 0.0023396 | 0.0023396 | 0.0023396 | 0.0 | 1.21
Output | 0.00025405 | 0.00025405 | 0.00025405 | 0.0 | 0.13
Modify | 0.013955 | 0.013955 | 0.013955 | 0.0 | 7.24
Other | | 0.001413 | | | 0.73
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 369 ave 369 max 369 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
create_atoms 2 region plane
Created 85849 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.015 seconds
set type 2 mass 0.01
Setting atom values ...
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 20 20 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
SRD per actual grid cell = 1.9275711
SRD viscosity = 0.68810145
big/SRD mass density ratio = 1.3736715
# of rescaled SRD velocities = 0
ave/max small velocity = 13.30933 24.335888
ave/max big velocity = 2.0802836 5.05672
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 26.726124, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.1884096 2.1884096 0.81792923 0.016786763 -0.7613492 2.4993811 1.1765894 13834 35 35 0 241 38416 11449 4172 0.81792923 16 50 0
2000 1.2708697 1.2708697 0.90821156 0.0069438942 -0.8597194 1.0338764 0.9801188 14658 35 35 0 372 38416 11449 4281 0.90821156 16 50 0
3000 1.1130928 1.1130928 0.9590586 0.0052557024 -0.8759868 0.78252152 0.70461705 15267 28 28 0 519 38416 11449 4292 0.9590586 16 50 0
4000 0.8649005 0.8649005 0.9947477 0.0026217985 -0.89834217 0.39035958 0.77420962 15681 36 36 0 698 38416 11449 4339 0.9947477 16 50 0
5000 1.1743692 1.1743692 0.98116608 0.0069116456 -0.72073526 1.0290749 0.8829165 15974 37 37 0 881 38416 11449 4328 0.98116608 16 50 0
6000 1.0190814 1.0190814 1.0138428 0.0048088112 -0.80244733 0.7159839 0.79743882 16092 36 36 0 1090 38416 11449 4319 1.0138428 16 50 0
7000 1.0824823 1.0824823 1.0415165 0.0049127988 -0.88143205 0.73146661 0.48157537 16178 46 46 0 1328 38416 11449 4370 1.0415165 23 50 0
8000 1.0482457 1.0482457 1.0336952 0.0051802902 -0.79059275 0.7712934 0.75744414 16622 33 33 0 1579 38416 11449 4340 1.0336952 24 50 0
9000 0.98889815 0.98889815 1.0126005 0.00397567 -0.88152073 0.59193751 0.52056685 16877 41 41 0 1811 38416 11449 4370 1.0126005 27 50 0
10000 0.96559538 0.96559538 1.0234124 0.0045683795 -0.7585511 0.68018602 0.70666049 16833 32 32 0 2038 38416 11449 4330 1.0234124 27 50 0
Loop time of 9.04639 on 1 procs for 10000 steps with 14889 atoms
Performance: 47753.873 tau/day, 1105.414 timesteps/s, 16.459 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.862 | 1.862 | 1.862 | 0.0 | 20.58
Neigh | 0.018395 | 0.018395 | 0.018395 | 0.0 | 0.20
Comm | 0.060502 | 0.060502 | 0.060502 | 0.0 | 0.67
Output | 0.00092704 | 0.00092704 | 0.00092704 | 0.0 | 0.01
Modify | 7.0482 | 7.0482 | 7.0482 | 0.0 | 77.91
Other | | 0.05636 | | | 0.62
Nlocal: 14889 ave 14889 max 14889 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 79 ave 79 max 79 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 416 ave 416 max 416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 416
Ave neighs/atom = 0.02794009
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:11

346
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
2 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
Setting atom values ...
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
Setting atom values ...
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair gayberne command: doi:10.1063/1.3058435
@Article{Brown09,
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
title = {Liquid Crystal Nanodroplets in Solution},
journal = {J.~Chem.\ Phys.},
year = 2009,
volume = 130,
number = 4,
pages = {044901}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
Step Temp c_rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
800 2.7632972 2.9060855 -0.52075354 2.2149107 0.77106773
900 2.9905599 2.8869667 -0.49099386 2.4696604 0.69616823
1000 2.8470131 2.9005016 -0.51282147 2.3057215 0.68817329
Loop time of 0.0666302 on 4 procs for 1000 steps with 100 atoms
Performance: 6483542.632 tau/day, 15008.201 timesteps/s, 1.501 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.039208 | 0.042833 | 0.045871 | 1.2 | 64.29
Neigh | 0.00065929 | 0.00071982 | 0.00076852 | 0.0 | 1.08
Comm | 0.013998 | 0.017169 | 0.02087 | 1.9 | 25.77
Output | 0.00018817 | 0.00020663 | 0.00025962 | 0.0 | 0.31
Modify | 0.0035046 | 0.0035933 | 0.003701 | 0.1 | 5.39
Other | | 0.002109 | | | 3.16
Nlocal: 25 ave 27 max 24 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 42.25 ave 45 max 38 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 92.25 ave 104 max 85 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
create_atoms 2 region plane
Created 85849 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.004 seconds
set type 2 mass 0.01
Setting atom values ...
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 20 20 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
SRD per actual grid cell = 1.9275711
SRD viscosity = 0.68810145
big/SRD mass density ratio = 1.3736715
# of rescaled SRD velocities = 0
ave/max small velocity = 13.30933 24.335888
ave/max big velocity = 2.080284 5.0567191
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 26.726124, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 16.89 | 16.9 | 16.91 Mbytes
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 2.9005016 2.9005016 0 0.025582147 -0.51282147 3.8089259 0.89862191 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.7138279 2.7138279 0.82437872 0.023781703 -0.50274582 3.5408578 1.6816604 13758 32 34 0 274 66564 11449 4238 0.82437872 24 50 0
2000 1.3183118 1.3183118 0.91362053 0.0077748292 -0.80669023 1.1575943 1.1678425 14118 23 23 0 414 66564 11449 4269 0.91362053 24 50 0
3000 1.3117991 1.3117991 0.96889539 0.0065133847 -0.98480276 0.96977785 0.51801823 14675 35 36 0 588 66564 11449 4291 0.96889539 26 50 0
4000 1.1034132 1.1034132 0.95899765 0.0042496304 -1.0113582 0.63272747 0.6382343 15146 38 38 0 776 66564 11449 4309 0.95899765 26 50 0
5000 1.0814177 1.0814177 1.0037423 0.0047549676 -0.90334518 0.70796713 0.76138491 15275 40 40 0 973 66564 11449 4285 1.0037423 26 50 0
6000 1.0515425 1.0515425 0.98728204 0.0041039749 -0.95575757 0.61104083 0.61253791 15685 34 34 0 1205 66564 11449 4328 0.98728204 26 50 0
7000 0.96229389 0.96229389 1.0146054 0.0031968892 -0.95783307 0.47598483 0.4469161 15944 43 43 0 1412 66564 11449 4391 1.0146054 27 50 0
8000 0.98798058 0.98798058 0.99692702 0.0037348841 -0.91600418 0.55608689 0.50558822 16250 43 43 0 1637 66564 11449 4330 0.99692702 27 50 0
9000 1.0120554 1.0120554 1.0099521 0.0039518454 -0.91957229 0.58839026 0.4092229 16367 43 44 0 1899 66564 11449 4309 1.0099521 27 50 0
10000 1.104152 1.104152 0.9993147 0.0053713858 -0.84544079 0.79974564 0.5119979 16331 50 50 0 2108 66564 11449 4353 0.9993147 27 50 0
Loop time of 2.95619 on 4 procs for 10000 steps with 14889 atoms
Performance: 146134.205 tau/day, 3382.736 timesteps/s, 50.366 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48773 | 0.52727 | 0.62879 | 8.1 | 17.84
Neigh | 0.0070094 | 0.0072204 | 0.0076255 | 0.3 | 0.24
Comm | 0.12898 | 0.22553 | 0.265 | 11.8 | 7.63
Output | 0.0005957 | 0.00064777 | 0.00075264 | 0.0 | 0.02
Modify | 2.1317 | 2.1512 | 2.166 | 0.9 | 72.77
Other | | 0.04427 | | | 1.50
Nlocal: 3722.25 ave 3968 max 3389 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 39.75 ave 44 max 35 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 101 ave 125 max 86 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 404
Ave neighs/atom = 0.027134126
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.000 seconds
set type 1 mass 1.0
Setting atom values ...
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
Setting atom values ...
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
Setting atom values ...
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair gayberne command: doi:10.1063/1.3058435
@Article{Brown09,
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
title = {Liquid Crystal Nanodroplets in Solution},
journal = {J.~Chem.\ Phys.},
year = 2009,
volume = 130,
number = 4,
pages = {044901}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
Step Temp c_rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678
900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841
1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567
Loop time of 0.192844 on 1 procs for 1000 steps with 100 atoms
Performance: 2240155.241 tau/day, 5185.545 timesteps/s, 518.554 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.32
Neigh | 0.0025614 | 0.0025614 | 0.0025614 | 0.0 | 1.33
Comm | 0.0024746 | 0.0024746 | 0.0024746 | 0.0 | 1.28
Output | 0.0001406 | 0.0001406 | 0.0001406 | 0.0 | 0.07
Modify | 0.014112 | 0.014112 | 0.014112 | 0.0 | 7.32
Other | | 0.001306 | | | 0.68
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 369 ave 369 max 369 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
create_atoms 2 region plane
Created 85849 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.015 seconds
set type 2 mass 0.01
Setting atom values ...
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 20 20 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
SRD per actual grid cell = 1.9275711
SRD viscosity = 0.68810145
big/SRD mass density ratio = 1.3736715
# of rescaled SRD velocities = 0
ave/max small velocity = 13.30933 24.335888
ave/max big velocity = 2.0802836 5.05672
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 26.726124, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.3102693 2.3102693 0.82371999 0.019779507 -0.49733043 2.9449709 1.9807143 13954 30 30 0 277 38416 11449 4255 0.82371999 15 50 0
2000 1.5312119 1.5312119 0.90846884 0.008532096 -1.011162 1.2703438 0.58038663 14523 37 37 0 439 38416 11449 4257 0.90846884 20 50 0
3000 1.3603443 1.3603443 0.95241399 0.0085403252 -0.75534393 1.271569 1.2262133 14864 34 35 0 599 38416 11449 4287 0.95241399 20 50 0
4000 2.2408861 2.2408861 0.99089404 0.016876315 -0.82620566 2.5127146 1.2664088 15457 35 35 0 809 38416 11449 4272 0.99089404 21 50 0
5000 1.7110067 1.7110067 0.99729333 0.011146301 -0.88982716 1.6595728 0.97334407 15555 36 36 0 1026 38416 11449 4324 0.99729333 24 50 0
6000 1.684666 1.684666 1.0235606 0.009751253 -1.0582882 1.4518641 0.62435255 15752 45 46 0 1256 38416 11449 4303 1.0235606 24 50 0
7000 2.1142261 2.1142261 1.0160206 0.014786886 -0.94857757 2.2016194 0.7761903 16144 30 30 0 1492 38416 11449 4401 1.0160206 27 50 0
8000 2.5622926 2.5622926 1.0125365 0.019933518 -0.84991443 2.9679015 0.93716383 16302 43 43 0 1720 38416 11449 4346 1.0125365 27 50 0
9000 2.6593623 2.6593623 1.0110535 0.020725053 -0.87669675 3.0857531 0.97818336 16856 44 44 0 2000 38416 11449 4298 1.0110535 30 50 0
10000 2.7567851 2.7567851 1.0379053 0.021598993 -0.8917358 3.2158741 0.74950846 16770 50 53 0 2284 38416 11449 4316 1.0379053 30 50 0
Loop time of 9.02679 on 1 procs for 10000 steps with 14889 atoms
Performance: 47857.551 tau/day, 1107.814 timesteps/s, 16.494 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8454 | 1.8454 | 1.8454 | 0.0 | 20.44
Neigh | 0.018708 | 0.018708 | 0.018708 | 0.0 | 0.21
Comm | 0.059853 | 0.059853 | 0.059853 | 0.0 | 0.66
Output | 0.00081453 | 0.00081453 | 0.00081453 | 0.0 | 0.01
Modify | 7.0469 | 7.0469 | 7.0469 | 0.0 | 78.07
Other | | 0.05507 | | | 0.61
Nlocal: 14889 ave 14889 max 14889 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 75 ave 75 max 75 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 382 ave 382 max 382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 382
Ave neighs/atom = 0.025656525
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:11

347
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.4 Normal file
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@ -0,0 +1,347 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
2 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
Setting atom values ...
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
Setting atom values ...
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair gayberne command: doi:10.1063/1.3058435
@Article{Brown09,
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
title = {Liquid Crystal Nanodroplets in Solution},
journal = {J.~Chem.\ Phys.},
year = 2009,
volume = 130,
number = 4,
pages = {044901}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 13 13 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
Step Temp c_rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
800 2.7632972 2.9060855 -0.52075354 2.2149107 0.77106773
900 2.9905599 2.8869667 -0.49099386 2.4696604 0.69616823
1000 2.8470131 2.9005016 -0.51282147 2.3057215 0.68817329
Loop time of 0.0905036 on 4 procs for 1000 steps with 100 atoms
Performance: 4773291.472 tau/day, 11049.286 timesteps/s, 1.105 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.039039 | 0.053443 | 0.065528 | 5.0 | 59.05
Neigh | 0.00068257 | 0.00086692 | 0.0010442 | 0.0 | 0.96
Comm | 0.016567 | 0.028689 | 0.043189 | 6.8 | 31.70
Output | 0.00016989 | 0.00018594 | 0.0002316 | 0.0 | 0.21
Modify | 0.0035809 | 0.0043052 | 0.0050755 | 1.0 | 4.76
Other | | 0.003013 | | | 3.33
Nlocal: 25 ave 27 max 24 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 42.25 ave 45 max 38 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 92.25 ave 104 max 85 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
create_atoms 2 region plane
Created 85849 atoms
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
create_atoms CPU = 0.007 seconds
set type 2 mass 0.01
Setting atom values ...
85849 settings made for mass
group small type 2
85849 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 20 20 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 71060 atoms, new total = 14889
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
SRD per actual grid cell = 1.9275711
SRD viscosity = 0.68810145
big/SRD mass density ratio = 1.3736715
# of rescaled SRD velocities = 0
ave/max small velocity = 13.30933 24.335888
ave/max big velocity = 2.080284 5.0567191
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 26.726124, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 16.89 | 16.9 | 16.91 Mbytes
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 2.9005016 2.9005016 0 0.025582147 -0.51282147 3.8089259 0.89862191 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.5269102 2.5269102 0.8207596 0.022784455 -0.37271861 3.3923775 2.0963085 13925 34 34 0 322 66564 11449 4235 0.8207596 24 50 0
2000 1.3685596 1.3685596 0.89115879 0.0089112146 -0.71236311 1.3267907 1.3970875 14444 25 25 0 454 66564 11449 4278 0.89115879 25 50 0
3000 1.5234001 1.5234001 0.9828293 0.0090168318 -0.92735003 1.3425161 0.70104224 14946 37 37 0 608 66564 11449 4331 0.9828293 27 50 0
4000 2.2536932 2.2536932 0.97648579 0.017005211 -0.82609701 2.5319058 1.190307 15428 43 43 0 827 66564 11449 4346 0.97648579 32 50 0
5000 1.8106358 1.8106358 1.0143347 0.012032652 -0.90630586 1.7915415 0.83451531 15438 26 26 0 1039 66564 11449 4314 1.0143347 32 50 0
6000 1.9880605 1.9880605 1.0142917 0.013767418 -0.91237924 2.0498309 0.87383026 15688 37 37 0 1279 66564 11449 4353 1.0142917 32 50 0
7000 2.4772098 2.4772098 0.99457682 0.018062012 -1.0017896 2.689253 0.74369504 15723 38 38 0 1521 66564 11449 4293 0.99457682 32 50 0
8000 2.5749419 2.5749419 1.0337514 0.019908918 -0.87242464 2.9642389 1.0460672 15932 33 34 0 1805 66564 11449 4320 1.0337514 32 50 0
9000 2.4877578 2.4877578 1.0366259 0.019125113 -0.85922105 2.847538 0.95616808 16292 52 53 0 2099 66564 11449 4291 1.0366259 33 50 0
10000 2.8498311 2.8498311 1.0117104 0.022669267 -0.87102125 3.3752271 0.98313087 16736 38 38 0 2415 66564 11449 4366 1.0117104 35 50 0
Loop time of 3.0339 on 4 procs for 10000 steps with 14889 atoms
Performance: 142390.919 tau/day, 3296.086 timesteps/s, 49.075 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46168 | 0.52303 | 0.69055 | 13.4 | 17.24
Neigh | 0.0068493 | 0.0072892 | 0.0081958 | 0.6 | 0.24
Comm | 0.12806 | 0.2911 | 0.34961 | 17.5 | 9.59
Output | 0.00055286 | 0.00057977 | 0.00065772 | 0.0 | 0.02
Modify | 2.1454 | 2.1674 | 2.1833 | 0.9 | 71.44
Other | | 0.04447 | | | 1.47
Nlocal: 3722.25 ave 4163 max 3210 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 46.25 ave 49 max 43 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 102.5 ave 143 max 79 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 410
Ave neighs/atom = 0.027537108
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:03

2
examples/ASPHERE/line/in.line
View File

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

2
examples/ASPHERE/poly/in.poly
View File

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

2
examples/ASPHERE/poly/in.poly.mp
View File

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

288
examples/ASPHERE/poly/log.1Feb14.poly.g++.8
View File

@ -1,288 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD diffusion demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
2 by 4 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Memory usage per processor = 2.7472 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.0221665 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.000323534 (1.45957)
Neigh time (%) = 0.000274181 (1.23692)
Comm time (%) = 0.0146933 (66.2864)
Outpt time (%) = 2.864e-05 (0.129204)
Other time (%) = 0.00684676 (30.8879)
Nlocal: 12.5 ave 18 max 10 min
Histogram: 1 3 1 1 0 1 0 0 0 1
Nghost: 27.75 ave 31 max 24 min
Histogram: 1 0 1 0 2 2 0 0 0 2
Neighs: 19 ave 30 max 16 min
Histogram: 4 1 2 0 0 0 0 0 0 1
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
create_atoms 4 region plane
Created 83521 atoms
set type 4 mass 0.1
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
delete_atoms overlap 1.0 small big
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.poly
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 100000
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
SRD per actual grid cell = 4.93717
SRD viscosity = 0.23322
big/SRD mass density ratio = 0.161311
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19344 7.74495
ave/max big velocity = 1.43991 3.5724
Memory usage per processor = 11.8633 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.84607633 3934 0.0065245151 0.058016014 1.3186697 4.2649214 7470 26 26 0 665 36480 5329 3934 0.95810956 0 2
2000 0.86586785 3944 0.0045898954 -0.36247933 0.92766376 2.1563866 7786 30 30 0 1374 36480 5329 3944 1.0799777 0 49
3000 0.78968677 4001 0.00417319 -0.33318986 0.84344343 1.9302042 7957 34 34 0 2129 36480 5329 4001 1.1247747 0 49
4000 0.7110667 4005 0.0031642256 -0.41996775 0.63952164 1.9679689 8188 24 24 0 2925 36480 5329 4005 1.1345941 0 49
5000 0.80379425 4052 0.0038912991 -0.41118297 0.78647047 1.6851034 8326 30 30 0 3794 36480 5329 4052 1.1310774 0 49
6000 0.96927432 4048 0.0054656969 -0.33954674 1.104672 1.8976158 8380 23 23 0 4643 36480 5329 4048 1.1861264 0 49
7000 0.75821666 4050 0.0036201309 -0.39807817 0.73166465 1.6087451 8450 51 51 0 5699 36480 5329 4050 1.1664119 0 49
8000 0.8712338 4035 0.0047243103 -0.343308 0.95483036 1.4707918 8458 42 42 0 6974 36480 5329 4035 1.1947807 0 91
9000 0.87995969 4048 0.0042778416 -0.44654537 0.86459457 1.5567027 8379 36 36 0 7965 36480 5329 4048 1.1675384 0 91
10000 0.83009098 4053 0.0042178709 -0.38436167 0.85247389 1.9119485 8373 34 34 0 8952 36480 5329 4053 1.1933986 0 91
11000 0.73595909 4015 0.0037439098 -0.33989742 0.75668162 1.6495307 8333 22 22 0 9983 36480 5329 4015 1.1959519 0 91
12000 0.84043443 4034 0.0041823741 -0.40694768 0.84529962 1.5115578 8566 31 31 0 11023 36480 5329 4034 1.2064988 0 91
13000 0.64253331 4044 0.0034868675 -0.25264383 0.7047308 1.739124 8528 31 31 0 12101 36480 5329 4044 1.1912336 0 91
14000 0.99330171 4042 0.0055047339 -0.36745778 1.1125618 1.8215191 8548 36 36 0 13098 36480 5329 4042 1.1819124 0 91
15000 0.90379859 4049 0.0049047446 -0.35536197 0.99129793 1.7159536 8459 37 37 0 14130 36480 5329 4049 1.1806762 0 91
16000 0.87446498 4034 0.0053318245 -0.22533777 1.0776151 2.0239395 8690 33 33 0 15176 36480 5329 4034 1.1912858 0 91
17000 0.95733995 4035 0.0053759665 -0.33989994 1.0865366 1.6243881 8518 27 27 0 16147 36480 5329 4035 1.2074487 0 91
18000 1.03543 4032 0.0052946469 -0.47268961 1.0701011 1.5444562 8464 28 28 0 17230 36480 5329 4032 1.1959755 0 91
19000 0.75997582 4051 0.0034371936 -0.43767278 0.6946912 1.4209137 8436 39 39 0 18276 36480 5329 4051 1.182461 0 91
20000 0.89615234 4037 0.0048910458 -0.34673773 0.98852926 1.5843879 8433 28 28 0 19275 36480 5329 4037 1.1850673 0 91
21000 0.85849578 4063 0.0044978314 -0.37010201 0.9090567 1.5445809 8504 40 40 0 20278 36480 5329 4063 1.1931031 0 91
22000 0.79050471 4066 0.0038260812 -0.40456274 0.77328927 1.6214277 8463 44 44 0 21287 36480 5329 4066 1.1948824 0 91
23000 0.89563532 4026 0.0051030186 -0.30312555 1.0313711 1.4848223 8548 35 35 0 22422 36480 5329 4026 1.1975081 0 91
24000 0.83528717 4036 0.0043136275 -0.37275064 0.87182725 1.5504059 8527 34 34 0 23404 36480 5329 4036 1.1755463 0 91
25000 0.64179358 4022 0.0035185741 -0.24513342 0.71113901 1.7238889 8452 47 47 0 24522 36480 5329 4022 1.2066339 0 91
26000 0.86710098 4028 0.0046099591 -0.36026164 0.93171883 1.4255297 8734 33 33 0 25524 36480 5329 4028 1.2001233 0 91
27000 0.8327003 4054 0.0045323379 -0.32469262 0.91603082 1.2654649 8468 34 34 0 26520 36480 5329 4054 1.1814901 0 91
28000 0.84396759 4049 0.0042805934 -0.39236096 0.86515074 1.2929473 8536 37 37 0 27657 36480 5329 4049 1.1897647 0 91
29000 0.77639299 4052 0.0038143413 -0.38590904 0.77091652 1.3627099 8637 36 36 0 28773 36480 5329 4052 1.1858017 0 91
30000 0.69994805 4046 0.0034430868 -0.34704032 0.69588228 1.5351247 8704 46 46 0 29818 36480 5329 4046 1.1724555 0 91
31000 0.73907898 4039 0.003034759 -0.48787254 0.61335514 1.2291035 8486 29 29 0 30848 36480 5329 4039 1.2063852 0 91
32000 0.84649298 4052 0.0044326201 -0.36539769 0.89587685 1.4591662 8513 28 28 0 31917 36480 5329 4052 1.1917883 0 91
33000 0.7188891 4031 0.0033440675 -0.39527528 0.67586949 1.2495703 8800 37 37 0 32938 36480 5329 4031 1.191087 0 91
34000 0.93588921 4054 0.0054112843 -0.30080024 1.0936747 1.3650172 8585 33 33 0 33913 36480 5329 4054 1.1840415 0 91
35000 0.86446961 4039 0.0053251497 -0.21179371 1.076266 1.3791947 8607 22 22 0 34865 36480 5329 4039 1.1916342 0 91
36000 0.90510006 4011 0.0054168442 -0.2538007 1.0947984 1.5747653 8479 31 31 0 35842 36480 5329 4011 1.1760305 0 91
37000 0.95332175 4058 0.0055020495 -0.30843018 1.1120192 1.4326924 8512 29 29 0 36751 36480 5329 4058 1.180738 0 91
38000 0.71413841 4043 0.0038380378 -0.2883604 0.77570582 1.4283837 8611 39 39 0 37689 36480 5329 4043 1.1693806 0 91
39000 0.81161335 4064 0.0044323475 -0.31348213 0.89582176 1.4378305 8697 28 28 0 38696 36480 5329 4064 1.1987209 0 91
40000 0.8294437 4062 0.0051262098 -0.19981285 1.0360583 1.6010501 8559 31 31 0 39743 36480 5329 4062 1.2092371 0 91
41000 0.79325147 4079 0.0045273868 -0.26691453 0.91503015 1.4080428 8775 53 53 0 40806 36480 5329 4079 1.1989619 0 91
42000 0.95693891 4027 0.005623893 -0.28919396 1.136645 1.5334192 8509 34 34 0 41793 36480 5329 4027 1.1931035 0 91
43000 0.66458435 4029 0.0035902162 -0.26461209 0.72561859 1.4253918 8559 44 44 0 42768 36480 5329 4029 1.2111853 0 91
44000 0.84442459 4022 0.0050980388 -0.22782802 1.0303646 1.4587515 8522 32 32 0 43812 36480 5329 4022 1.1943268 0 91
45000 0.96505326 4051 0.0057148128 -0.28290855 1.1550208 1.3014361 8496 32 32 0 44803 36480 5329 4051 1.1912109 0 91
46000 0.75345782 4064 0.0040245838 -0.30924351 0.81340864 1.7179797 8568 29 29 0 45795 36480 5329 4064 1.1975591 0 91
47000 0.87187806 4017 0.004406241 -0.40855293 0.89054538 1.3105257 8586 36 36 0 46822 36480 5329 4017 1.1834816 0 91
48000 0.83729235 4078 0.0045115864 -0.33572888 0.91183673 1.3856733 8513 38 38 0 47866 36480 5329 4078 1.1996374 0 91
49000 0.65112065 4048 0.0030445536 -0.35483503 0.61533473 1.2659451 8705 32 32 0 48907 36480 5329 4048 1.1907782 0 91
50000 0.82730473 4066 0.0045492584 -0.31323342 0.91945063 1.1803982 8562 41 41 0 49965 36480 5329 4066 1.1696702 0 91
51000 0.74252279 4048 0.0046741422 -0.16166808 0.94469088 1.5539445 8564 35 35 0 50948 36480 5329 4048 1.1748481 0 91
52000 0.85671386 4051 0.0058575179 -0.092640701 1.183863 1.6307333 8609 19 19 0 51894 36480 5329 4051 1.1770671 0 91
53000 0.7233951 4068 0.0043421658 -0.20026358 0.87759512 1.453924 8582 28 28 0 52893 36480 5329 4068 1.2027667 0 91
54000 0.72117217 4051 0.0040247209 -0.26111018 0.81343635 1.3496518 8679 25 25 0 53831 36480 5329 4051 1.1823115 0 91
55000 0.87940919 4044 0.0047057065 -0.35924936 0.95107033 1.240057 8559 34 34 0 54813 36480 5329 4044 1.1815144 0 91
56000 0.83192698 4044 0.0046298732 -0.30382753 0.93574367 1.547229 8441 37 37 0 55740 36480 5329 4044 1.1761232 0 91
57000 0.91043729 4058 0.0050029377 -0.34540782 1.0111437 1.4951603 8550 32 32 0 56678 36480 5329 4058 1.2024504 0 91
58000 0.97648852 4036 0.0053292287 -0.37787747 1.0770904 1.4058278 8554 31 31 0 57683 36480 5329 4036 1.1746239 0 91
59000 0.72239185 4018 0.0046615138 -0.1342253 0.94213856 1.8337414 8716 35 35 0 58640 36480 5329 4018 1.1697661 0 91
60000 0.73800253 4032 0.0037590001 -0.33989225 0.75973152 1.399426 8561 32 32 0 59593 36480 5329 4032 1.1958194 0 91
61000 0.72778603 4060 0.0042599892 -0.22341476 0.86098642 1.3778202 8541 31 31 0 60573 36480 5329 4060 1.1980875 0 91
62000 0.80350669 4044 0.0042316822 -0.34195968 0.85526529 1.4379455 8487 37 37 0 61608 36480 5329 4044 1.1942365 0 91
63000 0.90084181 4066 0.0043040273 -0.47236734 0.86988695 1.4672845 8504 32 32 0 62670 36480 5329 4066 1.1829834 0 91
64000 0.87220486 4059 0.0047840275 -0.33268544 0.9668998 1.5398216 8588 34 34 0 63605 36480 5329 4059 1.1884975 0 91
65000 0.82469157 4057 0.004405933 -0.33830733 0.89048312 1.5284565 8783 32 32 0 64693 36480 5329 4057 1.1952722 0 91
66000 0.88692288 4081 0.0047264561 -0.36625105 0.95526405 1.3151847 8745 36 36 0 65755 36480 5329 4081 1.1834684 0 91
67000 0.83322374 4031 0.0047732147 -0.27678896 0.96471442 1.5085732 8415 34 34 0 66796 36480 5329 4031 1.1969 0 91
68000 0.75375865 4020 0.0044379413 -0.22614806 0.89695233 1.6351001 8573 30 30 0 67876 36480 5329 4020 1.1911308 0 91
69000 0.91169697 4055 0.0050371842 -0.34036318 1.0180653 1.2495539 8625 20 20 0 68979 36480 5329 4055 1.1860768 0 91
70000 0.80502435 4075 0.0042565586 -0.33919322 0.86029306 1.3194042 8571 36 36 0 69947 36480 5329 4075 1.18994 0 91
71000 0.8928873 4055 0.0050586026 -0.3080079 1.0223942 1.3949364 8698 32 32 0 71037 36480 5329 4055 1.2154821 0 91
72000 0.95397384 4050 0.0052866702 -0.35293209 1.0684889 1.2950893 8613 35 35 0 72090 36480 5329 4050 1.1790804 0 91
73000 0.78742879 4053 0.004378612 -0.28830762 0.88496127 1.5168042 8624 30 30 0 73174 36480 5329 4053 1.2008591 0 91
74000 0.79498726 4046 0.0042999917 -0.31545969 0.86907133 1.3751647 8562 22 22 0 74250 36480 5329 4046 1.1921334 0 91
75000 0.88929145 4051 0.0048995187 -0.33480254 0.99024172 1.6589606 8393 33 33 0 75296 36480 5329 4051 1.1753137 0 91
76000 0.98366685 4045 0.0049217494 -0.47092883 0.99473478 1.5271346 8555 29 29 0 76301 36480 5329 4045 1.2031327 0 91
77000 0.72618119 4051 0.0035028638 -0.37404618 0.7079638 1.5178344 8565 37 37 0 77315 36480 5329 4051 1.1993308 0 91
78000 0.80445682 4028 0.003992176 -0.39178196 0.8068587 1.3682816 8624 32 32 0 78299 36480 5329 4028 1.2065456 0 91
79000 1.091703 4052 0.0063793569 -0.33730561 1.2893318 1.5717928 8677 39 39 0 79249 36480 5329 4052 1.1725194 0 91
80000 0.77212865 4052 0.0041275152 -0.31625959 0.8342121 1.5583982 8526 33 33 0 80284 36480 5329 4052 1.1981751 0 91
81000 0.80732682 4061 0.004618782 -0.26941493 0.93350203 1.5517327 8444 36 36 0 81331 36480 5329 4061 1.2095831 0 91
82000 0.80166933 4057 0.0042732734 -0.33081602 0.86367129 1.3937505 8476 29 29 0 82335 36480 5329 4057 1.2047807 0 91
83000 0.76980598 4049 0.0041331379 -0.31166241 0.83534851 1.1411979 8561 34 34 0 83375 36480 5329 4049 1.1810941 0 91
84000 0.85529188 4076 0.0046148117 -0.34168531 0.93269959 1.3284464 8664 27 27 0 84510 36480 5329 4076 1.192734 0 91
85000 0.96167157 4034 0.0053261317 -0.35642617 1.0764645 1.3195071 8557 36 36 0 85517 36480 5329 4034 1.2000123 0 91
86000 0.88130862 4047 0.0046646382 -0.37037981 0.94277003 1.3595079 8634 36 36 0 86578 36480 5329 4047 1.1654584 0 91
87000 0.68799517 4037 0.0042184867 -0.17251446 0.85259834 1.5087731 8363 40 40 0 87606 36480 5329 4037 1.1833599 0 91
88000 0.83191621 4041 0.0048307277 -0.26321678 0.97633838 1.4008912 8597 39 39 0 88490 36480 5329 4041 1.1607031 0 91
89000 0.71456519 4036 0.0039378285 -0.26882761 0.79587453 1.2251569 8397 36 36 0 89436 36480 5329 4036 1.1991362 0 91
90000 0.75198251 4048 0.0043377839 -0.24374445 0.87670949 1.4896261 8551 29 29 0 90453 36480 5329 4048 1.1899998 0 91
91000 0.83310145 4032 0.0049902932 -0.232733 1.0085882 1.4140378 8583 48 48 0 91563 36480 5329 4032 1.1953029 0 91
92000 0.8819465 4050 0.0058087956 -0.14008461 1.1740157 1.753218 8610 46 46 0 92618 36480 5329 4050 1.1972268 0 91
93000 0.76721608 4048 0.0041923848 -0.29582907 0.8473229 1.4126521 8671 32 32 0 93690 36480 5329 4048 1.2027935 0 91
94000 0.8942606 4050 0.0051973822 -0.28200539 1.0504429 1.5743434 8751 21 21 0 94750 36480 5329 4050 1.1804594 0 91
95000 0.73609582 4036 0.0035091666 -0.38754512 0.70923765 1.28494 8660 31 31 0 95713 36480 5329 4036 1.1883125 0 91
96000 0.79430429 4078 0.0043400156 -0.30635284 0.87716056 1.4351927 8600 38 38 0 96695 36480 5329 4078 1.1704833 0 91
97000 0.74817621 4044 0.0038163094 -0.34346826 0.77131429 1.255104 8377 36 36 0 97683 36480 5329 4044 1.1756023 0 91
98000 0.78160255 4048 0.0039385343 -0.36857064 0.79601716 1.5320263 8350 25 25 0 98631 36480 5329 4048 1.181196 0 91
99000 0.804448 4053 0.004503827 -0.28835905 0.91026848 1.7569548 8506 35 35 0 99687 36480 5329 4053 1.1950898 0 91
100000 0.74975993 4032 0.004263269 -0.255493 0.86164929 1.5983872 8621 33 33 0 100701 36480 5329 4032 1.1910217 0 91
Loop time of 13.4746 on 8 procs for 100000 steps with 20211 atoms
Pair time (%) = 0.0563478 (0.418178)
Neigh time (%) = 0.794382 (5.89541)
Comm time (%) = 1.23773 (9.18569)
Outpt time (%) = 0.00554895 (0.0411809)
Other time (%) = 11.3806 (84.4595)
Nlocal: 2526.38 ave 2725 max 2337 min
Histogram: 2 0 0 1 1 1 1 0 1 1
Nghost: 23.875 ave 27 max 21 min
Histogram: 1 1 0 2 0 2 0 0 0 2
Neighs: 17 ave 25 max 12 min
Histogram: 3 1 0 1 1 0 0 0 0 2
Total # of neighbors = 136
Ave neighs/atom = 0.00672901
Neighbor list builds = 5008
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
# SRD viscosity demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
2 by 4 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Memory usage per processor = 2.7472 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.0173425 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00033614 (1.93825)
Neigh time (%) = 0.000266045 (1.53407)
Comm time (%) = 0.0115004 (66.3132)
Outpt time (%) = 2.78056e-05 (0.160332)
Other time (%) = 0.00521213 (30.0541)
Nlocal: 12.5 ave 18 max 10 min
Histogram: 1 3 1 1 0 1 0 0 0 1
Nghost: 27.75 ave 31 max 24 min
Histogram: 1 0 1 0 2 2 0 0 0 2
Neighs: 19 ave 30 max 16 min
Histogram: 4 1 2 0 0 0 0 0 0 1
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
create_atoms 4 region plane
Created 83521 atoms
set type 4 mass 0.1
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
delete_atoms overlap 1.0 small big
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 500 dump.poly.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 50000
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
SRD per actual grid cell = 4.93717
SRD viscosity = 0.23322
big/SRD mass density ratio = 0.161311
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19344 7.74495
ave/max big velocity = 1.43991 3.5724
Memory usage per processor = 11.8633 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.76223471 3964 0.0058318994 0.042955471 1.1786852 3.9611295 7412 29 29 0 611 36480 5329 3964 0.97424113 0 1
2000 0.83394503 3951 0.0050432506 -0.22328672 1.0192914 2.7492771 7829 30 30 0 1225 36480 5329 3951 1.0832295 0 3
3000 0.86856945 3991 0.0048205728 -0.31988251 0.97428597 2.4105317 7961 34 34 0 2000 36480 5329 3991 1.1243219 0 6
4000 0.88106888 4009 0.0066731082 0.035909261 1.3487019 3.025346 8002 33 33 0 2895 36480 5329 4009 1.1359575 0 6
5000 1.0764198 4036 0.0070136315 -0.18634051 1.4175251 2.7617336 8117 36 36 0 3808 36480 5329 4036 1.1147743 0 6
6000 1.0433139 4004 0.0059532709 -0.35132214 1.2032156 2.3597383 8004 23 23 0 4845 36480 5329 4004 1.1192873 0 6
7000 1.1551053 4026 0.0074766715 -0.20999681 1.5111101 2.280806 8269 36 36 0 5873 36480 5329 4026 1.1704244 0 6
8000 1.2222713 4008 0.0078175708 -0.24117508 1.5800092 1.967726 8218 33 33 0 7077 36480 5329 4008 1.1496529 0 6
9000 1.2240884 4012 0.0081583857 -0.17500037 1.6488913 2.3684675 8502 27 27 0 8359 36480 5329 4012 1.1664455 0 6
10000 1.2071315 4035 0.0073838443 -0.30627724 1.4923488 2.124366 8376 33 33 0 9778 36480 5329 4035 1.1942304 0 6
11000 1.1694272 4036 0.0077950192 -0.16699527 1.5754513 2.4203067 8623 40 40 0 11210 36480 5329 4036 1.1802896 0 42
12000 1.0911561 4044 0.0074117515 -0.12783343 1.4979891 2.4859591 8490 30 30 0 12647 36480 5329 4044 1.171701 0 42
13000 1.3535072 4023 0.0091503262 -0.16735325 1.8493724 2.7718999 8320 33 33 0 14082 36480 5329 4023 1.1841757 0 42
14000 1.4191753 4043 0.0095368758 -0.18707328 1.927498 2.8442438 8422 25 25 0 15462 36480 5329 4043 1.1567854 0 42
15000 1.703769 4053 0.010892787 -0.33707457 2.2015412 2.4160876 8123 34 34 0 16985 36480 5329 4053 1.1875794 0 42
16000 1.4270161 4032 0.010142553 -0.076342616 2.0499114 2.9568071 8360 34 34 0 18487 36480 5329 4032 1.164586 0 42
17000 1.2267528 4013 0.0080642511 -0.19799584 1.6298658 2.5084784 8477 27 27 0 20101 36480 5329 4013 1.1529604 0 42
18000 1.4228586 4050 0.01009573 -0.079611446 2.0404479 2.8013833 8519 33 33 0 21633 36480 5329 4050 1.1549291 0 42
19000 1.3041379 4040 0.0082901927 -0.26763462 1.6755308 1.9403854 8483 30 30 0 23194 36480 5329 4040 1.1592747 0 42
20000 1.3837406 4030 0.0092446911 -0.19332904 1.8684445 2.4550531 8425 25 25 0 24761 36480 5329 4030 1.1757648 0 42
21000 1.7882552 4031 0.012076007 -0.22381856 2.4406817 2.4206092 8581 40 40 0 26371 36480 5329 4031 1.1591574 0 42
22000 1.5079803 4015 0.010373742 -0.15025377 2.0966369 2.6321039 8383 33 33 0 27989 36480 5329 4015 1.1495522 0 42
23000 1.3835348 4044 0.0087922321 -0.28446888 1.776998 2.2729548 8441 30 30 0 29575 36480 5329 4044 1.1616377 0 42
24000 1.5854836 4044 0.0099174248 -0.35795983 2.0044107 2.2250073 8462 35 35 0 31298 36480 5329 4044 1.1796851 0 42
25000 1.5314412 4062 0.010880793 -0.082730301 2.1991171 2.6858232 8473 28 28 0 33079 36480 5329 4062 1.1726593 0 54
26000 1.2896316 4070 0.0090198232 -0.098554631 1.8229965 2.3437649 8453 40 40 0 34816 36480 5329 4070 1.1764482 0 54
27000 1.6956611 4035 0.012064024 -0.088275024 2.43826 2.8138661 8380 32 32 0 36453 36480 5329 4035 1.1622504 0 54
28000 1.3560979 4043 0.0088193796 -0.23810107 1.7824848 2.1799536 8611 30 30 0 38202 36480 5329 4043 1.1681248 0 54
29000 1.5837646 4029 0.010790526 -0.17893612 2.1808731 2.3116753 8480 26 26 0 39846 36480 5329 4029 1.1774511 0 54
30000 1.6549448 4035 0.01137773 -0.16631482 2.2995529 2.6236656 8637 30 30 0 41461 36480 5329 4035 1.1538405 0 54
31000 1.445315 4050 0.01013447 -0.1052417 2.0482777 2.4440312 8504 38 38 0 43099 36480 5329 4050 1.1690375 0 54
32000 1.5572315 4037 0.010828477 -0.13173155 2.1885434 2.5911192 8453 30 30 0 44760 36480 5329 4037 1.1612147 0 54
33000 2.018109 4068 0.013467519 -0.28506208 2.7219203 2.5784978 8701 40 40 0 46462 36480 5329 4068 1.1727186 0 54
34000 1.2455134 4066 0.0083640288 -0.16536113 1.6904539 2.3054829 8428 32 32 0 48055 36480 5329 4066 1.1712016 0 54
35000 1.6248596 4012 0.011213824 -0.15461501 2.2664259 2.8697537 8453 31 31 0 49658 36480 5329 4012 1.1693962 0 54
36000 1.5485873 4039 0.01112737 -0.058442367 2.2489527 3.0386676 8529 42 42 0 51330 36480 5329 4039 1.1750818 0 54
37000 1.5561543 4024 0.011313246 -0.032149816 2.2865202 2.7583779 8484 45 45 0 52981 36480 5329 4024 1.1613247 0 54
38000 1.5174762 4043 0.010120957 -0.21549294 2.0455467 2.2489655 8528 37 37 0 54637 36480 5329 4043 1.1692017 0 54
39000 1.5936544 4045 0.010946409 -0.16216642 2.2123787 2.7579117 8460 35 35 0 56452 36480 5329 4045 1.1670575 0 54
40000 1.7884514 4051 0.011913021 -0.2570519 2.4077408 2.494169 8539 37 37 0 58163 36480 5329 4051 1.1744075 0 54
41000 1.4173685 4042 0.0096196931 -0.16764288 1.9442362 1.9949409 8511 42 42 0 59967 36480 5329 4042 1.1747318 0 54
42000 1.4946304 4055 0.0098254549 -0.24117659 1.9858227 1.9958514 8395 39 39 0 61697 36480 5329 4055 1.1745062 0 54
43000 1.6486882 4041 0.011190255 -0.19488288 2.2616625 2.2173122 8473 28 28 0 63447 36480 5329 4041 1.1631975 0 54
44000 1.7473914 4055 0.011743128 -0.23020951 2.3734036 2.3913609 8421 30 30 0 65095 36480 5329 4055 1.1567659 0 54
45000 1.7826681 4027 0.011993913 -0.23208563 2.4240898 2.4582759 8539 35 35 0 66749 36480 5329 4027 1.1513285 0 54
46000 1.3988187 4049 0.0091738733 -0.23010838 1.8541315 2.3866226 8447 38 38 0 68459 36480 5329 4049 1.1728215 0 54
47000 1.8402398 4064 0.01271321 -0.17249031 2.569467 2.7748374 8524 33 33 0 70139 36480 5329 4064 1.1555276 0 54
48000 1.5634287 4042 0.011047794 -0.096639164 2.2328696 2.7173437 8561 33 33 0 71923 36480 5329 4042 1.177462 0 54
49000 1.789207 4058 0.012453079 -0.14902655 2.5168918 2.9310418 8545 38 38 0 73721 36480 5329 4058 1.1581934 0 54
50000 1.3475703 4010 0.0092484369 -0.13867816 1.8692016 2.1619389 8664 32 32 0 75439 36480 5329 4010 1.1589691 0 54
Loop time of 6.84 on 8 procs for 50000 steps with 20211 atoms
Pair time (%) = 0.0295508 (0.432029)
Neigh time (%) = 0.400359 (5.8532)
Comm time (%) = 0.622996 (9.10813)
Outpt time (%) = 0.00241029 (0.0352382)
Other time (%) = 5.78468 (84.5714)
Nlocal: 2526.38 ave 2651 max 2342 min
Histogram: 1 0 0 2 1 0 0 1 1 2
Nghost: 24.5 ave 27 max 23 min
Histogram: 1 0 4 0 0 2 0 0 0 1
Neighs: 17.375 ave 24 max 13 min
Histogram: 2 2 0 1 1 0 0 0 0 2
Total # of neighbors = 139
Ave neighs/atom = 0.00687744
Neighbor list builds = 2502
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.000 seconds
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
Setting atom values ...
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
Setting atom values ...
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
Setting atom values ...
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 1.27, bins = 15 15 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.00622873 on 1 procs for 1000 steps with 100 atoms
Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015709 | 0.0015709 | 0.0015709 | 0.0 | 25.22
Neigh | 0.0014016 | 0.0014016 | 0.0014016 | 0.0 | 22.50
Comm | 0.0012066 | 0.0012066 | 0.0012066 | 0.0 | 19.37
Output | 6.169e-06 | 6.169e-06 | 6.169e-06 | 0.0 | 0.10
Modify | 0.0013508 | 0.0013508 | 0.0013508 | 0.0 | 21.69
Other | | 0.0006926 | | | 11.12
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 152 ave 152 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms 4 region plane
Created 83521 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.016 seconds
set type 4 mass 0.1
Setting atom values ...
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.poly
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
SRD per actual grid cell = 4.9371727
SRD viscosity = 0.23321983
big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1934421 7.74495
ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 18.257419, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 1.0181191 3924 0.0076572255 0.030604433 1.5476019 3.7992573 7242 26 26 0 635 15876 5329 3924 0.98110339 0 3
2000 0.69783736 3992 0.0027817464 -0.47755891 0.56221876 1.9887267 7740 34 34 1 1186 15876 5329 3992 1.0611575 0 24
3000 0.89084297 3981 0.004323119 -0.45361044 0.87374558 1.7342893 7775 24 24 0 1923 15876 5329 3981 1.1207371 0 24
4000 0.84391846 4036 0.0045581483 -0.33619115 0.92124735 1.8456288 8060 43 43 0 2734 15876 5329 4036 1.1481354 0 24
5000 0.69548234 4056 0.0030033315 -0.42926535 0.60700333 1.6113509 8260 33 33 0 3638 15876 5329 4056 1.148749 0 24
6000 0.71729125 4023 0.0035318938 -0.35493291 0.71383106 1.673491 8224 29 29 0 4528 15876 5329 4023 1.1602572 0 24
7000 0.90145513 4032 0.0047423524 -0.38469129 0.95847685 1.7537778 8382 31 31 0 5395 15876 5329 4032 1.1543513 0 24
8000 0.6739295 4026 0.0029910322 -0.39963744 0.60451751 1.646528 8409 35 35 0 6293 15876 5329 4026 1.1540519 0 24
9000 0.80563959 4041 0.0042947965 -0.33238166 0.86802133 1.6597032 8429 29 29 0 7164 15876 5329 4041 1.1880521 0 24
10000 0.90407954 4022 0.0046865656 -0.39987673 0.94720178 1.445708 8349 30 30 0 8189 15876 5329 4022 1.171667 0 24
Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms
Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.019832 | 0.019832 | 0.019832 | 0.0 | 0.35
Neigh | 0.020738 | 0.020738 | 0.020738 | 0.0 | 0.37
Comm | 0.056875 | 0.056875 | 0.056875 | 0.0 | 1.01
Output | 0.00083247 | 0.00083247 | 0.00083247 | 0.0 | 0.01
Modify | 5.4828 | 5.4828 | 5.4828 | 0.0 | 97.05
Other | | 0.06854 | | | 1.21
Nlocal: 20211 ave 20211 max 20211 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 49 ave 49 max 49 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 160
Ave neighs/atom = 0.0079164811
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:11

317
examples/ASPHERE/poly/log.1Feb24.poly.g++.4 Normal file
View File

@ -0,0 +1,317 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
2 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.000 seconds
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
Setting atom values ...
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
Setting atom values ...
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
Setting atom values ...
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 1.27, bins = 15 15 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.00891987 on 4 procs for 1000 steps with 100 atoms
Performance: 48431181.463 tau/day, 112109.216 timesteps/s, 11.211 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00039835 | 0.00043547 | 0.00047558 | 0.0 | 4.88
Neigh | 0.00033856 | 0.00036829 | 0.00038548 | 0.0 | 4.13
Comm | 0.0065535 | 0.0065882 | 0.0066353 | 0.0 | 73.86
Output | 1.0991e-05 | 1.2359e-05 | 1.4677e-05 | 0.0 | 0.14
Modify | 0.00043639 | 0.00045662 | 0.00050811 | 0.0 | 5.12
Other | | 0.001059 | | | 11.87
Nlocal: 25 ave 29 max 23 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 33.75 ave 35 max 31 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 38 ave 46 max 34 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms 4 region plane
Created 83521 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.006 seconds
set type 4 mass 0.1
Setting atom values ...
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.poly
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
SRD per actual grid cell = 4.9371727
SRD viscosity = 0.23321983
big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1934421 7.74495
ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 18.257419, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.98459665 3968 0.0086216557 0.27547381 1.7425228 4.4010488 7403 34 34 0 663 25600 5329 3968 0.98292304 0 5
2000 0.74381104 4003 0.0041077507 -0.27806095 0.8302175 2.6170187 7746 32 32 0 1272 25600 5329 4003 1.0631936 0 5
3000 0.86305095 3969 0.0048953507 -0.29654658 0.98939933 2.1215334 7834 35 35 0 1974 25600 5329 3969 1.1209619 0 5
4000 0.8262932 4022 0.0049907905 -0.2224882 1.0086887 2.079935 8196 27 27 0 2753 25600 5329 4022 1.1040604 0 5
5000 0.85908819 4038 0.0043301633 -0.40487209 0.87516931 1.7917343 8347 28 28 0 3622 25600 5329 4038 1.1575336 0 5
6000 0.8048766 4024 0.0047529981 -0.2386377 0.96062844 1.8195477 8103 26 26 0 4536 25600 5329 4024 1.1818796 0 5
7000 0.84561126 4047 0.0039459142 -0.46245206 0.79750871 1.4432235 8154 20 20 0 5483 25600 5329 4047 1.1817402 0 5
8000 0.81543891 4037 0.0037591562 -0.45524091 0.75976306 1.7501338 8377 27 27 0 6472 25600 5329 4037 1.168956 0 5
9000 0.71960112 4045 0.0035243955 -0.3598901 0.71231557 1.7333111 8440 30 30 0 7386 25600 5329 4045 1.1765277 0 5
10000 1.0831334 4043 0.0053045911 -0.54175788 1.0721109 1.7434822 8283 33 33 0 8331 25600 5329 4043 1.1696048 0 5
Loop time of 1.82855 on 4 procs for 10000 steps with 20211 atoms
Performance: 472504.837 tau/day, 5468.806 timesteps/s, 110.530 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0057481 | 0.0069625 | 0.0087051 | 1.3 | 0.38
Neigh | 0.0067658 | 0.0070766 | 0.0076303 | 0.4 | 0.39
Comm | 0.10613 | 0.10693 | 0.10786 | 0.2 | 5.85
Output | 0.00053606 | 0.00059075 | 0.00063891 | 0.0 | 0.03
Modify | 1.6117 | 1.6525 | 1.6763 | 1.9 | 90.37
Other | | 0.05449 | | | 2.98
Nlocal: 5052.75 ave 5483 max 4509 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 27 ave 28 max 26 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 39.5 ave 55 max 26 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 158
Ave neighs/atom = 0.0078175251
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:03

318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.1 Normal file
View File

@ -0,0 +1,318 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.000 seconds
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
Setting atom values ...
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
Setting atom values ...
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
Setting atom values ...
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 1.27, bins = 15 15 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.00627198 on 1 procs for 1000 steps with 100 atoms
Performance: 68877814.583 tau/day, 159439.386 timesteps/s, 15.944 Matom-step/s
97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016224 | 0.0016224 | 0.0016224 | 0.0 | 25.87
Neigh | 0.0014238 | 0.0014238 | 0.0014238 | 0.0 | 22.70
Comm | 0.0011671 | 0.0011671 | 0.0011671 | 0.0 | 18.61
Output | 6.058e-06 | 6.058e-06 | 6.058e-06 | 0.0 | 0.10
Modify | 0.0013659 | 0.0013659 | 0.0013659 | 0.0 | 21.78
Other | | 0.0006868 | | | 10.95
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 152 ave 152 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms 4 region plane
Created 83521 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.017 seconds
set type 4 mass 0.1
Setting atom values ...
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 500 dump.poly.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
SRD per actual grid cell = 4.9371727
SRD viscosity = 0.23321983
big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1934421 7.74495
ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 18.257419, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.9260989 3936 0.007125623 0.060272296 1.4401597 3.9323 7454 34 34 0 666 15876 5329 3936 0.98459206 0 28
2000 0.90353395 4000 0.0052889652 -0.27731283 1.0689528 2.6405627 7698 23 23 0 1382 15876 5329 4000 1.0797162 0 46
3000 0.90859187 3993 0.0052873224 -0.28518115 1.0686207 2.2965966 7968 31 31 0 2142 15876 5329 3993 1.1267833 0 46
4000 0.84755099 4048 0.005174979 -0.21693597 1.045915 2.3794577 8137 36 36 0 3087 15876 5329 4048 1.1357649 0 46
5000 0.970415 4034 0.0070498808 -0.021066942 1.4248514 2.7424457 8202 29 29 0 4119 15876 5329 4034 1.1354594 0 46
6000 1.3230208 4023 0.0094580142 -0.059741745 1.9115593 3.1405056 8259 36 36 0 5151 15876 5329 4023 1.1508111 0 46
7000 1.2356555 4022 0.0076141503 -0.30223075 1.5388959 2.2740088 8336 33 33 0 6277 15876 5329 4022 1.1814599 0 46
8000 1.0470467 4044 0.0077098735 -0.001857114 1.5582425 2.97413 8285 40 40 0 7399 15876 5329 4044 1.1644871 0 46
9000 1.0827168 4054 0.0062150407 -0.35712609 1.2561219 2.0991523 8454 31 31 0 8664 15876 5329 4054 1.1744383 0 46
10000 1.3953419 4031 0.0091083246 -0.23817595 1.8408835 2.4493963 8468 34 34 0 10227 15876 5329 4031 1.1657737 0 62
Loop time of 5.74914 on 1 procs for 10000 steps with 20211 atoms
Performance: 150283.390 tau/day, 1739.391 timesteps/s, 35.155 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.021224 | 0.021224 | 0.021224 | 0.0 | 0.37
Neigh | 0.020586 | 0.020586 | 0.020586 | 0.0 | 0.36
Comm | 0.057881 | 0.057881 | 0.057881 | 0.0 | 1.01
Output | 0.00093386 | 0.00093386 | 0.00093386 | 0.0 | 0.02
Modify | 5.579 | 5.579 | 5.579 | 0.0 | 97.04
Other | | 0.06951 | | | 1.21
Nlocal: 20211 ave 20211 max 20211 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 50 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 141 ave 141 max 141 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141
Ave neighs/atom = 0.006976399
Neighbor list builds = 503
Dangerous builds = 0
Total wall time: 0:00:11

318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.4 Normal file
View File

@ -0,0 +1,318 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
2 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.000 seconds
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
Setting atom values ...
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
Setting atom values ...
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
Setting atom values ...
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 1.27, bins = 15 15 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.00883083 on 4 procs for 1000 steps with 100 atoms
Performance: 48919544.759 tau/day, 113239.687 timesteps/s, 11.324 Matom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00040021 | 0.00044336 | 0.00050371 | 0.0 | 5.02
Neigh | 0.00033682 | 0.00036617 | 0.00038566 | 0.0 | 4.15
Comm | 0.006519 | 0.0065578 | 0.0066015 | 0.0 | 74.26
Output | 1.1215e-05 | 1.2252e-05 | 1.4089e-05 | 0.0 | 0.14
Modify | 0.00043326 | 0.00044482 | 0.00046058 | 0.0 | 5.04
Other | | 0.001006 | | | 11.40
Nlocal: 25 ave 29 max 23 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 33.75 ave 35 max 31 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 38 ave 46 max 34 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
create_atoms 4 region plane
Created 83521 atoms
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
create_atoms CPU = 0.006 seconds
set type 4 mass 0.1
Setting atom values ...
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 14 14 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 63410 atoms, new total = 20211
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 500 dump.poly.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 20111 100
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
SRD per actual grid cell = 4.9371727
SRD viscosity = 0.23321983
big/SRD mass density ratio = 0.16131131
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1934421 7.74495
ave/max big velocity = 1.4399093 3.5724039
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.54
ghost atom cutoff = 2.54
binsize = 18.257419, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.83735494 3964 0.0071370659 0.19481352 1.4424724 3.9770741 7472 25 25 0 603 25600 5329 3964 0.96475118 0 2
2000 0.89694821 3981 0.0057098818 -0.18242861 1.1540242 3.1251883 7672 28 28 0 1238 25600 5329 3981 1.0589985 0 2
3000 0.99778172 3975 0.0051822049 -0.43931933 1.0473754 1.8970896 7814 24 24 0 1968 25600 5329 3975 1.1192504 0 3
4000 0.90067439 4030 0.0045096255 -0.43056442 0.91144042 1.8769981 8104 33 33 0 2911 25600 5329 4030 1.1382082 0 3
5000 0.90625848 4018 0.0055622776 -0.22613322 1.1241919 2.1866405 8287 26 26 0 3900 25600 5329 4018 1.1429442 0 3
6000 1.1284139 4022 0.0065653291 -0.354418 1.3269187 2.0312152 8268 35 35 0 5013 25600 5329 4022 1.1559733 0 3
7000 1.0073477 4043 0.0063924548 -0.2089691 1.291979 2.3332058 8433 39 39 0 6093 25600 5329 4043 1.1308958 0 3
8000 1.0621801 4050 0.00731979 -0.10324558 1.4794028 2.6610716 8353 40 40 0 7194 25600 5329 4050 1.1539521 0 3
9000 1.3173319 4046 0.0085268497 -0.23946297 1.7233616 2.4074596 8290 33 33 0 8498 25600 5329 4046 1.1601502 0 3
10000 1.1754738 4009 0.0074264713 -0.25049186 1.5009641 2.4237351 8305 30 30 0 9811 25600 5329 4009 1.1489476 0 43
Loop time of 1.85719 on 4 procs for 10000 steps with 20211 atoms
Performance: 465218.852 tau/day, 5384.477 timesteps/s, 108.826 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0056791 | 0.0069765 | 0.0089852 | 1.6 | 0.38
Neigh | 0.006991 | 0.0073805 | 0.0079507 | 0.4 | 0.40
Comm | 0.10756 | 0.10836 | 0.10942 | 0.2 | 5.83
Output | 0.00052479 | 0.0005511 | 0.00062567 | 0.0 | 0.03
Modify | 1.6443 | 1.6772 | 1.7031 | 1.7 | 90.31
Other | | 0.0567 | | | 3.05
Nlocal: 5052.75 ave 5381 max 4651 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 28.5 ave 30 max 26 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 34.75 ave 55 max 26 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 139
Ave neighs/atom = 0.006877443
Neighbor list builds = 501
Dangerous builds = 0
Total wall time: 0:00:03

4
examples/ASPHERE/star/in.star
View File

@ -7,7 +7,7 @@ dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
set type 1 mass 1.0
@ -108,4 +108,4 @@ thermo 1000
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

4
examples/ASPHERE/star/in.star.mp
View File

@ -7,7 +7,7 @@ dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
set type 1 mass 1.0
@ -109,4 +109,4 @@ thermo 1000
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

290
examples/ASPHERE/star/log.1Feb14.star.g++.8
View File

@ -1,290 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD diffusion demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.star fix molprop NULL Molecules
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
270 atoms
set type 1 mass 1.0
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
thermo 100
run 1000
Memory usage per processor = 2.64859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0.24721146
100 0 3.291475 0 3.291475 0.69158089
200 0 4.6176595 0 4.6176595 0.71737945
300 0 7.0921814 0 7.0921814 1.2163497
400 0 8.3666709 0 8.3666709 0.50645957
500 0 10.630838 0 10.630838 0.72764487
600 0 12.42157 0 12.42157 1.0130599
700 0 14.349074 0 14.349074 0.74795509
800 0 16.464746 0 16.464746 1.054549
900 0 18.253108 0 18.253108 0.51551753
1000 0 20.699563 0 20.699563 1.8084662
Loop time of 0.040709 on 8 procs for 1000 steps with 270 atoms
Pair time (%) = 0.00249004 (6.11668)
Neigh time (%) = 0.000995547 (2.44552)
Comm time (%) = 0.0116902 (28.7165)
Outpt time (%) = 0.000232756 (0.571755)
Other time (%) = 0.0253005 (62.1496)
Nlocal: 33.75 ave 42 max 22 min
Histogram: 1 0 1 0 0 2 0 1 1 2
Nghost: 23.375 ave 30 max 14 min
Histogram: 1 0 1 0 0 2 1 0 1 2
Neighs: 52.25 ave 69 max 27 min
Histogram: 1 0 1 0 1 0 1 1 1 2
Total # of neighbors = 418
Ave neighs/atom = 1.54815
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 60025 atoms
set type 2 mass 0.1
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.star
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
SRD per actual grid cell = 5.55866
SRD viscosity = 0.235582
big/SRD mass density ratio = 0.144099
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19085 7.72582
ave/max big velocity = 2.20262 5.4168
Memory usage per processor = 7.83759 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.3155168 8201 0.22979575 37.225304 37.439685 8.9588433 14577 56 56 0 687 57680 11236 8201 1.0283377 0 5 0
2000 0.82290815 8187 0.22918912 37.206746 37.340849 6.0607727 14326 56 56 0 1524 57680 11236 8187 1.0127464 0 5 0
3000 0.99928391 8168 0.22921842 37.182777 37.345623 10.268998 14389 68 68 0 2274 57680 11236 8168 1.023497 0 5 0
4000 1.0348458 8200 0.22920437 37.174693 37.343335 9.8954805 14335 51 51 0 3047 57680 11236 8200 1.0156984 0 5 0
5000 1.1496765 8199 0.22939095 37.186379 37.373733 8.0143223 14444 74 74 0 3868 57680 11236 8199 1.0104858 0 5 0
6000 0.91767381 8225 0.2292466 37.200668 37.350215 8.6189298 14131 61 61 0 4594 57680 11236 8225 1.0147272 0 5 0
7000 0.74806752 8203 0.22888634 37.169611 37.291518 9.8613421 14121 53 53 1 5322 57680 11236 8203 1.0198289 0 19 0
8000 1.1177867 8213 0.22924801 37.168286 37.350444 7.911691 14380 62 62 0 6024 57680 11236 8213 1.0066799 0 19 0
9000 1.1258411 8209 0.22939703 37.191253 37.374723 6.7377179 14350 51 51 0 6821 57680 11236 8209 1.0081225 0 19 0
10000 1.0597344 8182 0.22919436 37.169006 37.341703 9.7769156 14372 48 48 0 7543 57680 11236 8182 1.0099373 0 19 0
11000 1.3337199 8159 0.22943046 37.162823 37.38017 6.0897666 14359 58 58 0 8245 57680 11236 8159 1.0046221 0 19 0
12000 1.0280975 8184 0.22894286 37.133186 37.300728 2.555317 14162 51 51 0 8935 57680 11236 8184 1.0010306 0 19 0
13000 1.2318533 8190 0.22921487 37.144299 37.345045 6.1739989 14285 64 64 0 9634 57680 11236 8190 1.0138112 0 19 0
14000 1.1851991 8215 0.22915708 37.142485 37.335629 7.8380175 14151 66 66 0 10407 57680 11236 8215 1.0008011 0 19 0
15000 0.89853218 8214 0.22897294 37.159201 37.305628 4.0743953 14077 61 61 0 11069 57680 11236 8214 1.0041341 0 19 0
16000 1.0295974 8176 0.22891205 37.127921 37.295708 8.7527117 14000 48 48 0 11832 57680 11236 8176 1.0089653 0 23 0
17000 1.1793664 8219 0.22906268 37.128056 37.320249 5.2583304 14268 57 57 0 12490 57680 11236 8219 1.0157079 0 23 0
18000 0.90486919 8180 0.22891008 37.147927 37.295387 4.8498125 13939 64 64 0 13154 57680 11236 8180 0.99700921 0 23 0
19000 0.81486319 8219 0.22881911 37.147773 37.280566 1.6338041 13934 59 59 1 13861 57680 11236 8219 1.0099189 0 23 0
20000 1.0146287 8180 0.22896254 37.138587 37.303934 2.1682593 14057 45 45 0 14593 57680 11236 8180 1.0009466 0 23 0
21000 1.3031463 8164 0.22920646 37.131309 37.343674 6.570906 13944 65 65 0 15323 57680 11236 8164 0.98955239 0 23 0
22000 1.1258162 8174 0.22915084 37.151147 37.334613 9.0817519 14052 56 56 0 16042 57680 11236 8174 1.0083228 0 23 0
23000 1.1421222 8217 0.22906722 37.134865 37.320989 8.0529401 14143 66 66 0 16797 57680 11236 8217 1.0111161 0 23 0
24000 0.77402445 8168 0.22883056 37.156294 37.282431 6.8609899 14258 62 62 0 17559 57680 11236 8168 1.0080535 0 23 0
25000 0.94006632 8215 0.22879533 37.123496 37.276692 3.8570839 14446 48 48 0 18267 57680 11236 8215 1.0087899 0 23 0
26000 1.2808563 8192 0.22933112 37.155253 37.363985 5.3591484 13960 54 54 1 19004 57680 11236 8192 1.0101851 0 79 0
27000 1.0266075 8171 0.22898652 37.140542 37.307841 2.9961422 14049 56 56 1 19683 57680 11236 8171 0.99950217 0 79 0
28000 0.98185838 8199 0.22867129 37.096475 37.256481 12.080529 14106 61 62 0 20417 57680 11236 8199 1.0026548 0 79 0
29000 0.96921352 8192 0.22861802 37.089856 37.247802 8.257635 13891 63 64 0 21169 57680 11236 8192 1.0128041 0 79 0
30000 1.0107665 8223 0.22866616 37.090929 37.255646 9.4280788 14021 61 61 1 21863 57680 11236 8223 1.0034994 0 79 0
31000 1.1859435 8195 0.22877222 37.079661 37.272926 7.3863353 14093 78 78 0 22480 57680 11236 8195 0.9945582 0 79 0
32000 1.2951374 8172 0.22897044 37.094161 37.30522 6.4322363 13792 52 52 0 23151 57680 11236 8172 1.0026092 0 79 0
33000 0.82899919 8176 0.22823894 37.050944 37.186041 0.60210493 13797 62 62 0 23903 57680 11236 8176 1.0051075 0 79 0
34000 0.96685714 8165 0.22828901 37.036637 37.194199 8.1409866 13837 50 50 0 24591 57680 11236 8165 1.0157895 0 79 0
35000 0.95645753 8206 0.22833008 37.045022 37.200889 8.9956195 14130 63 63 0 25340 57680 11236 8206 1.0030424 0 79 0
36000 1.2933379 8197 0.22879201 37.065383 37.27615 8.3938627 13978 80 80 0 26085 57680 11236 8197 1.0094497 0 79 0
37000 1.1511434 8176 0.22861016 37.058929 37.246523 4.9481995 13856 49 49 1 26759 57680 11236 8176 1.0063722 0 79 0
38000 0.93310274 8181 0.22837532 37.056199 37.20826 5.9575015 13949 51 51 0 27445 57680 11236 8181 1.0152607 0 79 0
39000 1.0352467 8215 0.22861437 37.078501 37.247208 9.8519532 14109 69 69 0 28245 57680 11236 8215 1.005523 0 79 0
40000 1.2696427 8193 0.22885162 37.078957 37.285862 8.4680587 13931 54 55 0 28960 57680 11236 8193 1.0014074 0 79 0
41000 1.3270531 8193 0.22909573 37.109374 37.325634 4.3731598 14115 62 62 0 29668 57680 11236 8193 1.0022493 0 79 0
42000 1.3650738 8183 0.22911257 37.105921 37.328377 6.6345101 13659 52 52 0 30400 57680 11236 8183 1.0145834 0 79 0
43000 1.0780084 8209 0.22855316 37.06156 37.237235 5.5147087 14062 52 52 0 31092 57680 11236 8209 1.0031365 0 79 0
44000 0.96146724 8193 0.22846546 37.066263 37.222946 9.7967735 13699 56 56 0 31771 57680 11236 8193 1.0072364 0 79 0
45000 1.1733618 8200 0.2286481 37.061489 37.252703 9.8058881 13967 51 52 0 32532 57680 11236 8200 1.0068663 0 79 0
46000 0.94784989 8211 0.22845052 37.066048 37.220513 5.8834756 13944 34 35 0 33213 57680 11236 8211 1.0080225 0 79 0
47000 1.2354771 8207 0.22859598 37.042876 37.244213 6.1458407 13851 56 56 0 33886 57680 11236 8207 1.0151781 0 79 0
48000 1.0834097 8164 0.22835968 37.029157 37.205712 6.7378814 13944 56 56 0 34578 57680 11236 8164 1.0128575 0 79 0
49000 0.9386786 8208 0.22837254 37.054838 37.207808 5.0809383 13618 53 53 0 35328 57680 11236 8208 1.0045622 0 79 0
50000 1.047176 8154 0.22859126 37.072791 37.243442 4.8016981 13847 55 55 0 36059 57680 11236 8154 1.0005378 0 79 0
51000 1.0943417 8222 0.22844191 37.040773 37.21911 7.9359541 13897 61 61 0 36711 57680 11236 8222 1.0036343 0 79 0
52000 1.2811259 8200 0.22871149 37.054255 37.263031 4.9958687 13744 56 56 0 37402 57680 11236 8200 1.0049188 0 79 0
53000 1.0997162 8218 0.22853173 37.05453 37.233743 4.6772882 13967 65 65 0 38082 57680 11236 8218 1.0054533 0 79 0
54000 0.97625718 8185 0.2283994 37.05309 37.212184 5.9026406 13741 69 69 0 38761 57680 11236 8185 0.99393606 0 79 0
55000 0.97919465 8192 0.22835234 37.044944 37.204516 6.8419755 13990 58 58 0 39453 57680 11236 8192 1.0103052 0 79 0
56000 0.86300824 8181 0.22842164 37.075169 37.215808 6.8288348 13751 57 57 0 40118 57680 11236 8181 0.99683099 0 79 0
57000 0.89429559 8181 0.22851743 37.085677 37.231414 9.378853 13746 72 72 0 40730 57680 11236 8181 1.0086882 0 79 0
58000 1.0853441 8172 0.22857719 37.064279 37.24115 7.4580035 13869 58 58 1 41462 57680 11236 8172 1.0092141 0 79 0
59000 1.0149632 8199 0.22868187 37.092803 37.258205 8.2913359 13720 54 54 0 42159 57680 11236 8199 1.0082738 0 79 0
60000 0.99214038 8241 0.22871146 37.101344 37.263026 7.9905647 13776 67 67 0 42858 57680 11236 8241 1.0027929 0 79 0
61000 0.95721926 8211 0.2285241 37.07651 37.232501 11.837258 13907 62 62 0 43565 57680 11236 8211 1.0201117 0 79 0
62000 1.1457294 8195 0.22866514 37.068769 37.25548 9.7934944 13796 40 40 1 44292 57680 11236 8195 1.005192 0 79 0
63000 1.1096177 8193 0.22863037 37.068989 37.249815 8.0809047 13984 54 55 0 44986 57680 11236 8193 1.0076438 0 79 0
64000 1.1643495 8168 0.22860016 37.055147 37.244893 4.7376475 13857 50 50 1 45657 57680 11236 8168 1.002011 0 79 0
65000 1.2172585 8201 0.22845803 37.023368 37.221736 8.9744616 13610 53 53 0 46295 57680 11236 8201 1.0033999 0 79 0
66000 0.99924611 8189 0.22807344 36.996237 37.159077 8.5854786 13849 49 49 0 46944 57680 11236 8189 1.015528 0 79 0
67000 1.2543542 8165 0.22831075 36.993327 37.19774 5.0081411 13906 57 58 1 47666 57680 11236 8165 1.0189753 0 79 0
68000 1.0360874 8205 0.22812149 36.99806 37.166904 2.2431831 13650 52 52 0 48363 57680 11236 8205 1.0076864 0 79 0
69000 0.69755552 8218 0.22766249 36.978446 37.092121 4.2769033 13654 51 51 0 49044 57680 11236 8218 1.009863 0 79 0
70000 0.90921994 8167 0.22796236 36.992809 37.140978 9.3555738 13927 52 52 0 49793 57680 11236 8167 1.0015807 0 79 0
71000 0.95608837 8177 0.22797832 36.987772 37.143579 8.0740708 13612 63 63 0 50464 57680 11236 8177 1.0097491 0 79 0
72000 1.0374855 8192 0.22803745 36.98414 37.153212 4.4789755 13561 52 52 0 51127 57680 11236 8192 0.99496724 0 79 0
73000 0.90636338 8214 0.22783374 36.97232 37.120024 9.3364171 13598 53 53 0 51799 57680 11236 8214 1.0078219 0 79 0
74000 1.1869638 8179 0.22834625 37.010094 37.203525 4.8292929 13771 51 51 0 52500 57680 11236 8179 0.98865277 0 79 0
75000 1.0177351 8188 0.22826506 37.024443 37.190296 5.1808505 13508 55 55 0 53183 57680 11236 8188 0.99903558 0 79 0
76000 1.062496 8230 0.22820987 37.008158 37.181305 8.1032524 13769 58 58 0 53864 57680 11236 8230 0.99397021 0 79 0
77000 0.9762027 8131 0.22831271 37.038975 37.19806 10.309798 13787 47 47 0 54553 57680 11236 8131 1.0066289 0 79 0
78000 1.0688533 8160 0.22855677 37.06364 37.237824 7.4800503 13224 58 58 0 55248 57680 11236 8160 1.0073477 0 79 0
79000 1.2598513 8151 0.22844942 37.015024 37.220333 7.4724924 13859 63 63 0 55911 57680 11236 8151 1.0065168 0 79 0
80000 1.1044575 8176 0.22834306 37.023019 37.203005 3.0142586 13579 62 62 0 56611 57680 11236 8176 1.0008704 0 79 0
81000 1.2756491 8205 0.22853748 37.026797 37.23468 6.434309 13702 52 52 0 57313 57680 11236 8205 1.0058366 0 79 0
82000 1.1276926 8193 0.22857049 37.056287 37.240059 11.825248 13621 63 63 0 58011 57680 11236 8193 1.0113537 0 79 0
83000 0.96941691 8173 0.22824759 37.029471 37.18745 2.9152799 13478 48 49 0 58712 57680 11236 8173 1.0168819 0 79 0
84000 1.0770325 8186 0.22821292 37.006285 37.181802 5.0626072 13733 60 61 0 59433 57680 11236 8186 1.0177757 0 79 0
85000 1.1959489 8175 0.2284266 37.021719 37.216615 5.3844747 13964 55 55 0 60226 57680 11236 8175 1.007371 0 79 0
86000 1.035779 8204 0.22845952 37.053185 37.221979 7.5428558 13713 64 64 0 60982 57680 11236 8204 1.0110801 0 79 0
87000 1.1878573 8204 0.22836412 37.012859 37.206436 3.1124447 13655 47 47 0 61668 57680 11236 8204 1.0034968 0 79 0
88000 0.98402924 8206 0.22815704 37.012337 37.172698 10.613422 13947 56 56 0 62325 57680 11236 8206 1.0081468 0 79 0
89000 0.83763529 8199 0.22807071 37.022127 37.158631 5.4628281 13966 50 50 0 63012 57680 11236 8199 0.99956322 0 79 0
90000 1.1976672 8187 0.22849599 37.032745 37.227921 5.5583762 13903 43 43 0 63697 57680 11236 8187 1.0047573 0 79 0
91000 0.94863742 8188 0.22818061 37.021945 37.176537 5.157692 13859 46 46 0 64382 57680 11236 8188 1.0041894 0 79 0
92000 1.2038427 8172 0.22846103 37.026042 37.222224 6.685059 13675 57 57 0 65081 57680 11236 8172 1.0036906 0 79 0
93000 0.95835618 8210 0.22828548 37.037446 37.193622 8.0038227 13826 57 58 0 65761 57680 11236 8210 1.0076646 0 79 0
94000 1.2451267 8197 0.22856138 37.035665 37.238575 3.6305666 13918 62 62 0 66462 57680 11236 8197 1.0110913 0 79 0
95000 0.82128549 8206 0.22809174 37.028218 37.162057 8.7024273 13817 44 44 0 67185 57680 11236 8206 1.0032224 0 79 0
96000 0.83473128 8199 0.22820935 37.04519 37.18122 8.1258155 14167 54 54 0 67912 57680 11236 8199 1.0035561 0 79 0
97000 0.98924493 8196 0.22847944 37.064014 37.225225 8.9964529 14039 48 51 0 68608 57680 11236 8196 1.0007515 0 79 0
98000 1.1749668 8211 0.22879851 37.085733 37.27721 7.0283734 13850 58 59 0 69305 57680 11236 8211 0.99525651 0 79 0
99000 1.3269705 8163 0.22890919 37.078994 37.295241 9.7962294 13885 63 63 0 69994 57680 11236 8163 1.011015 0 107 0
100000 1.0020436 8171 0.22867221 37.093336 37.256632 4.9455304 14102 55 56 0 70707 57680 11236 8171 1.0072865 0 107 0
Loop time of 33.9872 on 8 procs for 100000 steps with 43990 atoms
Pair time (%) = 0.379981 (1.11801)
Neigh time (%) = 2.01801 (5.93757)
Comm time (%) = 2.30255 (6.77476)
Outpt time (%) = 0.00694308 (0.0204285)
Other time (%) = 29.2797 (86.1492)
Nlocal: 5498.75 ave 6445 max 4431 min
Histogram: 1 0 0 2 1 1 0 1 1 1
Nghost: 62.5 ave 70 max 57 min
Histogram: 3 0 0 1 1 0 1 0 1 1
Neighs: 207 ave 365 max 92 min
Histogram: 1 1 1 1 2 0 1 0 0 1
Total # of neighbors = 1656
Ave neighs/atom = 0.0376449
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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examples/ASPHERE/star/log.1Feb14.star.mp.g++.8
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@ -1,291 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD viscosity demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.star fix molprop NULL Molecules
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
270 atoms
set type 1 mass 1.0
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
thermo 100
run 1000
Memory usage per processor = 2.64859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0.24721146
100 0 3.291475 0 3.291475 0.69158089
200 0 4.6176595 0 4.6176595 0.71737945
300 0 7.0921814 0 7.0921814 1.2163497
400 0 8.3666709 0 8.3666709 0.50645957
500 0 10.630838 0 10.630838 0.72764487
600 0 12.42157 0 12.42157 1.0130599
700 0 14.349074 0 14.349074 0.74795509
800 0 16.464746 0 16.464746 1.054549
900 0 18.253108 0 18.253108 0.51551753
1000 0 20.699563 0 20.699563 1.8084662
Loop time of 0.0484946 on 8 procs for 1000 steps with 270 atoms
Pair time (%) = 0.00250834 (5.17242)
Neigh time (%) = 0.000999629 (2.06132)
Comm time (%) = 0.0154877 (31.9369)
Outpt time (%) = 0.000273734 (0.564464)
Other time (%) = 0.0292252 (60.2649)
Nlocal: 33.75 ave 42 max 22 min
Histogram: 1 0 1 0 0 2 0 1 1 2
Nghost: 23.375 ave 30 max 14 min
Histogram: 1 0 1 0 0 2 1 0 1 2
Neighs: 52.25 ave 69 max 27 min
Histogram: 1 0 1 0 1 0 1 1 1 2
Total # of neighbors = 418
Ave neighs/atom = 1.54815
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 60025 atoms
set type 2 mass 0.1
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.star.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
SRD per actual grid cell = 5.55866
SRD viscosity = 0.235582
big/SRD mass density ratio = 0.144099
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19085 7.72582
ave/max big velocity = 2.20262 5.4168
Memory usage per processor = 7.83759 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.3197888 8196 0.2296966 37.208454 37.42353 7.4694369 14388 59 59 0 707 57680 11236 8196 1.0259754 0 5 0
2000 1.5789784 8192 0.22993088 37.204387 37.461702 7.6252927 14352 56 56 0 1521 57680 11236 8192 1.0168955 0 7 0
3000 1.286186 8153 0.2296947 37.213621 37.423222 8.8624394 14533 73 73 0 2299 57680 11236 8153 1.0109574 0 7 0
4000 2.0862082 8194 0.23044604 37.20566 37.545635 7.8064365 14228 48 48 0 3068 57680 11236 8194 1.0046224 0 7 0
5000 1.892401 8172 0.23019301 37.196017 37.504409 7.9041579 14290 55 55 0 3866 57680 11236 8172 1.005673 0 7 0
6000 2.1063411 8138 0.23041636 37.197543 37.540799 4.8468885 13803 47 47 0 4638 57680 11236 8138 1.0083722 0 7 0
7000 2.3549938 8174 0.23071159 37.205123 37.5889 6.5703154 13773 58 58 0 5398 57680 11236 8174 1.0039365 0 7 0
8000 3.0660305 8216 0.23155654 37.226914 37.726563 11.977404 13898 65 65 0 6180 57680 11236 8216 0.99586836 0 7 0
9000 3.1510761 8203 0.23143756 37.19367 37.707178 7.2978028 13815 54 54 0 6985 57680 11236 8203 0.99794556 0 7 0
10000 2.7472522 8196 0.23096076 37.181796 37.629496 11.336568 14012 59 59 0 7812 57680 11236 8196 0.99210203 0 11 0
11000 2.1776587 8186 0.23038876 37.181424 37.536302 9.2106614 14063 64 64 0 8627 57680 11236 8186 1.003993 0 11 0
12000 3.0146734 8196 0.2312123 37.179198 37.670478 5.9303705 14077 60 60 0 9436 57680 11236 8196 0.98496016 0 23 0
13000 3.0029829 8179 0.23150759 37.229214 37.718589 7.3329148 14116 74 74 0 10339 57680 11236 8179 1.0039911 0 23 0
14000 3.2942972 8191 0.23166868 37.207985 37.744833 9.6428846 14019 56 57 0 11290 57680 11236 8191 0.99410574 0 23 0
15000 3.8480961 8213 0.23228155 37.217589 37.844686 2.1025549 13746 68 68 0 12175 57680 11236 8213 1.0011325 0 23 0
16000 3.2573043 8195 0.2316418 37.209634 37.740454 8.1255708 13682 55 55 0 13104 57680 11236 8195 1.0061399 0 23 0
17000 3.3579037 8186 0.2315443 37.177356 37.72457 9.8606039 13833 54 54 0 14034 57680 11236 8186 1.004156 0 23 0
18000 4.7903055 8194 0.23307181 37.192799 37.973441 3.8090185 13914 55 55 1 15012 57680 11236 8194 0.98633014 0 23 0
19000 4.4696839 8183 0.23293212 37.222288 37.950681 7.1931333 13499 54 54 0 15960 57680 11236 8183 0.98359656 0 23 0
20000 5.0239019 8126 0.23355887 37.234085 38.052794 5.1504203 13600 58 58 0 16972 57680 11236 8126 0.98555755 0 23 0
21000 4.6595948 8155 0.23275722 37.162845 37.922186 9.0375076 13965 73 74 0 17966 57680 11236 8155 0.99574348 0 23 0
22000 4.043444 8124 0.23247599 37.217434 37.876366 3.9265975 13584 53 53 2 18989 57680 11236 8124 0.9943952 0 23 0
23000 4.9981028 8127 0.23314549 37.170939 37.985445 4.2352191 13589 47 47 0 19958 57680 11236 8127 0.99276741 0 47 0
24000 4.7542655 8145 0.23295434 37.179533 37.954302 7.365415 13753 51 51 0 20955 57680 11236 8145 0.99024306 0 47 0
25000 4.2987054 8177 0.23252979 37.184601 37.885131 10.735771 13536 58 58 0 21994 57680 11236 8177 0.99215977 0 47 0
26000 4.4136261 8170 0.23331629 37.294015 38.013272 14.25925 13842 58 58 0 22979 57680 11236 8170 0.99283174 0 47 0
27000 4.0546007 8173 0.23283443 37.274016 37.934766 6.22969 13877 51 51 0 23997 57680 11236 8173 0.98496361 0 47 0
28000 4.5919614 8151 0.23364384 37.318319 38.066638 4.9917488 13836 60 61 1 25071 57680 11236 8151 0.99390956 0 47 0
29000 4.8025535 8189 0.23313849 37.201667 37.984305 4.7895172 13978 46 47 0 26121 57680 11236 8189 0.99018295 0 47 0
30000 4.2835226 8139 0.23247583 37.178284 37.87634 8.994878 13988 61 61 0 27141 57680 11236 8139 0.98735471 0 47 0
31000 5.4049428 8133 0.23373767 37.201121 38.081927 7.6419291 13771 58 58 0 28207 57680 11236 8133 0.98354883 0 47 0
32000 5.0299584 8177 0.23336211 37.201041 38.020738 8.1206741 14036 55 55 0 29303 57680 11236 8177 0.98239013 0 47 0
33000 4.2993816 8158 0.23320229 37.29406 37.9947 10.745167 13583 51 51 0 30344 57680 11236 8158 0.98952524 0 47 0
34000 5.8334257 8179 0.23458355 37.269109 38.219741 11.094625 13921 62 62 0 31432 57680 11236 8179 0.98822406 0 47 0
35000 6.481318 8168 0.23501133 37.233224 38.289439 7.9397445 13942 56 56 0 32518 57680 11236 8168 0.98830425 0 47 0
36000 4.967891 8186 0.23366927 37.261199 38.070782 8.3979019 13952 51 51 0 33626 57680 11236 8186 0.99579665 0 47 0
37000 5.3458808 8145 0.2337339 37.210132 38.081312 5.4177865 13659 55 55 0 34715 57680 11236 8145 1.0009582 0 47 0
38000 6.3597955 8159 0.23479285 37.217431 38.253842 6.1408411 13754 55 56 0 35754 57680 11236 8159 0.98853252 0 47 0
39000 6.1217173 8195 0.23447066 37.203737 38.20135 9.6016075 13756 70 70 0 36807 57680 11236 8195 0.98652299 0 47 0
40000 5.0218059 8159 0.23370899 37.258886 38.077254 6.6460004 13603 56 56 1 37933 57680 11236 8159 0.98674585 0 47 0
41000 5.5873722 8138 0.23429215 37.26173 38.172265 1.4183057 13634 51 52 1 39050 57680 11236 8138 0.98833769 0 47 0
42000 5.5502013 8170 0.23405343 37.228895 38.133372 7.8338637 13913 72 72 0 40105 57680 11236 8170 0.99124609 0 47 0
43000 4.6854143 8161 0.23326283 37.241013 38.004562 7.857085 13759 48 48 0 41187 57680 11236 8161 0.99649848 0 47 0
44000 6.3172352 8180 0.2348893 37.240081 38.269557 12.59288 13810 55 55 0 42292 57680 11236 8180 0.99164669 0 47 0
45000 6.1213322 8166 0.23449878 37.208381 38.205931 6.3760889 13854 48 49 0 43406 57680 11236 8166 0.98981447 0 47 0
46000 5.0015874 8195 0.23354809 37.235965 38.051038 10.992836 13962 62 62 0 44527 57680 11236 8195 0.99128184 0 47 0
47000 5.0499615 8190 0.23376151 37.262854 38.085811 8.7985849 14105 64 64 0 45653 57680 11236 8190 0.99020272 0 47 0
48000 5.202255 8170 0.23400688 37.278013 38.125788 4.7389097 13754 51 51 0 46705 57680 11236 8170 0.98792999 0 47 0
49000 5.6144741 8167 0.23429848 37.258346 38.173297 6.3247626 13953 51 51 1 47846 57680 11236 8167 0.99270232 0 47 0
50000 6.3027505 8145 0.2347122 37.213588 38.240703 6.4424496 13843 59 59 0 49061 57680 11236 8145 0.99810926 0 47 0
51000 5.2050769 8154 0.23390178 37.26043 38.108665 6.6143765 13999 51 51 0 50075 57680 11236 8154 0.99525977 0 47 0
52000 5.4749884 8175 0.23418567 37.262697 38.154917 8.7256782 13916 51 51 0 51249 57680 11236 8175 0.99508289 0 47 0
53000 5.1367735 8158 0.23393299 37.276645 38.113748 9.3248422 13910 41 41 0 52381 57680 11236 8158 0.98956839 0 47 0
54000 4.8680584 8211 0.23402832 37.335968 38.129281 4.8979582 14214 63 64 0 53439 57680 11236 8211 0.98838908 0 47 0
55000 4.6223848 8167 0.23347097 37.285196 38.038473 6.1898955 14162 46 46 0 54504 57680 11236 8167 0.97935238 0 47 0
56000 4.9075747 8168 0.23409393 37.340218 38.139971 12.20686 13980 60 60 0 55540 57680 11236 8168 0.99885966 0 47 0
57000 4.8736147 8143 0.23354696 37.256636 38.050854 3.9348529 13857 59 59 0 56680 57680 11236 8143 0.98434054 0 47 0
58000 5.6134201 8162 0.23393276 37.198932 38.113711 3.7493067 13866 55 55 2 57767 57680 11236 8162 0.99041155 0 47 0
59000 5.440371 8197 0.23353392 37.162151 38.04873 4.1297786 13748 67 67 0 58894 57680 11236 8197 0.98824623 0 47 0
60000 5.2754075 8148 0.23359083 37.198307 38.058003 7.1427242 13781 55 55 0 60028 57680 11236 8148 0.9831827 0 47 0
61000 5.8228233 8153 0.23438274 37.23812 38.187025 8.8839625 14019 48 48 0 61204 57680 11236 8153 0.98566731 0 47 0
62000 5.7623285 8129 0.23480056 37.316052 38.255098 9.992341 13791 67 68 0 62385 57680 11236 8129 0.97338459 0 47 0
63000 6.095315 8178 0.23455792 37.222257 38.215567 10.722535 14210 54 54 0 63448 57680 11236 8178 0.98135973 0 47 0
64000 5.2494942 8189 0.23380158 37.236866 38.092339 4.4010329 13869 51 51 0 64538 57680 11236 8189 0.98071569 0 47 0
65000 5.6534858 8151 0.23405328 37.212039 38.133348 8.9144953 14065 53 53 0 65661 57680 11236 8151 0.99589337 0 47 0
66000 5.3999138 8165 0.23453061 37.33113 38.211116 7.3102657 13994 61 62 0 66785 57680 11236 8165 0.98715854 0 47 0
67000 6.3619419 8183 0.23459518 37.184875 38.221636 4.0425684 13859 49 49 0 67944 57680 11236 8183 0.98479883 0 47 0
68000 6.2170116 8157 0.23470153 37.225822 38.238965 9.3090925 13598 50 50 0 69121 57680 11236 8157 0.98683618 0 47 0
69000 6.8545121 8179 0.23542272 37.239433 38.356465 9.4175179 13911 59 59 0 70316 57680 11236 8179 0.99828763 0 47 0
70000 5.1476232 8154 0.23389653 37.268937 38.107809 7.6438157 13882 55 55 0 71380 57680 11236 8154 0.99088995 0 47 0
71000 5.9284504 8161 0.23499148 37.320087 38.286205 9.1242845 13968 60 60 0 72478 57680 11236 8161 0.98627289 0 47 0
72000 5.8044136 8180 0.23473312 37.298207 38.244111 6.6084298 14066 56 56 0 73653 57680 11236 8180 0.97959812 0 47 0
73000 5.3690655 8148 0.23424676 37.289911 38.16487 8.7025002 14433 55 55 1 74740 57680 11236 8148 0.97949605 0 47 0
74000 4.8144157 8192 0.23361625 37.277572 38.062144 7.6685178 14425 58 58 1 75918 57680 11236 8192 0.98949387 0 47 0
75000 4.9424688 8143 0.23362551 37.258213 38.063652 5.5882668 13938 42 42 0 77080 57680 11236 8143 0.99602516 0 47 0
76000 6.3017203 8178 0.23500247 37.261048 38.287995 5.2760401 13952 47 47 0 78240 57680 11236 8178 0.98484281 0 47 0
77000 5.3086333 8208 0.23389726 37.242817 38.107928 4.034731 14052 47 47 0 79331 57680 11236 8208 0.9896033 0 47 0
78000 6.1152265 8157 0.23546115 37.366171 38.362726 11.521489 13980 58 58 0 80446 57680 11236 8157 0.98562154 0 47 0
79000 6.5034669 8173 0.23569944 37.341726 38.40155 5.0939756 14030 74 74 0 81663 57680 11236 8173 0.98837711 0 47 0
80000 6.1688245 8182 0.23495003 37.274162 38.279451 6.3337593 14292 50 50 0 82872 57680 11236 8182 0.99316806 0 47 0
81000 6.3818913 8189 0.23516767 37.274899 38.314911 9.0232294 14259 56 56 0 84072 57680 11236 8189 0.98467136 0 47 0
82000 6.502454 8171 0.23498158 37.224932 38.284591 7.6685939 13970 63 63 0 85190 57680 11236 8171 0.99511647 0 47 0
83000 7.2245962 8142 0.23564338 37.215075 38.392416 6.0363083 13789 61 61 0 86416 57680 11236 8142 0.99223565 0 47 0
84000 6.3529888 8192 0.23477435 37.215526 38.250828 7.2109855 14062 52 52 0 87555 57680 11236 8192 0.98623425 0 47 0
85000 6.5185235 8177 0.23516364 37.251976 38.314254 5.266764 14325 52 53 0 88732 57680 11236 8177 0.97895516 0 47 0
86000 5.742959 8170 0.23432816 37.242243 38.178133 6.0834874 13922 48 48 0 89836 57680 11236 8170 0.99203022 0 47 0
87000 6.548676 8177 0.23495538 37.213132 38.280324 6.2502744 14147 48 48 0 91035 57680 11236 8177 0.98829721 0 47 0
88000 5.9500587 8193 0.23446634 37.231006 38.200645 6.2196893 13960 44 44 0 92206 57680 11236 8193 0.98956808 0 47 0
89000 5.0591447 8174 0.23386574 37.278339 38.102793 11.164066 14071 54 54 0 93437 57680 11236 8174 0.99827748 0 47 0
90000 6.4930795 8181 0.23544182 37.301445 38.359576 6.6167028 14183 63 63 1 94640 57680 11236 8181 0.99559871 0 47 0
91000 6.489104 8187 0.23523152 37.267829 38.325313 6.4932786 14223 51 51 1 95718 57680 11236 8187 0.99090796 0 47 0
92000 6.3543839 8184 0.23502776 37.256587 38.292116 7.1553807 14265 66 66 1 96903 57680 11236 8184 0.98979354 0 47 0
93000 5.3818591 8195 0.23393122 37.236417 38.11346 7.9445503 14327 70 70 0 98138 57680 11236 8195 1.0030252 0 47 0
94000 5.6818206 8171 0.2343696 37.258958 38.184885 5.7311019 13943 63 63 0 99306 57680 11236 8171 0.99691591 0 47 0
95000 4.8295204 8160 0.23371941 37.291918 38.078951 4.5703653 13682 48 48 1 100491 57680 11236 8160 1.0078235 0 47 0
96000 6.7415726 8191 0.23539566 37.253429 38.352056 11.837168 13783 53 53 1 101761 57680 11236 8191 1.0010125 0 49 0
97000 6.5298825 8160 0.2354153 37.291126 38.355255 7.6012271 13688 65 65 0 103010 57680 11236 8160 0.99694671 0 49 0
98000 6.2804965 8175 0.23496877 37.259015 38.282504 5.4636503 14041 55 55 0 104259 57680 11236 8175 1.0042653 0 49 0
99000 5.7684681 8173 0.2344998 37.26605 38.206096 1.7807753 14082 58 59 0 105418 57680 11236 8173 0.99124491 0 49 0
100000 6.1371898 8170 0.23495644 37.28036 38.280495 7.7665232 13908 53 53 0 106633 57680 11236 8170 0.98281247 0 49 0
Loop time of 34.1892 on 8 procs for 100000 steps with 43990 atoms
Pair time (%) = 0.361362 (1.05695)
Neigh time (%) = 2.01143 (5.88324)
Comm time (%) = 2.27139 (6.64359)
Outpt time (%) = 0.00694269 (0.0203067)
Other time (%) = 29.5381 (86.3959)
Nlocal: 5498.75 ave 6478 max 4726 min
Histogram: 2 0 1 0 1 2 1 0 0 1
Nghost: 52.875 ave 59 max 44 min
Histogram: 1 0 1 0 1 0 1 0 2 2
Neighs: 186.25 ave 293 max 81 min
Histogram: 1 0 1 3 0 0 1 0 0 2
Total # of neighbors = 1490
Ave neighs/atom = 0.0338713
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
270 atoms
read_data CPU = 0.011 seconds
set type 1 mass 1.0
Setting atom values ...
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 38 38 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.3101488 0 0 0.21350573 0.32876464
100 5.0954142 3.291475 0 4.1218387 1.0087565
200 13.041252 4.6176595 0 6.7429006 1.5291618
300 11.912727 7.0921814 0 9.0335147 1.9578844
400 17.60886 8.3666709 0 11.236263 1.602563
500 16.786375 10.630838 0 13.366396 1.7725508
600 18.470347 12.42157 0 15.431552 2.1627885
700 19.39794 14.349074 0 17.510219 1.9554238
800 19.082984 16.464746 0 19.574566 2.2424126
900 20.702091 18.253108 0 21.626782 1.8041661
1000 18.299191 20.699563 0 23.681654 2.9475408
Loop time of 0.0585091 on 1 procs for 1000 steps with 270 atoms
Performance: 7383466.593 tau/day, 17091.358 timesteps/s, 4.615 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017165 | 0.017165 | 0.017165 | 0.0 | 29.34
Neigh | 0.0058479 | 0.0058479 | 0.0058479 | 0.0 | 9.99
Comm | 0.0028221 | 0.0028221 | 0.0028221 | 0.0 | 4.82
Output | 0.00017384 | 0.00017384 | 0.00017384 | 0.0 | 0.30
Modify | 0.03015 | 0.03015 | 0.03015 | 0.0 | 51.53
Other | | 0.00235 | | | 4.02
Nlocal: 270 ave 270 max 270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 73 ave 73 max 73 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 418 ave 418 max 418 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 60025 atoms
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
create_atoms CPU = 0.013 seconds
set type 2 mass 0.1
Setting atom values ...
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 19 19 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.star
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
SRD per actual grid cell = 5.5586635
SRD viscosity = 0.23558168
big/SRD mass density ratio = 0.14409881
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1908497 7.725824
ave/max big velocity = 2.202625 5.4167964
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 26.586808, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 41.29 | 41.29 | 41.29 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.2074332 8227 0.22959643 37.210444 37.407211 7.9007359 14317 47 47 0 649 28900 11236 8227 1.0260288 0 3 0
2000 1.2044605 8206 0.22945824 37.188414 37.384697 5.8738384 14470 63 63 0 1423 28900 11236 8206 1.018589 0 4 0
3000 1.1060368 8226 0.22936549 37.189341 37.369584 4.7013136 14255 51 51 0 2207 28900 11236 8226 1.0007203 0 4 0
4000 1.2395587 8236 0.2294891 37.187723 37.389725 5.7916781 14371 56 56 0 2916 28900 11236 8236 1.0229966 0 4 0
5000 1.3332555 8236 0.22962818 37.195112 37.412383 10.662157 14373 61 61 0 3740 28900 11236 8236 1.0094713 0 4 0
6000 1.2991744 8192 0.22957221 37.191547 37.403264 1.2016626 14145 56 58 0 4425 28900 11236 8192 1.0215234 0 4 0
7000 1.0110737 8147 0.22923336 37.18329 37.348057 6.2493424 14200 59 59 0 5102 28900 11236 8147 1.0163405 0 4 0
8000 0.79508387 8168 0.22908516 37.194343 37.323912 9.832591 14355 45 45 0 5839 28900 11236 8168 1.0063207 0 4 0
9000 1.0340542 8207 0.2292515 37.1825 37.351013 11.458942 14220 54 54 0 6606 28900 11236 8207 1.0074421 0 4 0
10000 0.96342976 8202 0.22912995 37.174206 37.33121 1.7523017 14308 53 53 0 7379 28900 11236 8202 1.0126923 0 4 0
Loop time of 18.5504 on 1 procs for 10000 steps with 43990 atoms
Performance: 46575.737 tau/day, 539.071 timesteps/s, 23.714 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21961 | 0.21961 | 0.21961 | 0.0 | 1.18
Neigh | 0.055763 | 0.055763 | 0.055763 | 0.0 | 0.30
Comm | 0.22073 | 0.22073 | 0.22073 | 0.0 | 1.19
Output | 0.0013822 | 0.0013822 | 0.0013822 | 0.0 | 0.01
Modify | 17.872 | 17.872 | 17.872 | 0.0 | 96.34
Other | | 0.1812 | | | 0.98
Nlocal: 43990 ave 43990 max 43990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 138 ave 138 max 138 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1587 ave 1587 max 1587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1587
Ave neighs/atom = 0.036076381
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:20

321
examples/ASPHERE/star/log.1Feb24.star.g++.4 Normal file
View File

@ -0,0 +1,321 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
270 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 38 38 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.554 | 5.554 | 5.555 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.3101488 0 0 0.21350573 0.32876464
100 5.0954142 3.291475 0 4.1218387 1.0087565
200 13.041252 4.6176595 0 6.7429006 1.5291618
300 11.912727 7.0921814 0 9.0335147 1.9578844
400 17.60886 8.3666709 0 11.236263 1.602563
500 16.786375 10.630838 0 13.366396 1.7725508
600 18.470347 12.42157 0 15.431552 2.1627885
700 19.39794 14.349074 0 17.510219 1.9554238
800 19.082984 16.464746 0 19.574566 2.2424126
900 20.702091 18.253108 0 21.626782 1.8041661
1000 18.299191 20.699563 0 23.681654 2.9475408
Loop time of 0.0312248 on 4 procs for 1000 steps with 270 atoms
Performance: 13835169.963 tau/day, 32025.856 timesteps/s, 8.647 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0026978 | 0.0031211 | 0.0033489 | 0.5 | 10.00
Neigh | 0.0011292 | 0.0013054 | 0.0014446 | 0.3 | 4.18
Comm | 0.010095 | 0.010474 | 0.010975 | 0.3 | 33.54
Output | 0.00019592 | 0.00021948 | 0.00027642 | 0.0 | 0.70
Modify | 0.013333 | 0.013668 | 0.013952 | 0.2 | 43.77
Other | | 0.002437 | | | 7.80
Nlocal: 67.5 ave 80 max 54 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 29.75 ave 33 max 26 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 104.5 ave 135 max 72 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 60025 atoms
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
create_atoms CPU = 0.003 seconds
set type 2 mass 0.1
Setting atom values ...
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 19 19 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.star
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
SRD per actual grid cell = 5.5586635
SRD viscosity = 0.23558168
big/SRD mass density ratio = 0.14409881
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1908497 7.725824
ave/max big velocity = 2.202625 5.4167964
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 26.586808, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 14.19 | 14.19 | 14.2 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.4057114 8217 0.22974151 37.20177 37.430849 11.548865 14197 56 57 0 682 42436 11236 8217 1.0187465 0 3 0
2000 1.0468288 8223 0.22932205 37.191914 37.362508 4.8322766 14185 60 60 0 1452 42436 11236 8223 1.0271433 0 64 0
3000 0.89541606 8240 0.22921893 37.199787 37.345707 9.7555289 14770 60 60 0 2175 42436 11236 8240 1.0157844 0 64 0
4000 1.021344 8222 0.22920858 37.177579 37.344021 6.2834235 14480 50 50 0 2951 42436 11236 8222 1.0130315 0 64 0
5000 1.045809 8222 0.2294309 37.209813 37.380241 2.8847497 14109 59 60 0 3667 42436 11236 8222 1.0126872 0 64 0
6000 1.1527336 8227 0.22933212 37.176296 37.364149 5.4760843 14597 42 42 0 4418 42436 11236 8227 1.0188272 0 64 0
7000 1.1799559 8216 0.22941075 37.18467 37.376959 10.243848 14281 57 57 0 5154 42436 11236 8216 1.0063617 0 64 0
8000 1.1913762 8188 0.22940126 37.181263 37.375413 5.7338518 14497 47 47 0 5878 42436 11236 8188 1.0076169 0 64 0
9000 1.0587094 8230 0.22928172 37.183406 37.355936 5.7323116 14267 62 62 0 6550 42436 11236 8230 1.0108237 0 64 0
10000 1.0359117 8165 0.22944086 37.21305 37.381865 9.4246373 14016 52 52 0 7246 42436 11236 8165 1.0147132 0 64 0
Loop time of 6.61179 on 4 procs for 10000 steps with 43990 atoms
Performance: 130675.562 tau/day, 1512.449 timesteps/s, 66.533 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041077 | 0.059027 | 0.07409 | 4.8 | 0.89
Neigh | 0.015706 | 0.017829 | 0.019903 | 1.1 | 0.27
Comm | 0.23742 | 0.25326 | 0.26722 | 2.1 | 3.83
Output | 0.00073333 | 0.00077549 | 0.00084859 | 0.0 | 0.01
Modify | 6.1477 | 6.174 | 6.2149 | 1.0 | 93.38
Other | | 0.1069 | | | 1.62
Nlocal: 10997.5 ave 11924 max 10204 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 64.25 ave 71 max 56 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 395.5 ave 497 max 271 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 1582
Ave neighs/atom = 0.035962719
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:07

322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.1 Normal file
View File

@ -0,0 +1,322 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
270 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 38 38 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.3101488 0 0 0.21350573 0.32876464
100 5.0954142 3.291475 0 4.1218387 1.0087565
200 13.041252 4.6176595 0 6.7429006 1.5291618
300 11.912727 7.0921814 0 9.0335147 1.9578844
400 17.60886 8.3666709 0 11.236263 1.602563
500 16.786375 10.630838 0 13.366396 1.7725508
600 18.470347 12.42157 0 15.431552 2.1627885
700 19.39794 14.349074 0 17.510219 1.9554238
800 19.082984 16.464746 0 19.574566 2.2424126
900 20.702091 18.253108 0 21.626782 1.8041661
1000 18.299191 20.699563 0 23.681654 2.9475408
Loop time of 0.0474374 on 1 procs for 1000 steps with 270 atoms
Performance: 9106745.092 tau/day, 21080.428 timesteps/s, 5.692 Matom-step/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01287 | 0.01287 | 0.01287 | 0.0 | 27.13
Neigh | 0.0050573 | 0.0050573 | 0.0050573 | 0.0 | 10.66
Comm | 0.0024616 | 0.0024616 | 0.0024616 | 0.0 | 5.19
Output | 0.00025461 | 0.00025461 | 0.00025461 | 0.0 | 0.54
Modify | 0.024714 | 0.024714 | 0.024714 | 0.0 | 52.10
Other | | 0.00208 | | | 4.38
Nlocal: 270 ave 270 max 270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 73 ave 73 max 73 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 418 ave 418 max 418 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 60025 atoms
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
create_atoms CPU = 0.014 seconds
set type 2 mass 0.1
Setting atom values ...
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 19 19 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.star.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
SRD per actual grid cell = 5.5586635
SRD viscosity = 0.23558168
big/SRD mass density ratio = 0.14409881
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1908497 7.725824
ave/max big velocity = 2.202625 5.4167964
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 26.586808, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 41.29 | 41.29 | 41.29 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 0.82328749 8250 0.22908506 37.18973 37.323895 6.0611499 14546 54 54 0 691 28900 11236 8250 1.025654 0 3 0
2000 1.314397 8198 0.22953802 37.183497 37.397695 7.6050033 14165 65 65 0 1503 28900 11236 8198 1.0137885 0 3 0
3000 1.4327928 8174 0.22973765 37.196727 37.430219 4.8441566 14378 43 43 0 2274 28900 11236 8174 1.0052401 0 5 0
4000 1.9637993 8194 0.23036966 37.213164 37.533191 4.9697216 14203 51 51 1 3241 28900 11236 8194 1.0129187 0 245 0
5000 1.6886675 8206 0.22987561 37.177507 37.452697 10.972628 14155 56 56 0 4073 28900 11236 8206 1.0024406 0 245 0
6000 1.7377657 8197 0.23000322 37.190296 37.473487 6.3971042 14331 57 57 0 4929 28900 11236 8197 1.0094945 0 245 0
7000 2.4106224 8199 0.23083719 37.216521 37.609363 5.1070917 14144 49 49 0 5822 28900 11236 8199 1.0074275 0 245 0
8000 2.5161884 8202 0.2306663 37.171475 37.581521 12.156127 14263 67 67 0 6667 28900 11236 8202 1.006502 0 245 0
9000 2.9100148 8188 0.23124828 37.202115 37.67634 6.1326598 14171 66 67 0 7443 28900 11236 8188 0.99544201 0 245 0
10000 3.4714177 8206 0.23192306 37.220567 37.78628 5.1293943 14100 48 49 0 8272 28900 11236 8206 1.0022763 0 245 0
Loop time of 17.933 on 1 procs for 10000 steps with 43990 atoms
Performance: 48179.444 tau/day, 557.632 timesteps/s, 24.530 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22008 | 0.22008 | 0.22008 | 0.0 | 1.23
Neigh | 0.054046 | 0.054046 | 0.054046 | 0.0 | 0.30
Comm | 0.20917 | 0.20917 | 0.20917 | 0.0 | 1.17
Output | 0.001317 | 0.001317 | 0.001317 | 0.0 | 0.01
Modify | 17.275 | 17.275 | 17.275 | 0.0 | 96.33
Other | | 0.1731 | | | 0.97
Nlocal: 43990 ave 43990 max 43990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 122 ave 122 max 122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1569 ave 1569 max 1569 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1569
Ave neighs/atom = 0.035667197
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:19

322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.4 Normal file
View File

@ -0,0 +1,322 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - rigid star particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.star fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
270 atoms
read_data CPU = 0.001 seconds
set type 1 mass 1.0
Setting atom values ...
270 settings made for mass
group big type 1
270 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 38 38 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.554 | 5.554 | 5.555 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.3101488 0 0 0.21350573 0.32876464
100 5.0954142 3.291475 0 4.1218387 1.0087565
200 13.041252 4.6176595 0 6.7429006 1.5291618
300 11.912727 7.0921814 0 9.0335147 1.9578844
400 17.60886 8.3666709 0 11.236263 1.602563
500 16.786375 10.630838 0 13.366396 1.7725508
600 18.470347 12.42157 0 15.431552 2.1627885
700 19.39794 14.349074 0 17.510219 1.9554238
800 19.082984 16.464746 0 19.574566 2.2424126
900 20.702091 18.253108 0 21.626782 1.8041661
1000 18.299191 20.699563 0 23.681654 2.9475408
Loop time of 0.0311841 on 4 procs for 1000 steps with 270 atoms
Performance: 13853197.664 tau/day, 32067.587 timesteps/s, 8.658 Matom-step/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0027957 | 0.0031644 | 0.0035219 | 0.5 | 10.15
Neigh | 0.001171 | 0.0012862 | 0.0014036 | 0.3 | 4.12
Comm | 0.0099068 | 0.010544 | 0.011053 | 0.4 | 33.81
Output | 0.00014281 | 0.00016091 | 0.00020823 | 0.0 | 0.52
Modify | 0.013319 | 0.013618 | 0.014047 | 0.2 | 43.67
Other | | 0.002411 | | | 7.73
Nlocal: 67.5 ave 80 max 54 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 29.75 ave 33 max 26 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 104.5 ave 135 max 72 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 60025 atoms
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
create_atoms CPU = 0.003 seconds
set type 2 mass 0.1
Setting atom values ...
60025 settings made for mass
group small type 2
60025 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 19 19 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 16305 atoms, new total = 43990
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo 1000
#dump 1 all atom 1000 dump.star.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 43720 270
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
SRD per actual grid cell = 5.5586635
SRD viscosity = 0.23558168
big/SRD mass density ratio = 0.14409881
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1908497 7.725824
ave/max big velocity = 2.202625 5.4167964
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 26.586808, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 14.19 | 14.19 | 14.2 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.3506473 8186 0.22968182 37.201018 37.421123 5.6398923 14572 54 54 0 654 42436 11236 8186 1.0228728 0 3 0
2000 0.99412905 8212 0.22952823 37.234094 37.3961 8.5863689 14257 69 69 0 1394 42436 11236 8212 1.0206297 0 12 0
3000 1.4469134 8192 0.22970951 37.189841 37.425634 8.0408437 14439 53 53 0 2178 42436 11236 8192 1.0121272 0 12 0
4000 1.6112802 8172 0.2303679 37.270324 37.532903 8.3379947 14098 57 57 0 2992 42436 11236 8172 1.0171443 0 12 0
5000 2.0436283 8191 0.23016186 37.166298 37.499334 7.1370191 14030 49 49 0 3804 42436 11236 8191 1.0054513 0 12 0
6000 2.2894073 8184 0.2303867 37.162878 37.535967 7.6496143 13970 50 50 0 4662 42436 11236 8184 1.0084738 0 12 0
7000 2.1640822 8183 0.23045121 37.193812 37.546477 7.1526683 13926 56 57 0 5445 42436 11236 8183 1.0046108 0 15 0
8000 2.8851243 8199 0.23121762 37.201176 37.671344 9.1644504 13849 58 58 0 6237 42436 11236 8199 1.0081629 0 15 0
9000 2.6422092 8180 0.23070839 37.157795 37.588377 2.4816571 13651 70 70 0 7007 42436 11236 8180 1.0089869 0 15 0
10000 2.7121051 8189 0.23087145 37.172972 37.614945 11.176036 13901 63 64 0 7845 42436 11236 8189 1.0023484 0 15 0
Loop time of 6.56969 on 4 procs for 10000 steps with 43990 atoms
Performance: 131513.146 tau/day, 1522.143 timesteps/s, 66.959 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037869 | 0.059232 | 0.073664 | 5.4 | 0.90
Neigh | 0.015688 | 0.017835 | 0.019891 | 1.1 | 0.27
Comm | 0.22905 | 0.24375 | 0.26098 | 2.3 | 3.71
Output | 0.00069058 | 0.00071614 | 0.00078869 | 0.0 | 0.01
Modify | 6.1124 | 6.1385 | 6.1881 | 1.2 | 93.44
Other | | 0.1096 | | | 1.67
Nlocal: 10997.5 ave 12305 max 10259 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 58.25 ave 73 max 48 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 402.75 ave 520 max 207 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Total # of neighbors = 1611
Ave neighs/atom = 0.03662196
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:06

4
examples/ASPHERE/tri/in.tri.srd
View File

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

812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8
View File

@ -1,812 +0,0 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.007 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.002 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4401779 0 -0.15917996 0 0
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
Other | | 0.2104 | | | 0.13
Nlocal: 2033.88 ave 2601 max 1413 min
Histogram: 1 2 0 0 0 0 2 1 1 1
Nghost: 1647.25 ave 1714 max 1617 min
Histogram: 4 0 1 0 0 1 1 0 0 1
Neighs: 12482.8 ave 17009 max 8679 min
Histogram: 1 1 1 0 1 1 2 0 0 1
Total # of neighbors = 99862
Ave neighs/atom = 6.1374224
Neighbor list builds = 562
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.14994 40
ave/max big velocity = 1.6952661 5.2200074
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
24300 6.7765706 1.0007065 4.3500477 9.4974154 1 16
24400 7.0853466 1.0013246 4.409163 9.2215823 1 17
24500 6.9603823 1.0004247 4.4866051 7.7870058 1 20
24600 6.9208291 0.99953329 4.2298144 6.5732392 1 21
24700 6.5005518 1.0026848 4.0003505 7.8094715 1 22
24800 5.8421948 1.0012055 3.6686768 7.6078157 1 26
24900 5.8410604 1.0023428 3.746177 6.8971309 1 22
25000 5.8728511 1.0001747 3.7170134 7.4456816 1 19
25100 6.0217168 1.000624 3.7756108 6.6542452 1 20
25200 6.1939015 1.0017861 3.8943084 9.395821 1 25
25300 6.161998 1.0010373 3.9255122 6.2228884 1 28
25400 5.5850406 1.0018505 3.5129832 7.2551309 1 24
25500 6.0286276 1.0009028 3.8580887 6.8065265 1 24
25600 5.6262228 1.0005097 3.4574446 7.5061246 1 21
25700 6.1348187 1.0009828 3.8073512 7.4818375 1 17
25800 6.09781 1.0026426 3.9585383 9.0915939 1 21
25900 6.2673667 1.0002269 3.8182813 9.2134822 1 21
26000 6.6001776 1.0020444 4.041386 8.0403555 1 18
26100 6.3063025 1.0016633 3.8649839 8.8149734 1 19
26200 6.0046983 1.002332 3.5380766 8.6145656 1 17
26300 5.9627788 1.0005401 3.56864 6.7821213 1 15
26400 5.0547314 0.9998295 3.2106781 9.2935351 1 15
26500 5.256781 1.0013131 3.2946631 8.8590275 1 15
26600 5.6250355 1.0023929 3.5243033 8.8985058 1 17
26700 6.0197165 1.0018323 3.7973947 7.3093402 1 17
26800 5.4556541 1.0015309 3.4295107 8.2342049 1 18
26900 5.420428 1.0024996 3.4374201 7.1444636 1 16
27000 6.165624 1.0019174 3.8726016 8.6588275 1 20
27100 6.7131697 1.0006541 4.266264 8.7063389 1 24
27200 6.4855163 1.0016139 4.2029778 7.667611 1 29
27300 6.0525608 1.000478 3.9169723 7.4515279 1 25
27400 6.1426194 1.0014522 3.9176108 6.8689671 1 24
27500 6.5981349 1.0001143 4.0620686 8.6804552 1 27
27600 6.7827138 1.0016694 4.2764286 9.3912843 1 21
27700 6.6368902 1.0025149 4.1452128 9.1814523 1 24
27800 6.9791025 1.0019486 4.3989933 7.9446882 1 24
27900 6.617142 1.0015736 4.360571 9.3732108 1 26
28000 7.2818263 1.0014101 4.6041512 8.2398587 1 28
28100 7.2543709 1.0007625 4.5724787 7.7373488 1 22
28200 7.0631847 1.0023922 4.4021705 8.3290554 1 29
28300 7.2999952 1.0012593 4.4655563 8.612666 1 27
28400 7.4124538 1.0014043 4.5011335 8.379391 1 29
28500 7.0350937 1.0011392 4.3528091 7.8167375 1 24
28600 7.9659642 1.0031684 4.8732467 8.0661929 1 30
28700 7.2865919 1.0010958 4.6650146 8.0325989 1 32
28800 7.7039529 1.0027912 4.8299888 9.5471747 1 30
28900 8.3288847 1.0012438 5.0785288 8.8964877 1 31
29000 7.9348665 1.0021794 4.9393968 9.5531767 1 31
29100 8.2473389 1.0013795 4.9890359 9.7697184 1 29
29200 8.6383362 1.0018356 4.9856954 7.6402719 1 25
29300 8.2504592 1.0011048 4.9631793 7.9466724 1 24
29400 8.0502922 1.0010516 5.2521065 8.4515028 1 26
29500 7.9475896 1.0012951 4.8584644 9.1225463 1 19
29600 8.5641641 1.0016228 5.4361335 9.2045399 1 23
29700 8.9932021 1.0011848 5.5727205 8.6045729 1 23
29800 8.0320178 1.0019073 5.2837013 8.9335413 1 22
29900 8.2676522 1.0012734 5.2213798 8.8966896 1 24
30000 9.1848984 1.001747 5.9147628 12.096129 1 27
30100 10.184519 0.99977427 6.4260136 11.140491 1 27
30200 9.271472 1.0023983 6.0252189 9.6954338 1 30
30300 9.0751572 1.000851 5.6010295 9.734426 1 28
30400 9.4581261 1.0018449 5.6987258 9.70456 1 34
30500 9.1574751 0.99944001 5.582217 9.300318 1 27
30600 8.619312 1.001388 5.3503985 8.2759155 1 26
30700 7.9370031 1.0026674 5.0702831 8.5368014 1 28
30800 7.9221619 1.0019077 5.1278637 11.046922 1 26
30900 9.9722884 1.0025903 6.4055506 10.167311 1 25
31000 8.8648667 0.99962676 5.4777514 10.142102 1 21
31100 8.576344 1.000906 5.3216342 8.7984921 1 18
31200 7.8480974 1.0010341 4.9584917 9.0696437 1 16
31300 8.3536183 1.0005758 5.208516 9.7971514 1 15
31400 8.5301933 1.0007603 5.2241536 9.0257241 1 17
31500 8.5196226 1.0018215 5.0576064 8.8847294 1 19
31600 8.1470823 1.0023147 4.9182956 9.0205413 1 20
31700 8.1475888 1.0005764 5.1814113 9.0603162 1 16
31800 7.8629717 1.0014194 4.9221218 9.366291 1 16
31900 7.7206559 1.0021082 4.9167636 7.4136735 1 16
32000 7.5152809 1.0004752 4.6330638 8.830959 1 16
32100 8.2693974 1.0011751 4.9094804 9.427636 1 13
32200 8.3067661 0.9997006 4.9036865 9.0374633 1 17
32300 7.2068514 1.0007866 4.3580755 8.6445065 1 17
32400 6.885063 1.0011887 4.1528011 8.1199454 1 16
32500 6.9147014 1.0020825 4.160405 7.5398034 1 19
32600 6.8809668 1.000971 4.3312782 8.2157688 1 16
32700 6.4818892 1.0000885 3.9433899 7.309605 1 22
32800 6.6875555 1.0018674 4.1017504 7.2327183 1 22
32900 7.6118502 0.99975736 4.4498951 8.5072395 1 19
33000 7.7576909 1.0022061 4.7239551 9.2132467 1 22
33100 7.8616235 1.000482 5.0031322 9.349805 1 20
33200 8.2620563 1.0015059 5.2482188 10.286446 1 17
33300 8.0217099 1.0015466 5.1166876 9.1381844 1 20
33400 7.6565746 1.0024855 4.7594208 9.2646824 1 22
33500 7.9633887 1.0010334 4.6754116 9.1085184 1 23
33600 7.9566834 1.0024542 4.6712679 9.2046594 1 25
33700 8.2639384 1.0003021 5.1326892 8.0930215 1 24
33800 8.5648917 1.0000947 5.2099387 8.8127486 1 21
33900 8.3593557 1.0002488 5.1291354 8.5938391 1 25
34000 8.1922068 1.0030011 5.1441189 7.1529563 1 24
34100 8.4260308 1.0004639 5.5876122 9.0450303 1 28
34200 8.3014654 1.0002204 5.1964772 8.4920822 1 33
34300 7.4736545 1.0010306 4.7932244 7.8442244 1 30
34400 7.0023126 1.0024002 4.5665168 8.4702188 1 29
34500 7.3797703 1.000813 4.7224014 8.4098954 1 30
34600 7.7158761 0.99973161 4.7441628 8.5818592 1 29
34700 7.6135895 1.0015768 4.6612844 7.2195952 1 28
34800 7.0458078 0.99992638 4.2805357 7.4162305 1 32
34900 7.6190708 1.0007146 4.8064968 8.2709405 1 27
35000 7.4614294 1.0006051 4.7807207 7.7137359 1 28
35100 7.7008336 1.0008263 4.6823621 7.0208513 1 26
35200 8.1510766 1.000271 5.1781834 7.3231692 1 24
35300 7.5106275 1.0010438 4.6988185 8.9418343 1 25
35400 7.8116652 1.0009688 4.8622216 7.4624002 1 17
35500 7.2159785 1.0027484 4.543984 8.3177043 1 21
35600 7.6978875 1.0004834 4.7021203 8.3706905 1 20
35700 7.7827655 1.0019919 4.775879 8.6083292 1 15
35800 7.8433537 1.001844 4.7506574 7.3250009 1 15
35900 7.9456497 1.0004336 4.7925775 7.9824359 1 18
36000 8.1044513 1.0022261 5.1213755 9.211699 1 16
36100 7.6657532 1.0025661 4.751804 8.9770412 1 19
36200 7.909323 1.0035462 4.8435293 10.232493 1 21
36300 8.4188244 1.0016775 5.4337725 9.2060079 1 24
36400 8.7352689 1.0011274 5.6313351 8.6202832 1 24
36500 8.3459273 1.0005659 5.187336 6.9333716 1 21
36600 7.7118105 1.0018769 4.9293347 8.2789615 1 14
36700 7.8069879 1.0014021 4.7782709 8.4841233 1 15
36800 7.862085 1.0005342 4.8680692 8.1055023 1 16
36900 7.9469362 1.0027815 4.9339095 9.157722 1 16
37000 7.9085375 1.0024851 5.0921374 8.9374239 1 16
37100 8.9464869 1.0005734 5.6837772 8.806998 1 16
37200 8.1482632 1.0021175 5.1266453 8.5772094 1 18
37300 7.7958072 1.0026336 4.788431 8.3233372 1 19
37400 7.3647655 1.0015482 4.4786134 9.6606112 1 23
37500 7.3071882 1.0003912 4.681549 8.6319438 1 17
37600 7.8672509 1.0000478 4.7981944 8.3051478 1 14
37700 7.9306696 0.99923102 4.9316544 9.3672856 1 15
37800 7.7397949 0.99948557 5.1168552 8.5978047 1 17
37900 7.9121039 1.0020122 4.9866234 7.640888 1 14
38000 7.433451 1.0007901 4.6254894 8.0853539 1 14
38100 7.4636908 1.0021552 4.8472833 8.1975615 1 10
38200 7.4453077 1.0010305 4.6910943 7.8192603 1 13
38300 7.0488536 1.0012587 4.5490462 8.190036 1 16
38400 8.0686748 1.0016782 5.0747029 7.7242015 1 15
38500 7.9575875 1.0007137 4.8361776 8.05268 1 15
38600 7.6690498 1.0027522 4.8823286 9.1926516 1 20
38700 7.1567 1.002374 4.5600354 10.098089 1 19
38800 6.9100518 1.0008695 4.4101446 7.8832032 1 19
38900 6.8021882 1.0017647 4.1844125 8.1858761 1 21
39000 8.3996464 1.0010263 4.8183813 8.0997387 1 16
39100 8.4533834 1.0021643 5.074254 11.291904 1 19
39200 8.2406701 1.002062 5.0117425 8.778159 1 24
39300 8.3134114 1.0008218 5.0067136 7.9871787 1 22
39400 7.4307571 1.0014205 4.5858283 8.8596594 1 25
39500 7.1146821 1.0016367 4.5021057 7.4890018 1 22
39600 8.0048978 0.99992107 4.9235747 7.8770845 1 24
39700 8.070853 1.0029024 5.0842957 9.020664 1 21
39800 7.6939108 1.0012543 4.8986595 8.3306129 1 20
39900 7.2915444 1.00267 4.5038291 8.3844384 1 20
40000 7.3023994 1.0020441 4.4960911 8.1023709 1 18
40100 7.0221648 1.0033695 4.6374149 8.3756822 1 24
40200 7.4114756 1.0019246 4.6733475 7.6547258 1 23
40300 7.5323108 1.0005472 4.8284493 8.2820085 1 26
40400 7.3890772 1.0010491 4.6599273 8.9203575 1 19
40500 7.5786764 1.0016114 4.8166885 8.6760107 1 25
40600 8.165763 1.0006961 5.1488995 7.9321524 1 22
40700 8.1277597 0.99933464 5.0441567 10.069551 1 16
40800 8.1050904 1.0024705 5.4408599 8.3244459 1 21
40900 7.805318 1.0022992 4.9965408 9.7193723 1 21
41000 9.0130932 1.0006842 5.7931112 6.1646073 1 20
41100 8.0387975 1.0017359 5.3355655 9.6123191 1 21
41200 8.4484723 1.0014151 5.4461007 8.5146504 1 27
41300 8.6181909 1.0007562 5.2963876 9.1122306 1 30
41400 9.6762899 1.0010931 5.950456 9.2851025 1 25
41500 9.9414226 1.0016186 6.1433384 10.741453 1 24
41600 9.3348435 1.0003483 5.9291766 11.460717 1 20
41700 9.6125587 1.0013661 5.8530052 9.2105722 1 19
41800 11.383056 1.0032034 7.1988684 10.312945 1 22
41900 10.884524 1.0034888 6.9126707 10.775457 1 20
42000 11.071218 1.0026753 7.0004189 10.740627 1 20
42100 11.054304 1.0008347 6.9602414 8.9885498 1 22
42200 22.478691 1.0020466 14.997099 12.72513 1 19
42300 18.303508 1.0027626 11.336523 12.638769 1 18
42400 15.998712 1.0030312 9.4092725 11.070501 1 24
42500 15.034488 1.0024472 9.3543751 11.48052 1 28
42600 14.538257 1.0033153 9.2523745 10.909576 1 27
42700 13.986613 1.001458 8.5544184 10.765136 1 29
42800 13.240256 1.0027899 8.2014429 10.506497 1 32
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
43000 13.374145 1.0012996 8.4207155 10.32817 1 31
43100 13.142334 1.0022503 8.5908808 10.152205 1 32
43200 12.669284 1.0018944 7.8511966 10.580104 1 32
43300 13.155032 1.001144 8.0337768 10.6652 1 39
43400 12.155928 1.0019472 7.5886584 11.234772 1 35
43500 12.385603 1.0007639 7.8865245 9.3868914 1 32
43600 12.236179 1.0027456 7.7521353 10.456701 1 42
43700 11.49535 1.0008758 7.3633144 8.8490079 1 40
43800 11.469157 1.0015845 7.0035577 10.594522 1 41
43900 11.228266 1.0013014 7.0137223 8.0653711 1 38
44000 10.56742 1.0016631 6.6908938 8.1094154 1 35
44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36
44200 9.041539 1.0019541 5.6721401 8.6518043 1 38
44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38
44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37
44500 9.458981 1.0030409 5.7612138 7.7679755 1 37
44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37
44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32
44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30
44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28
45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26
45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32
45200 7.7001199 1.001626 4.9315953 7.4926686 1 25
45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26
45400 7.493909 1.0016257 4.7631808 8.0330626 1 26
45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23
45600 7.9028612 1.0017008 4.9561022 8.440428 1 23
45700 7.2285584 1.0006033 4.5521456 9.385579 1 23
45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23
45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26
46000 8.318466 1.0020803 5.4761811 8.2227801 1 25
46100 7.9169512 1.0024598 5.0406355 8.64365 1 27
46200 7.5535458 1.0016318 4.8010133 9.370726 1 26
46300 7.8926896 1.0001525 5.18463 7.9830196 1 27
46400 7.487145 1.002671 4.7718312 8.300134 1 29
46500 7.3564658 1.0006114 4.6762189 7.34947 1 26
46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25
46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25
46900 10.176752 1.0023799 6.0456779 9.4050423 1 16
47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22
47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28
47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25
47300 9.3543283 1.0013246 6.0873147 10.41657 1 24
47400 8.594101 1.0020068 5.6864295 9.2388304 1 24
47500 9.3191964 1.002411 6.0537511 9.3506828 1 23
47600 8.1615734 1.001364 5.3757905 10.303962 1 30
47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32
47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33
47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33
48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34
48100 8.4495256 1.000088 4.9940422 10.01023 1 27
48200 8.8068097 1.0014275 5.4732649 8.410093 1 31
48300 8.0008187 1.0017459 4.7732764 9.25726 1 27
48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30
48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29
48700 9.3623061 1.0001767 5.7117062 8.396895 1 25
48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27
48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24
49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22
49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24
49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25
49300 7.9703755 1.0010628 5.2328567 7.968278 1 28
49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
Other | | 1.023 | | | 0.10
Nlocal: 2033.88 ave 2657 max 1198 min
Histogram: 2 0 0 0 0 2 1 0 1 2
Nghost: 1628.12 ave 1719 max 1569 min
Histogram: 2 0 1 1 2 1 0 0 0 1
Neighs: 13566 ave 18212 max 8488 min
Histogram: 1 0 0 1 2 1 2 0 0 1
Total # of neighbors = 108528
Ave neighs/atom = 6.6700264
Neighbor list builds = 2447
Dangerous builds = 2
Total wall time: 0:19:22

343
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@ -0,0 +1,343 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
1 by 1 by 1 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.013 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.014 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 381.8 | 381.8 | 381.8 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4502537 0 -0.15976045 0 0
100 0.41802172 1.152223 0.27557714 1.0421065 1.1470081 283
200 0.79710339 1.0669332 0.5813323 0.97699684 1.0361619 534
300 1.3739181 1.0275476 1.0869716 0.81001536 1.0211312 658
400 1.9355117 1.0155457 1.5813236 1.7798798 0.99354559 831
500 2.8557382 1.0005021 2.267698 3.3903849 0.98597972 927
600 4.7851916 1.0156689 3.730334 2.838776 0.99140534 1053
700 5.3647697 1.0176657 3.9593121 5.1189107 0.9972029 1218
800 8.23688 1.0268086 5.899689 6.8199153 0.99310516 1349
900 9.9330758 1.0356047 7.0260595 7.2596589 0.98360014 1607
1000 9.8719995 1.043178 6.9903792 10.05101 1.0045416 1805
Loop time of 79.2664 on 1 procs for 1000 steps with 16271 atoms
Performance: 1089.995 tau/day, 12.616 timesteps/s, 205.270 katom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 57.961 | 57.961 | 57.961 | 0.0 | 73.12
Neigh | 0.34589 | 0.34589 | 0.34589 | 0.0 | 0.44
Comm | 0.28615 | 0.28615 | 0.28615 | 0.0 | 0.36
Output | 0.0022784 | 0.0022784 | 0.0022784 | 0.0 | 0.00
Modify | 20.644 | 20.644 | 20.644 | 0.0 | 26.04
Other | | 0.02724 | | | 0.03
Nlocal: 16271 ave 16271 max 16271 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4612 ave 4612 max 4612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99463 ave 99463 max 99463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99463
Ave neighs/atom = 6.1129003
Neighbor list builds = 72
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 2000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
# of rescaled SRD velocities = 3
ave/max small velocity = 16.23763 40
ave/max big velocity = 1.9825234 5.257255
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 278.4 | 278.4 | 278.4 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
1000 9.8719995 1.0317167 6.98982 4.0948969 0 0
1100 7.6460335 1.0028444 5.2446585 6.6348814 1 1320
1200 6.2789381 1.0012003 4.5257435 6.3278972 1 1024
1300 5.5060209 1.002182 3.7063549 7.0004503 1 794
1400 5.4107119 1.002291 3.594515 7.9511695 1 621
1500 5.072582 1.0001037 3.2501353 8.6993671 1 503
1600 4.7912016 0.99982803 3.1208274 6.464157 1 416
1700 4.5518848 1.0030059 2.9084074 6.3278992 1 346
1800 4.368682 1.000831 2.807184 6.7382017 1 282
1900 4.458655 1.0012568 2.7966515 6.0124309 1 246
2000 4.1256128 1.0004032 2.763649 6.3707442 1 208
2100 3.7040346 1.0004125 2.4398152 5.4213931 1 181
2200 4.2347861 1.002625 2.6206986 6.6832437 1 151
2300 4.254984 1.0028871 2.6794167 7.1661525 1 127
2400 4.1017692 1.0028508 2.6371178 8.388599 1 105
2500 3.9285571 1.0002888 2.5002741 6.0806187 1 95
2600 3.6239964 1.0012152 2.2573993 6.7863124 1 80
2700 3.4085702 1.0023974 2.1179914 6.7351139 1 68
2800 3.1399303 1.0005349 2.0163219 6.4502765 1 61
2900 3.1277562 1.0004013 2.0453134 6.6485498 1 51
3000 3.0737732 1.0022962 1.997382 6.797214 1 44
Loop time of 206.387 on 1 procs for 2000 steps with 16271 atoms
Performance: 837.264 tau/day, 9.691 timesteps/s, 157.675 katom-step/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 173.6 | 173.6 | 173.6 | 0.0 | 84.12
Neigh | 1.0077 | 1.0077 | 1.0077 | 0.0 | 0.49
Comm | 0.58656 | 0.58656 | 0.58656 | 0.0 | 0.28
Output | 0.0042824 | 0.0042824 | 0.0042824 | 0.0 | 0.00
Modify | 31.128 | 31.128 | 31.128 | 0.0 | 15.08
Other | | 0.05664 | | | 0.03
Nlocal: 16271 ave 16271 max 16271 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4521 ave 4521 max 4521 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 94777 ave 94777 max 94777 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94777
Ave neighs/atom = 5.8249032
Neighbor list builds = 100
Dangerous builds = 0
Total wall time: 0:04:47

343
examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.4 Normal file
View File

@ -0,0 +1,343 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
1 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.010 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.005 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 184.3 | 184.9 | 185.4 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4502537 0 -0.15949051 0 0
100 0.39689465 1.1495173 0.26931663 1.0004927 1.1170389 279
200 0.82155086 1.0684809 0.60689485 0.81307973 1.0433122 467
300 1.3210872 1.0334277 1.0368935 1.0853416 0.99443391 621
400 1.9755695 1.0149146 1.6438403 1.7258285 0.9925525 788
500 3.0111365 1.0121291 2.4285289 2.5210058 0.99688885 922
600 4.5413799 1.014305 3.4727946 3.8290233 0.99002027 1063
700 6.6071849 1.0062952 4.9025772 3.9595327 0.99573591 1186
800 7.6256618 1.0151252 5.3662442 5.0088255 0.99640985 1371
900 8.1578206 1.0148959 5.7716683 6.6059298 0.96053165 1555
1000 10.749617 1.0282309 7.6209538 11.277602 1.0012602 1844
Loop time of 28.4136 on 4 procs for 1000 steps with 16271 atoms
Performance: 3040.793 tau/day, 35.194 timesteps/s, 572.647 katom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.454 | 15.242 | 17.781 | 48.4 | 53.64
Neigh | 0.093078 | 0.094516 | 0.097759 | 0.6 | 0.33
Comm | 0.48732 | 2.9927 | 5.7363 | 107.5 | 10.53
Output | 0.00080706 | 0.0008431 | 0.00086933 | 0.0 | 0.00
Modify | 10.015 | 10.063 | 10.111 | 1.4 | 35.42
Other | | 0.02046 | | | 0.07
Nlocal: 4067.75 ave 4467 max 3606 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 2313.5 ave 2327 max 2296 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 24883 ave 26066 max 24145 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 99532
Ave neighs/atom = 6.1171409
Neighbor list builds = 70
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 2000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
# of rescaled SRD velocities = 3
ave/max small velocity = 16.10299 40
ave/max big velocity = 2.0311414 11.34118
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/atomonly/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 148.8 | 149.5 | 150 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
1000 10.749616 1.0167438 7.6203704 5.4893075 0 0
1100 9.0727748 1.003438 6.1822573 8.6707036 1 1339
1200 7.1960998 1.0003968 4.8077632 6.7809972 1 1039
1300 6.2680889 1.0011134 4.3139658 8.2260362 1 861
1400 5.8199503 1.0024475 3.9876867 7.0322957 1 692
1500 5.399935 0.99757802 3.4552534 7.905565 1 577
1600 5.0830248 1.0023727 3.1330433 7.6897887 1 479
1700 4.8728937 1.0027203 3.0838267 7.606406 1 389
1800 4.8443541 1.0018057 3.115321 7.4547572 1 317
1900 5.0622362 1.0007126 2.9336473 6.514338 1 268
2000 5.022699 1.0030275 3.1244763 7.2999286 1 223
2100 4.4605894 1.0019457 2.9262733 8.3475145 1 196
2200 4.6544992 1.0023701 3.0140329 7.3670747 1 164
2300 4.1954825 1.0012089 2.5802739 7.5553707 1 142
2400 4.0806819 1.0000292 2.6492187 7.5648723 1 122
2500 3.7437189 0.99949605 2.3660722 8.2155316 1 104
2600 4.2333926 1.0002823 2.5704515 7.2839635 1 106
2700 3.7542455 1.001394 2.4146222 6.3785983 1 86
2800 3.4011329 0.99832028 2.141193 6.3869497 1 78
2900 3.4579019 1.0007319 2.1839274 6.241817 1 64
3000 3.6128019 1.0017345 2.2982426 5.8975992 1 55
Loop time of 67.0194 on 4 procs for 2000 steps with 16271 atoms
Performance: 2578.358 tau/day, 29.842 timesteps/s, 485.561 katom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 36.774 | 43.583 | 50.126 | 71.5 | 65.03
Neigh | 0.29299 | 0.3134 | 0.32399 | 2.2 | 0.47
Comm | 0.75102 | 7.2688 | 14.075 | 174.8 | 10.85
Output | 0.0016347 | 0.0017229 | 0.0018802 | 0.2 | 0.00
Modify | 15.794 | 15.808 | 15.828 | 0.3 | 23.59
Other | | 0.04379 | | | 0.07
Nlocal: 4067.75 ave 4560 max 3583 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 2256.75 ave 2292 max 2241 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 23706 ave 24669 max 22450 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 94824
Ave neighs/atom = 5.8277918
Neighbor list builds = 108
Dangerous builds = 0
Total wall time: 0:01:36

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -110,6 +110,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_variable);
ADDSYM(extract_variable_datatype);
ADDSYM(set_variable);
ADDSYM(set_string_variable);
ADDSYM(set_internal_variable);
ADDSYM(variable_info);
ADDSYM(gather_atoms);

6
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -152,9 +152,11 @@ struct _liblammpsplugin {
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
void *(*extract_variable)(void *, const char *, const char *);
int (*extract_variable_datatype)(void *, const char *);
int (*set_variable)(void *, char *, char *);
int (*set_variable)(void *, const char *, const char *);
int (*set_string_variable)(void *, const char *, const char *);
int (*set_internal_variable)(void *, const char *, double);
int (*variable_info)(void *, int, char *, int);
void (*gather_atoms)(void *, const char *, int, int, void *);

95
examples/PACKAGES/cgdna/util/generate.py
View File

@ -22,6 +22,10 @@
"""
Import basic modules
"""
# for python2/3 compatibility
from __future__ import print_function
import sys, os, timeit
from timeit import default_timer as timer
@ -33,7 +37,7 @@ which needs to be provided
try:
import numpy as np
except:
print >> sys.stderr, "numpy not found. Exiting."
print("numpy not found. Exiting.", file=sys.stderr)
sys.exit(1)
"""
@ -45,8 +49,8 @@ try:
box_length = float(sys.argv[2])
infile = sys.argv[3]
except:
print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences")
print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences"), file=sys.stderr)
sys.exit(1)
box = np.array ([box_length, box_length, box_length])
@ -57,8 +61,7 @@ try:
inp = open (infile, 'r')
inp.close()
except:
print >> sys.stderr, "Could not open file '%s' for reading. \
Aborting." % infile
print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
sys.exit(2)
# return parts of a string
@ -174,21 +177,21 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
# placed particles i we check whether it overlaps with any of the
# newly created particles j
print >> sys.stdout, "## Checking for overlaps"
print( "## Checking for overlaps", file=sys.stdout)
for i in xrange(len(positions)):
for i in range(len(positions)):
p = positions[i]
pa1 = a1s[i]
for j in xrange (len(mynewpositions)):
for j in range (len(mynewpositions)):
q = mynewpositions[j]
qa1 = mynewa1s[j]
# skip particles that are anyway too far away
dr = p - q
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) > RC2:
continue
@ -200,13 +203,13 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
# check for no overlap between the two backbone sites
dr = p_pos_back - q_pos_back
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BACK:
overlap = True
# check for no overlap between the two base sites
dr = p_pos_base - q_pos_base
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BASE:
overlap = True
@ -238,7 +241,7 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
for p in mynewa3s:
a3s.append (p)
# calculate quaternion from local body frame and append
for ia in xrange(len(mynewpositions)):
for ia in range(len(mynewpositions)):
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
quaternions.append(mynewquaternions)
@ -301,13 +304,12 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
elif len(sequence) != bp:
n = bp - len(sequence)
sequence += np.random.randint(1, 5, n)
print >> sys.stderr, "sequence is too short, adding %d random bases" % n
print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
# normalize direction
dir_norm = np.sqrt(np.dot(dir,dir))
if dir_norm < 1e-10:
print >> sys.stderr, "direction must be a valid vector, \
defaulting to (0, 0, 1)"
print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
dir = np.array([0, 0, 1])
else: dir /= dir_norm
@ -391,7 +393,7 @@ def read_strands(filename):
try:
infile = open (filename)
except:
print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
sys.exit(2)
# This block works out the number of nucleotides and strands by reading
@ -406,28 +408,27 @@ def read_strands(filename):
if line[:6] == 'DOUBLE':
line = line.split()[1]
length = len(line)
print >> sys.stdout, "## Found duplex of %i base pairs" % length
print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
nnucl += 2*length
nstrands += 2
nbonds += (2*length-2)
else:
line = line.split()[0]
length = len(line)
print >> sys.stdout, \
"## Found single strand of %i bases" % length
print( "## Found single strand of %i bases" % length, file=sys.stdout)
nnucl += length
nstrands += 1
nbonds += length-1
# rewind the sequence input file
infile.seek(0)
print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
# generate the data file in LAMMPS format
try:
out = open ("data.oxdna", "w")
except:
print >> sys.stderr, "Could not open data file for writing. Aborting."
print( "Could not open data file for writing. Aborting.", file=sys.stderr)
sys.exit(2)
lines = infile.readlines()
@ -452,11 +453,11 @@ def read_strands(filename):
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
@ -467,16 +468,16 @@ def read_strands(filename):
seq2.reverse()
myns += 1
for b in xrange(length):
for b in range(length):
basetype.append(seq2[b])
strandnum.append(myns)
for b in xrange(length-1):
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
# generate random position of the first nucleotide
cdm = box_offset + np.random.random_sample(3) * box
@ -499,10 +500,10 @@ def read_strands(filename):
axis /= np.sqrt(np.dot(axis, axis))
newpositions, newa1s, newa3s = generate_strand(len(line), \
sequence=seq, dir=axis, start_pos=cdm, double=True)
print >> sys.stdout, "## Trying %i" % i
print( "## Trying %i" % i, file=sys.stdout)
end = timer()
print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl)
print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
# block for single strands: last argument of the generate function
# is set to 'False'
@ -511,11 +512,11 @@ def read_strands(filename):
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
@ -527,8 +528,7 @@ def read_strands(filename):
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
print >> sys.stdout, \
"## Created single strand of %i bases" % length
print("## Created single strand of %i bases" % length, file=sys.stdout)
newpositions, newa1s, newa3s = generate_strand(length, \
sequence=seq, dir=axis, start_pos=cdm, double=False)
@ -541,14 +541,14 @@ def read_strands(filename):
sequence=seq, dir=axis, start_pos=cdm, double=False)
print >> sys.stdout, "## Trying %i" % (i)
end = timer()
print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl)
print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
i += 1
# sanity check
if not len(positions) == nnucl:
print len(positions), nnucl
print( len(positions), nnucl )
raise AssertionError
out.write('# LAMMPS data file\n')
@ -580,18 +580,16 @@ def read_strands(filename):
out.write('Atoms\n')
out.write('\n')
for i in xrange(nnucl):
for i in range(nnucl):
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
% (i+1, basetype[i], \
positions[i][0], positions[i][1], positions[i][2], \
strandnum[i]))
% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
out.write('\n')
out.write('# Atom-ID, translational, rotational velocity\n')
out.write('Velocities\n')
out.write('\n')
for i in xrange(nnucl):
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
@ -600,9 +598,8 @@ def read_strands(filename):
out.write('Ellipsoids\n')
out.write('\n')
for i in xrange(nnucl):
out.write(\
"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
@ -611,13 +608,13 @@ def read_strands(filename):
out.write('Bonds\n')
out.write('\n')
for i in xrange(nbonds):
for i in range(nbonds):
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
out.close()
print >> sys.stdout, "## Wrote data to 'data.oxdna'"
print >> sys.stdout, "## DONE"
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
print("## DONE", file=sys.stdout)
# call the above main() function, which executes the program
read_strands (infile)
@ -627,4 +624,6 @@ runtime = end_time-start_time
hours = runtime/3600
minutes = (runtime-np.rint(hours)*3600)/60
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)

3
examples/PACKAGES/cgdna/util/generate_simple.py
View File

@ -1,5 +1,8 @@
# Setup tool for oxDNA input in LAMMPS format.
# for python2/3 compatibility
from __future__ import print_function
import math,numpy as np,sys,os
# system size

4
examples/PACKAGES/mgpt/in.bcc0
View File

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

4
examples/PACKAGES/mgpt/in.vac0-bcc
View File

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

4
examples/PACKAGES/mgpt/in.vacmin-bcc
View File

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

134
examples/PACKAGES/mgpt/log.7Feb24.bcc0.g++.1 Normal file
View File

@ -0,0 +1,134 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos in bulk bcc structure
units electron
atom_style atomic
# Atomic volume for MGPT potential in a.u.
variable atomic_vol equal 121.6
# Derive lattice constant from volume
variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.6*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.24196300283154
Lattice spacing in x,y,z = 6.241963 6.241963 6.241963
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
create_atoms CPU = 0.000 seconds
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Create velocities at 0 K
velocity all create 0.0 87287
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Set up microcanonical integrator
fix 1 all nve
# Dump coordinates to file every 50 timesteps
#dump id all atom 50 dump.bcc0
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# Run 0 timesteps
run 0
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 = 13.161827
ghost atom cutoff = 13.161827
binsize = 6.5809134, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes
Step Volume Temp PotEng TotEng Press
0 30400 0 -74.412503 -74.412503 -1.1594626e+09
Loop time of 1.019e-06 on 1 procs for 0 steps with 250 atoms
98.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.019e-06 | | |100.00
Nlocal: 250 ave 250 max 250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1479 ave 1479 max 1479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 16000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 250
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.6
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.59530002488734
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -1.15946260887554
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
250 121.6 -148.825006221835 -1.15946260887554
print "${atvol} ${etotry} ${ptotgpa}"
121.6 -0.59530002488734 -1.15946260887554
Total wall time: 0:00:00

134
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos in bulk bcc structure
units electron
atom_style atomic
# Atomic volume for MGPT potential in a.u.
variable atomic_vol equal 121.6
# Derive lattice constant from volume
variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.6*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.24196300283154
Lattice spacing in x,y,z = 6.241963 6.241963 6.241963
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
create_atoms CPU = 0.000 seconds
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Create velocities at 0 K
velocity all create 0.0 87287
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Set up microcanonical integrator
fix 1 all nve
# Dump coordinates to file every 50 timesteps
#dump id all atom 50 dump.bcc0
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# Run 0 timesteps
run 0
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 = 13.161827
ghost atom cutoff = 13.161827
binsize = 6.5809134, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.73 | 3.73 | 3.73 Mbytes
Step Volume Temp PotEng TotEng Press
0 30400 0 -74.412503 -74.412503 -1.1594626e+09
Loop time of 3.56525e-06 on 4 procs for 0 steps with 250 atoms
119.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.565e-06 | | |100.00
Nlocal: 62.5 ave 65 max 60 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 868.5 ave 871 max 866 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 2000 ave 2110 max 1890 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 4000 ave 4160 max 3840 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 16000
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 250
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.6
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.595300024887348
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -1.15946260887575
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
250 121.6 -148.825006221837 -1.15946260887575
print "${atvol} ${etotry} ${ptotgpa}"
121.6 -0.595300024887348 -1.15946260887575
Total wall time: 0:00:00

144
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
# input for unrelaxed vacancy formation energy at constant atomic volume
units electron
atom_style atomic
# Atomic volume for MGPT potential in a.u.
variable atomic_vol equal 121.6
# Derive effective lattice volume from atomic volume for 249-site cell
variable lat_vol equal ${atomic_vol}*249/250
variable lat_vol equal 121.6*249/250
# Derive lattice constant from lattice volume
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.1136*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.23362926394575
Lattice spacing in x,y,z = 6.2336293 6.2336293 6.2336293
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
create_atoms CPU = 0.000 seconds
# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Create velocities at 0 K
velocity all create 0.0 87287
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Set up microcanonical integrator
fix 1 all nve
# Dump coordinates to file every 50 timesteps
# dump id all atom 50 dump.vac0-bcc
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# Run 0 timesteps
run 0
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 = 13.161827
ghost atom cutoff = 13.161827
binsize = 6.5809134, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes
Step Volume Temp PotEng TotEng Press
0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
Loop time of 1.016e-06 on 1 procs for 0 steps with 249 atoms
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.016e-06 | | |100.00
Nlocal: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1479 ave 1479 max 1479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7936 ave 7936 max 7936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15872 ave 15872 max 15872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 0
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.6
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594348488796036
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -0.634267307139553
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
249 121.6 -147.992773710213 -0.634267307139553
print "${atvol} ${etotry} ${ptotgpa}"
121.6 -0.594348488796036 -0.634267307139553
Total wall time: 0:00:00

144
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
# input for unrelaxed vacancy formation energy at constant atomic volume
units electron
atom_style atomic
# Atomic volume for MGPT potential in a.u.
variable atomic_vol equal 121.6
# Derive effective lattice volume from atomic volume for 249-site cell
variable lat_vol equal ${atomic_vol}*249/250
variable lat_vol equal 121.6*249/250
# Derive lattice constant from lattice volume
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.1136*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.23362926394575
Lattice spacing in x,y,z = 6.2336293 6.2336293 6.2336293
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
create_atoms CPU = 0.000 seconds
# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Create velocities at 0 K
velocity all create 0.0 87287
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Set up microcanonical integrator
fix 1 all nve
# Dump coordinates to file every 50 timesteps
# dump id all atom 50 dump.vac0-bcc
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# Run 0 timesteps
run 0
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 = 13.161827
ghost atom cutoff = 13.161827
binsize = 6.5809134, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.73 | 3.73 | 3.73 Mbytes
Step Volume Temp PotEng TotEng Press
0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
Loop time of 2.64725e-06 on 4 procs for 0 steps with 249 atoms
37.8% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.647e-06 | | |100.00
Nlocal: 62.25 ave 65 max 60 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 867.75 ave 870 max 865 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 1984 ave 2099 max 1875 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 3968 ave 4149 max 3825 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 0
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.6
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594348488795831
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -0.634267307088164
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
249 121.6 -147.992773710162 -0.634267307088164
print "${atvol} ${etotry} ${ptotgpa}"
121.6 -0.594348488795831 -0.634267307088164
Total wall time: 0:00:00

162
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
# input for relaxed vacancy formation energy at constant pressure
units electron
atom_style atomic
# Atomic volume for MGPT potential
variable atomic_vol equal 121.863
# Derive effective lattice volume from atomic volume for 249-site cell
variable lat_vol equal ${atomic_vol}*249/250
variable lat_vol equal 121.863*249/250
# Derive lattice constant from lattice volume
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.375548*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.23812011912273
Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
create_atoms CPU = 0.000 seconds
# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Dump coordinates to file every 50 timesteps
# dump id all atom 50 dump.vacmin-bcc
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# minimize total energy
min_style cg
minimize 1.0e-10 1.0e-10 5000 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 = 13.171237
ghost atom cutoff = 13.171237
binsize = 6.5856184, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.88 | 4.88 | 4.88 Mbytes
Step Volume Temp PotEng TotEng Press
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
Loop time of 2.58636 on 1 procs for 139 steps with 249 atoms
90.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-73.9945109564338 -74.0063705487283 -74.0063705557007
Force two-norm initial, final = 0.036622686 8.090814e-05
Force max component initial, final = 0.0073094815 8.0524205e-06
Final line search alpha, max atom move = 1 8.0524205e-06
Iterations, force evaluations = 139 139
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5671 | 2.5671 | 2.5671 | 0.0 | 99.26
Neigh | 0.015241 | 0.015241 | 0.015241 | 0.0 | 0.59
Comm | 0.001446 | 0.001446 | 0.001446 | 0.0 | 0.06
Output | 0.00038428 | 0.00038428 | 0.00038428 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002161 | | | 0.08
Nlocal: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1479 ave 1479 max 1479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7936 ave 7936 max 7936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15872 ave 15872 max 15872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 4
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.863
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594428679162253
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -1.15783109516516
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
249 121.863 -148.012741111401 -1.15783109516516
print "${atvol} ${etotry} ${ptotgpa}"
121.863 -0.594428679162253 -1.15783109516516
Total wall time: 0:00:02

162
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
# input for relaxed vacancy formation energy at constant pressure
units electron
atom_style atomic
# Atomic volume for MGPT potential
variable atomic_vol equal 121.863
# Derive effective lattice volume from atomic volume for 249-site cell
variable lat_vol equal ${atomic_vol}*249/250
variable lat_vol equal 121.863*249/250
# Derive lattice constant from lattice volume
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
variable lattice_constant equal (121.375548*2.0)^(1.0/3.0)
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
lattice bcc ${lattice_constant}
lattice bcc 6.23812011912273
Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 250 atoms
using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
create_atoms CPU = 0.000 seconds
# Remove central atom from bcc lattice to create vacancy
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
delete_atoms region vacancy
Deleted 1 atoms, new total = 249
# Define potential for use in simulation
pair_style mgpt
# Set parameters for potential:
# parameter files atomic volume
#pair_coeff * * parmin potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
# Set neighbor list parameters
neighbor 0.1 bin
neigh_modify every 1 delay 0 check yes
# Dump coordinates to file every 50 timesteps
# dump id all atom 50 dump.vacmin-bcc
# Output thermodynamical data every 10 timesteps
thermo 10
# Set output quantities and output format
thermo_style custom step vol temp pe etotal press
## Example: Output floating point number with 5 digits exponential notation.
#thermo_modify format float %15.5e
# minimize total energy
min_style cg
minimize 1.0e-10 1.0e-10 5000 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 = 13.171237
ghost atom cutoff = 13.171237
binsize = 6.5856184, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mgpt, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair mgpt, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.855 | 4.855 | 4.855 Mbytes
Step Volume Temp PotEng TotEng Press
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
Loop time of 0.972735 on 4 procs for 139 steps with 249 atoms
89.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-73.9945109564331 -74.0063705487423 -74.0063705556773
Force two-norm initial, final = 0.036622686 8.090814e-05
Force max component initial, final = 0.0073094815 8.0524207e-06
Final line search alpha, max atom move = 1 8.0524207e-06
Iterations, force evaluations = 139 139
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.9418 | 0.94514 | 0.9488 | 0.3 | 97.16
Neigh | 0.0083827 | 0.0084423 | 0.0085002 | 0.0 | 0.87
Comm | 0.011833 | 0.015482 | 0.01882 | 2.0 | 1.59
Output | 0.0002579 | 0.00029089 | 0.000389 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003376 | | | 0.35
Nlocal: 62.25 ave 68 max 59 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 867.75 ave 871 max 862 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 1984 ave 2211 max 1853 min
Histogram: 1 1 1 0 0 0 0 0 0 1
FullNghs: 3968 ave 4334 max 3761 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 15872
Ave neighs/atom = 63.742972
Neighbor list builds = 4
Dangerous builds = 0
# Convert energy to rydbergs and pressure to gpa
variable natoms equal "count(all)"
variable voltot equal "vol"
variable atvol equal "v_voltot/v_natoms"
variable etot equal "2.0*pe"
variable etotry equal "v_etot/v_natoms"
variable ptot equal "press"
variable ptotgpa equal "v_ptot/1.0e+09"
print "number of atoms = ${natoms}"
number of atoms = 249
print "atomic volume (a.u.) = ${atvol}"
atomic volume (a.u.) = 121.863
print "total energy (ry/atom) = ${etotry}"
total energy (ry/atom) = -0.594428679162068
print "pressure (gpa) = ${ptotgpa}"
pressure (gpa) = -1.15783109519336
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
249 121.863 -148.012741111355 -1.15783109519336
print "${atvol} ${etotry} ${ptotgpa}"
121.863 -0.594428679162068 -1.15783109519336
Total wall time: 0:00:00

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