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Merge branch 'master' of github.com:lammps/lammps into kokkos_double_free

This commit is contained in:
Stan Gerald Moore 2021-05-14 09:38:21 -06:00
parent 7b4fdb92df e5cc4409a5
commit eedd726edb
2659 changed files with 86364 additions and 24436 deletions
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1
.gitattributes vendored
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@ -1,3 +1,4 @@
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore

6
.github/CONTRIBUTING.md vendored
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@ -26,11 +26,11 @@ __
## I don't want to read this whole thing I just have a question!
> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
## How Can I Contribute?
There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
### Discussing How To Use LAMMPS
@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not
If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
### Reporting Bugs
While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.

4
.github/codeql/cpp.yml vendored Normal file
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@ -0,0 +1,4 @@
paths:
- src
- lib
- tools

5
.github/codeql/python.yml vendored Normal file
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@ -0,0 +1,5 @@
paths:
- python/lammps
queries:
- uses: security-and-quality

8
.github/workflows/codeql-analysis.yml vendored
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@ -31,16 +31,18 @@ jobs:
uses: github/codeql-action/init@v1
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
if: ${{ matrix.language == 'cpp' }}
run: mkdir build
- name: Building LAMMPS via CMake
if: ${{ matrix.language == 'cpp' }}
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
cmake -C ../cmake/presets/most.cmake ../cmake
cmake --build . --parallel 2
- name: Perform CodeQL Analysis

32
.github/workflows/unittest-macos.yml vendored
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@ -10,6 +10,8 @@ jobs:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
@ -17,20 +19,36 @@ jobs:
with:
fetch-depth: 2
- name: Install ccache
run: brew install ccache
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
run: mkdir build
- name: Set up ccache
uses: actions/cache@v2
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}
restore-keys: macos-ccache-
- name: Building LAMMPS via CMake
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
-C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
$GITHUB_WORKSPACE/cmake \
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
ccache -z
cmake -C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D ENABLE_TESTING=on \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
../cmake
cmake --build . --parallel 2
ccache -s
- name: Run Tests
working-directory: ${{github.workspace}}/build
working-directory: build
shell: bash
run: ctest -V

14
.lgtm.yml Normal file
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@ -0,0 +1,14 @@
extraction:
cpp:
configure:
command:
- "mkdir build"
- "cd build"
- "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
index:
build_command:
- "cd build"
- "ninja"
python:
python_setup:
version: 3

65
cmake/CMakeLists.txt
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@ -124,7 +124,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -245,69 +245,6 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(C)
find_package(LAPACK)

4
cmake/Modules/Documentation.cmake
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@ -55,8 +55,8 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
# download mathjax distribution and unpack to folder "mathjax"

3
cmake/Modules/GenerateOpenCLHeader.cmake Normal file
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@ -0,0 +1,3 @@
# utility script to call WriteOpenCLHeader function
include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

4
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

20
cmake/Modules/OpenCLUtils.cmake
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@ -1,10 +1,8 @@
function(GenerateOpenCLHeader varname outfile files)
message("Creating ${outfile}...")
function(WriteOpenCLHeader varname outfile files)
file(WRITE ${outfile} "const char * ${varname} = \n")
math(EXPR ARG_END "${ARGC}-1")
separate_arguments(files)
foreach(IDX RANGE 2 ${ARG_END})
list(GET ARGV ${IDX} filename)
foreach(filename ${files})
file(READ ${filename} content)
string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
endforeach()
file(APPEND ${outfile} ";\n")
endfunction(WriteOpenCLHeader)
function(GenerateOpenCLHeader varname outfile files)
list(REMOVE_AT ARGV 0 1)
add_custom_command(OUTPUT ${outfile}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
-D VARNAME=${varname}
-D HEADER_FILE=${outfile}
-D SOURCE_FILES="${ARGV}"
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
DEPENDS ${ARGV}
COMMENT "Generating ${outfile}...")
endfunction(GenerateOpenCLHeader)

19
cmake/Modules/Packages/GPU.cmake
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@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@ -145,7 +145,14 @@ if(GPU_API STREQUAL "CUDA")
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
# the static OpenCL loader doesn't seem to work on macOS. use the system provided
# version by default instead (for as long as it will be available)
if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
set(_opencl_static_default OFF)
else()
set(_opencl_static_default ON)
endif()
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader)
@ -289,18 +296,18 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()

6
cmake/Modules/Packages/KOKKOS.cmake
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@ -37,8 +37,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -58,7 +58,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
find_package(Kokkos 3.4.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()

8
cmake/Modules/Packages/USER-INTEL.cmake
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@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
if(COMPILER_SUPPORTS${_FLAGX})
separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
target_compile_options(lammps PRIVATE ${_FLAG})
endif()
endforeach()

2
cmake/Modules/Packages/USER-PACE.cmake
View File

@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE})
set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)

73
cmake/Modules/Testing.cmake
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@ -56,3 +56,76 @@ if(ENABLE_TESTING)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
# enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif()
# detect the "native" header folder so we can include them first
execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
#######################################
# select code sanitizer options
#######################################
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()

2
cmake/Modules/generate_lmpgitversion.cmake
View File

@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}

20
cmake/presets/all_off.cmake
View File

@ -2,16 +2,16 @@
# an existing package selection without losing any other settings
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
SNAP SPIN SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

20
cmake/presets/all_on.cmake
View File

@ -4,16 +4,16 @@
# with just a working C++ compiler and an MPI library.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
SNAP SPIN SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

6
cmake/presets/most.cmake
View File

@ -5,9 +5,9 @@
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})

9
cmake/presets/nolib.cmake
View File

@ -1,10 +1,11 @@
# preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent.
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

2
doc/Makefile
View File

@ -236,7 +236,7 @@ $(VENV):
)
$(MATHJAX):
@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \

10
doc/src/Build_extras.rst
View File

@ -467,6 +467,9 @@ They must be specified in uppercase.
* - ARMV8_THUNDERX2
- HOST
- ARMv8 Cavium ThunderX2 CPU
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
@ -539,6 +542,9 @@ They must be specified in uppercase.
* - AMPERE80
- GPU
- NVIDIA Ampere generation CC 8.0 GPU
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
* - VEGA900
- GPU
- AMD GPU MI25 GFX900
@ -547,12 +553,12 @@ They must be specified in uppercase.
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- GPU
- AMD GPU GFX908
- AMD GPU MI100 GFX908
* - INTEL_GEN
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.3 of the Kokkos library.
This list was last updated for version 3.4 of the Kokkos library.
.. tabs::

3
doc/src/Commands_fix.rst
View File

@ -39,6 +39,9 @@ OPT.
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`brownian <fix_brownian>`
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`

4
doc/src/Commands_pair.rst
View File

@ -87,6 +87,8 @@ OPT.
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (gio) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/ext <pair_dpd_ext>`
* :doc:`dpd/ext/tstat <pair_dpd_ext>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (go) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -169,7 +171,7 @@ OPT.
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`lj96/cut (go) <pair_lj96>`

40
doc/src/Developer_utils.rst
View File

@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of
strings into specific types of numbers with checking for validity. This
reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
I/O with status check and similar functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like
``fgets()`` or ``fread()``. They will check if there were errors
on reading or an unexpected end-of-file state was reached. In that
case, the functions will stop the calculation with an error message,
indicating the name of the problematic file, if possible.
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
were errors on reading or an unexpected end-of-file state was reached.
In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
but it will read in a whole line (i.e. until the end of line or end
of file), but store only as many characters as will fit into the buffer
including a final newline character and the terminating NULL byte.
If the line in the file is longer it will thus be truncated in the buffer.
This function is used by :cpp:func:`read_lines_from_file` to read individual
lines but make certain they follow the size constraints.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
NULL character.
----------
@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible.
.. doxygenfunction:: sfread
:project: progguide
.. doxygenfunction:: fgets_trunc
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
----------
String to number conversions with validity check
@ -164,7 +185,10 @@ Argument processing
Convenience functions
^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: logmesg
.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
:project: progguide
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: getsyserror

2
doc/src/Examples.rst
View File

@ -108,6 +108,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |
+-------------+------------------------------------------------------------------+
| nb3b | use of non-bonded 3-body harmonic pair style |
+-------------+------------------------------------------------------------------+
| neb | nudged elastic band (NEB) calculation for barrier finding |

2
doc/src/Howto_drude2.rst
View File

@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
Example input scripts available: examples/USER/drude
----------
**Overview of Drude induced dipoles**

12
doc/src/Library_config.rst
View File

@ -15,6 +15,8 @@ This section documents the following functions:
- :cpp:func:`lammps_config_package_count`
- :cpp:func:`lammps_config_package_name`
- :cpp:func:`lammps_config_accelerator`
- :cpp:func:`lammps_has_gpu_device`
- :cpp:func:`lammps_gpu_device_info`
- :cpp:func:`lammps_has_style`
- :cpp:func:`lammps_style_count`
- :cpp:func:`lammps_style_name`
@ -132,6 +134,16 @@ approach.
-----------------------
.. doxygenfunction:: lammps_has_gpu_device
:project: progguide
-----------------------
.. doxygenfunction:: lammps_get_gpu_device_info
:project: progguide
-----------------------
.. doxygenfunction:: lammps_has_style
:project: progguide

21
doc/src/Packages_details.rst
View File

@ -69,6 +69,7 @@ page gives those details.
* :ref:`USER-ATC <PKG-USER-ATC>`
* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
* :ref:`USER-BOCS <PKG-USER-BOCS>`
* :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
@ -1266,6 +1267,26 @@ Example inputs are in the examples/USER/bocs folder.
----------
.. _PKG-USER-BROWNIAN:
USER-BROWNIAN package
---------------------
**Contents:**
This package provides :doc:`fix brownian, fix brownian/sphere, and
fix brownian/asphere <fix_brownian>` as well as
:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
Dynamics time integration of point, spherical and aspherical particles
and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
Example inputs are in the examples/USER/brownian folder.
----------
.. _PKG-USER-CGDNA:
USER-CGDNA package

2
doc/src/Packages_user.rst
View File

@ -39,6 +39,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |

98
doc/src/Tools.rst
View File

@ -94,6 +94,7 @@ Miscellaneous tools
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
----------
.. _offline:
Scripts for building LAMMPS when offline
----------------------------------------
In some situations it might be necessary to build LAMMPS on a system
without direct internet access. The scripts in ``tools/offline`` folder
allow you to pre-load external dependencies for both the documentation
build and for building LAMMPS with CMake.
It does so by
#. downloading necessary ``pip`` packages,
#. cloning ``git`` repositories
#. downloading tarballs
to a designated cache folder.
As of April 2021, all of these downloads make up around 600MB. By
default, the offline scripts will download everything into the
``$HOME/.cache/lammps`` folder, but this can be changed by setting the
``LAMMPS_CACHING_DIR`` environment variable.
Once the caches have been initialized, they can be used for building the
LAMMPS documentation or compiling LAMMPS using CMake on an offline
system.
The ``use_caches.sh`` script must be sourced into the current shell
to initialize the offline build environment. Note that it must use
the same ``LAMMPS_CACHING_DIR``. This script does the following:
#. Set up environment variables that modify the behavior of both,
``pip`` and ``git``
#. Start a simple local HTTP server using Python to host files for CMake
Afterwards, it will print out instruction on how to modify the CMake
command line to make sure it uses the local HTTP server.
To undo the environment changes and shutdown the local HTTP server,
run the ``deactivate_caches`` command.
Examples
^^^^^^^^
For all of the examples below, you first need to create the cache, which
requires an internet connection.
.. code-block:: bash
./tools/offline/init_caches.sh
Afterwards, you can disconnect or copy the contents of the
``LAMMPS_CACHING_DIR`` folder to an offline system.
Documentation Build
^^^^^^^^^^^^^^^^^^^
The documentation build will create a new virtual environment that
typically first installs dependencies from ``pip``. With the offline
environment loaded, these installations will instead grab the necessary
packages from your local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
cd doc/
make html
deactivate_caches
CMake Build
^^^^^^^^^^^
When compiling certain packages with external dependencies, the CMake
build system will download necessary files or sources from the web. For
more flexibility the CMake configuration allows users to specify the URL
of each of these dependencies. What the ``init_caches.sh`` script does
is create a CMake "preset" file, which sets the URLs for all of the known
dependencies and redirects the download to the local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
mkdir build
cd build
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
make -j 8
deactivate_caches
----------
.. _phonon:
phonon tool

54
doc/src/comm_modify.rst
View File

@ -11,13 +11,17 @@ Syntax
comm_modify keyword value ...
* zero or more keyword/value pairs may be appended
* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
.. parsed-literal::
*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
*mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
*cutoff* value = Rcut (distance units) = communicate atoms from this far away
*cutoff/multi* type value
*cutoff/multi* collection value
collection = atom collection or collection range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
*cutoff/multi/old* type value
type = atom type or type range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*group* value = group-ID = only communicate atoms in the group
@ -28,7 +32,7 @@ Examples
.. code-block:: LAMMPS
comm_modify mode multi
comm_modify mode multi reduce/multi
comm_modify mode multi group solvent
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor
cutoff across all atom type pairs.
For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* mode can
be faster. In this case, each atom type is assigned its own distance
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
be faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs.
In this case, each atom collection is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. See the :doc:`neighbor multi <neighbor>` command for a
neighbor list construction option that may also be beneficial for
simulations of this kind.
communicated. in *multi/old*, a similar technique is used but atoms
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
:doc:`neighbor multi/old <neighbor>` commands for
neighbor list construction options that may also be beneficial for
simulations of this kind. The *multi* communiction mode is only compatable
with the *multi* neighbor style. The *multi/old* communication mode is compatble
with both the *multi* and *multi/old* neighbor styles.
The *cutoff* keyword allows you to extend the ghost cutoff distance
for communication mode *single*\ , which is the distance from the borders
@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since in this case the communication
cutoffs are determined per atom type, a type specifier is needed and
cutoff for one or multiple types can be extended. Also ranges of types
using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
communication mode *multi* instead. Since the communication
cutoffs are determined per atom collections, a collection specifier is needed and
cutoff for one or multiple collections can be extended. Also ranges of collections
using the usual asterisk notation can be given.
Collections are indexed from 1 to N where N is the total number of collections.
Note that the arguments for *cutoff/multi* are parsed right before each
simulation to account for potential changes in the number of collections.
Custom cutoffs are preserved between runs but if collections are redefined,
one may want to respecify communication cutoffs.
For granular pair styles,the default cutoff is set to the sum of the
current maximum atomic radii for each collection.
The *cutoff/multi/old* option is similar to *cutoff/multi* except it
operates on atom types as opposed to collections.
The *reduce/multi* option applies to *multi* and sets the communication
cutoff for a particle equal to the maximum interaction distance between particles
in the same collection. This reduces the number of
ghost atoms that need to be communicated. This method is only compatible with the
*multi* neighbor style and requires a half neighbor list and Newton on.
See the :doc:`neighbor multi <neighbor>` command for more information.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:

2
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@ -48,6 +48,8 @@ Examples
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
doc/src/compute_temp_drude.rst
View File

@ -20,6 +20,8 @@ Examples
compute TDRUDE all temp/drude
Example input scripts available: examples/USER/drude
Description
"""""""""""

3
doc/src/fix.rst
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@ -182,6 +182,9 @@ accelerated styles exist.
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
* :doc:`brownian <fix_brownian>` - overdamped translational brownian motion
* :doc:`brownian/asphere <fix_brownian>` - overdamped translational and rotational brownian motion for ellipsoids
* :doc:`brownian/sphere <fix_brownian>` - overdamped translational and rotational brownian motion for spheres
* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
* :doc:`bond/create <fix_bond_create>` - create bonds on the fly

3
doc/src/fix_adapt_fep.rst
View File

@ -56,6 +56,9 @@ Examples
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
Example input scripts available: examples/USER/fep
Description
"""""""""""

43
doc/src/fix_bond_react.rst
View File

@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', and 'rmsd'.
six types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
A sample map file is given below:
@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
The constraint of type 'custom' has the following syntax:
.. parsed-literal::
custom *varstring*
where 'custom' is the required keyword, and *varstring* is a
variable expression. The expression must be a valid equal-style
variable formula that can be read by the :doc:`variable <variable>` command,
after any special reaction functions are evaluated. If the resulting
expression is zero, the reaction is prevented from occurring;
otherwise, it is permitted to occur. There are two special reaction
functions available, 'rxnsum' and 'rxnave'. These functions operate
over the atoms in a given reaction site, and have one mandatory
argument and one optional argument. The mandatory argument is the
identifier for an atom-style variable. The second, optional argument
is the name of a molecule fragment in the pre-reaction template, and
can be used to operate over a subset of atoms in the reaction site.
The 'rxnsum' function sums the atom-style variable over the reaction
site, while the 'rxnave' returns the average value. For example, a
constraint on the total potential energy of atoms involved in the
reaction can be imposed as follows:
.. code-block:: LAMMPS
compute 1 all pe/atom # in LAMMPS input script
variable my_pe atom c_1 # in LAMMPS input script
.. code-block:: LAMMPS
custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
The above example prevents the reaction from occurring unless the
total potential energy of the reaction site is above 100. The variable
expression can be interpreted as the probability of the reaction
occurring by using an inequality and the 'random(x,y,z)' function
available as an equal-style variable input, similar to the 'arrhenius'
constraint above.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
logical values using the logical AND operator "&&". More complex logic

216
doc/src/fix_brownian.rst Normal file
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@ -0,0 +1,216 @@
.. index:: fix brownian
.. index:: fix brownian/sphere
.. index:: fix brownian/asphere
fix brownian command
===========================
fix brownian/sphere command
===========================
fix brownian/sphere command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID style_name temp seed keyword args
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
* temp = temperature
* seed = random number generator seed
* one or more keyword/value pairs may be appended
* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
.. parsed-literal::
*rng* value = *uniform* or *gaussian* or *none*
*uniform* = use uniform random number generator
*gaussian* = use gaussian random number generator
*none* = turn off noise
*dipole* value = *mux* and *muy* and *muz* for *brownian/asphere*
*mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body
*gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere*
*gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor
*gamma_r* values = *gr* for *brownian/sphere*
*gr* = magnitude of the (isotropic) rotational friction tensor
*gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere*
*gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor
*gamma_t* values = *gt* for *brownian* and *brownian/sphere*
*gt* = magnitude of the (isotropic) translational friction tensor
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all brownian 1.0 12908410 gamma_t 1.0
fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
Description
"""""""""""
Perform Brownian Dynamics time integration to update position, velocity,
dipole orientation (for spheres) and quaternion orientation (for
ellipsoids, with optional dipole update as well) of all particles in the
fix group in each timestep. Brownian Dynamics uses Newton's laws of
motion in the limit that inertial forces are negligible compared to
viscous forces. The stochastic equation of motion for the center of mass
positions is
.. math::
d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
only depends on orientation and so the noise is still additive).
The rotational motion for the spherical and ellipsoidal particles is not
as simple an expression, but is chosen to replicate the Boltzmann
distribution for the case of conservative torques (see :ref:`(Ilie)
<Ilie1>` or :ref:`(Delong) <Delong1>`).
For the style *brownian*, only the positions of the particles are
updated. This is therefore suitable for point particle simulations.
For the style *brownian/sphere*, the positions of the particles are
updated, and a dipole slaved to the spherical orientation is also
updated. This style therefore requires the hybrid atom style
:doc:`atom_style dipole <atom_style>` and :doc:`atom_style sphere
<atom_style>`.
For the style *brownian/asphere*, the center of mass positions and the
quaternions of ellipsoidal particles are updated. This fix style is
suitable for equations of motion where the rotational and translational
friction tensors can be diagonalized in a certain (body) reference frame.
---------
.. note::
This integrator does not by default assume a relationship between the
rotational and translational friction tensors, though such a relationship
should exist in the case of no-slip boundary conditions between the particles and
the surrounding (implicit) solvent. E.g. in the case of spherical particles,
the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly
accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
:math:`\sigma` is the spherical diameter). A similar (though more complex)
relationship holds for ellipsoids and rod-like particles.
---------
.. note::
Temperature computation using the :doc:`compute temp <compute_temp>`
will not correctly compute temperature of these overdamped dynamics
since we are explicitly neglecting inertial effects.
Furthermore, this time integrator does not add the stochastic terms or
viscous terms to the force and/or torques. Rather, they are just added
in to the equations of motion to update the degrees of freedom.
---------
If the *rng* keyword is used with the *uniform* value, then the noise
is generated from a uniform distribution (see
:ref:`(Dunweg) <Dunweg7>` for why this works). This is the same method
of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
If the *rng* keyword is used with the *gaussian* value, then the noise
is generated from a gaussian distribution. Typically this added
complexity is unnecessary, and one should be fine using the *uniform*
value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
If the *rng* keyword is used with the *none* value, then the noise
terms are set to zero.
The *gamma_t* keyword sets the (isotropic) translational viscous damping.
Required for (and only compatible with) *brownian* and *brownian/sphere*.
The units of *gamma_t* are mass/time.
The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
Required for (and only compatible with) *brownian/sphere*.
The units of *gamma_r* are mass*length**2/time.
The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
the rotational and viscous damping tensors (having the same units as
their isotropic counterparts). Required for (and only compatible with)
*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen*
must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen*
must be inf (only diffusion in xy plane).
If the *dipole* keyword is used, then the dipole moments of the particles
are updated as described above. Only compatible with *brownian/asphere*
(as *brownian/sphere* updates dipoles automatically).
----------
.. note::
For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
*gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
*brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega)
as defined by the :doc:`atom_style sphere <atom_style>` command.
The style *brownian/asphere* fix requires that atoms store torque and quaternions
as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
If the *dipole* keyword is used, they must also store a dipole moment
as defined by the :doc:`atom_style dipole <atom_style>` command.
This fix is part of the USER-BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`fix propel/self <fix_propel_self>`,
:doc:`fix langevin <fix_langevin>`, :doc:`fix nve/sphere <fix_nve_sphere>`,
Default
"""""""
The default for *rng* is *uniform*. The default for the rotational and translational friction
tensors are the identity tensor.
----------
.. _Ilie1:
**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
.. _Delong1:
**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015)
.. _Dunweg7:
**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

2
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@ -22,6 +22,8 @@ Examples
fix 1 all drude 1 1 0 1 0 2 2 2
fix 1 all drude C C N C N D D D
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_drude_transform.rst
View File

@ -25,6 +25,8 @@ Examples
fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_langevin_drude.rst
View File

@ -35,6 +35,8 @@ Examples
fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
Example input scripts available: examples/USER/drude
Description
"""""""""""

16
doc/src/fix_precession_spin.rst
View File

@ -125,10 +125,10 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c >
diagonals. See chapter 2 of :ref:`(Skomski) <Skomski1>` for more
details on cubic anisotropies.
Style *stt* is used to simulate the interaction between the spins and
Style *stt* is used to simulate the interaction between the spins and
a spin-transfer torque.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
In all cases, the choice of :math:`(x y z)` only imposes the vector
directions for the forces. Only the direction of the vector is
@ -139,12 +139,12 @@ Those styles can be combined within one single command line.
.. note::
The norm of all vectors defined with the precession/spin command
The norm of all vectors defined with the precession/spin command
have to be non-zero. For example, defining
"fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result
in an error message.
in an error message.
Since those vector components are used to compute the inverse of the
field (or anisotropy) vector norm, setting a zero-vector would result
field (or anisotropy) vector norm, setting a zero-vector would result
in a division by zero.
----------
@ -197,6 +197,6 @@ Oxford University Press.
.. _Chirac1:
**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
**(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
Physical Review B 102.13 (2020): 134415.

183
doc/src/fix_propel_self.rst
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@ -8,52 +8,121 @@ Syntax
.. parsed-literal::
fix ID group-ID propel/self mode magnitude keyword values ...
fix ID group-ID propel/self mode magnitude keyword values
* ID, group-ID are documented in :doc:`fix <fix>` command
* propel/self = style name of this fix command
* mode = velocity or quat
* magnitude = magnitude of the active force
* one or more keyword/value pairs may be appended to args
* keyword = *types*
* mode = *dipole* or *velocity* or *quat*
* magnitude = magnitude of self-propulsion force
* zero or one keyword/value pairs may be appended
* keyword = *qvector*
.. parsed-literal::
*qvector* value = direction of force in ellipsoid frame
*sx*, *sy*, *sz* = components of *qvector*
*types* values = one or more atom types
Examples
""""""""
.. code-block:: LAMMPS
fix active_group all propel/self velocity 1.0
fix constant_velocity all viscous 1.0
fix active_group all propel/self quat 1.0
fix active all propel/self quat 1.0 types 1 2 4
fix active all propel/self dipole 40.0
fix active all propel/self velocity 10.0
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
Description
"""""""""""
Adds a force of a constant magnitude to each atom in the group. The nature in
which the force is added depends on the mode.
Add a force to each atom in the group due to a self-propulsion force. The
force is given by
For *mode* = *velocity*, the active force acts along the velocity vector of
each atom. This can be interpreted as a velocity-dependent friction,
such as proposed by :ref:`(Erdmann) <Erdmann>`.
.. math::
For *mode* = *quat* the force is applied along the axis obtained
by rotating the x-axis along the atom's quaternion. In other words, the
force is along the x-axis in the atom's body frame. This mode requires
all atoms in the group to have a quaternion, so atom_style should
either be ellipsoid or body. In combination with Langevin thermostat
for translation and rotation in the overdamped regime, the quaternion
mode corresponds to the active Brownian particle model introduced by
:ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily)
<Fily>`.
F_i = f_P e_i
By default, this fix is applied to all atoms in the group. You can
override this behavior by specifying the atom types the fix should work
on through the *types* keyword.
where *i* is the particle the force is being applied to, :math:`f_P`
is the magnitude of the force, and :math:`e_i` is the vector direction
of the force. The specification of :math:`e_i` is based on which of the
three keywords (*dipole* or *velocity* or *quat*) one selects.
For mode *dipole*, :math:`e_i` is just equal to
the dipole vectors of the atoms in the group. Therefore, if the dipoles
are not unit vectors, the :math:`e_i` will not be unit vectors.
.. note::
If another command changes the magnitude of the dipole, this force will
change accordingly (since :math:`|e_i|` will change, which is physically
equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant),
and no warning will be provided by LAMMPS. This is almost never what you
want, so ensure you are not changing dipole magnitudes with another LAMMPS
fix or pair style. Furthermore, self-propulsion forces (almost) always
set :math:`e_i` to be a unit vector for all times, so it's best to set
all the dipole magnitudes to 1.0 unless you have a good reason not to
(see the :doc:`set <set>` command on how to do this).
For mode *velocity*, :math:`e_i` points in the direction
of the current velocity (a unit-vector). This can be interpreted as a
velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) <Erdmann1>`.
For mode *quat*, :math:`e_i` points in the direction of a unit
vector, oriented in the coordinate frame of the ellipsoidal particles,
which defaults to point along the x-direction. This default behavior
can be changed by via the *quatvec* keyword.
The optional *quatvec* keyword specifies the direction of self-propulsion
via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are
defined within the coordinate frame of the atom's
ellipsoid. For instance, for an ellipsoid with long axis along
its x-direction, if one wanted the self-propulsion force to also
be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
to zero. This keyword may only be specified for mode *quat*.
.. note::
In using keyword *quatvec*, the three arguments *sx*,
*sy*, and *sz* will be automatically normalized to components
of a unit vector internally to avoid users having to explicitly
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
will always be of unit length.
Along with adding a force contribution, this fix can also
contribute to the virial (pressure) of the system, defined as
:math:`f_P \sum_i <e_i . r_i>/(d V)`, where :math:`r_i` is the
*unwrapped* coordinate of particle i in the case of periodic
boundary conditions. See :ref:`(Winkler) <Winkler1>` for a
discussion of this active pressure contribution.
For modes *dipole* and *quat*, this fix is by default
included in pressure computations.
For mode *velocity*, this fix is by default not included
in pressure computations.
.. note::
In contrast to equilibrium systems, pressure of active systems
in general depends on the geometry of the container.
The active pressure contribution as calculated in this fix
is only valid for certain boundary conditions (spherical
walls, rectangular walls, or periodic boundary conditions).
For other geometries, the pressure must be measured via
explicit calculation of the force per unit area on a wall,
and so one must not calculate it using this fix.
(Use :doc:`fix_modify <fix_modify>` as described below
to turn off the virial contribution of this fix). Again,
see :ref:`(Winkler) <Winkler1>` for discussion of why this
is the case.
Furthermore, when dealing with active systems, the temperature
is no longer well defined. Therefore, one should ensure that
the *virial* flag is used in the
:doc:`compute pressure <compute_pressure>` command (turning
off temperature contributions).
----------
@ -62,40 +131,48 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
This fix is not imposed during minimization.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial yes* for keywords *dipole* and *quat*. The
default is *virial no* for keyword *velocity*.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
Restrictions
""""""""""""
In quat mode, this fix makes use of per-atom quaternions to take
into account the fact that the orientation can rotate and hence the
direction of the active force can change. The quat mode
of this fix only works with atom_style ellipsoid.
With keyword *dipole*, this fix only works when the DIPOLE package is enabled.
See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the USER-BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
.. _Erdmann:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Henkes:
**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
.. _Bialke:
**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
.. _Fily:
**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
:doc:`fix efield <fix_efield>` , :doc:`fix setforce <fix_setforce>`,
:doc:`fix addforce <fix_addforce>`
Default
"""""""
types
none
----------
.. _Erdmann1:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Winkler1:
**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).

2
doc/src/fix_tgnh_drude.rst
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@ -62,6 +62,8 @@ Examples
fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0
fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
Example input scripts available: examples/USER/drude
Description
"""""""""""

39
doc/src/neigh_modify.rst
View File

@ -14,7 +14,7 @@ Syntax
.. parsed-literal::
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize*
keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
*delay* value = N
N = delay building until this many steps since last build
*every* value = M
@ -47,6 +47,12 @@ Syntax
N = max number of neighbors of one atom
*binsize* value = size
size = bin size for neighbor list construction (distance units)
*collection/type* values = N arg1 ... argN
N = number of custom collections
arg = N separate lists of types (see below)
*collection/interval* values = N arg1 ... argN
N = number of custom collections
arg = N separate cutoffs for intervals (see below)
Examples
""""""""
@ -58,6 +64,8 @@ Examples
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule/intra rigid
neigh_modify collection/type 2 1*2,5 3*4
neigh_modify collection/interval 2 1.0 10.0
Description
"""""""""""
@ -188,8 +196,9 @@ atom can have.
The *binsize* option allows you to specify what size of bins will be
used in neighbor list construction to sort and find neighboring atoms.
By default, for :doc:`neighbor style bin <neighbor>`, LAMMPS uses bins
that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`, the bins are 1/2 the size of the minimum pair
cutoff. Typically these are good values for minimizing the time for
that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`,
the bins are 1/2 the size of the collection interaction cutoff.
Typically these are good values for minimizing the time for
neighbor list construction. This setting overrides the default.
If you make it too big, there is little overhead due to
looping over bins, but more atoms are checked. If you make it too
@ -197,6 +206,30 @@ small, the optimal number of atoms is checked, but bin overhead goes
up. If you set the binsize to 0.0, LAMMPS will use the default
binsize of 1/2 the cutoff.
The *collection/type* option allows you to define collections of atom
types, used by the *multi* neighbor mode. By grouping atom types with
similar physical size or interaction cutoff lengths, one may be able
to improve performance by reducing
overhead. You must first specify the number of collections N to be
defined followed by N lists of types. Each list consists of a series of type
ranges separated by commas. The range can be specified as a
single numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, if M = the number of atom types, then an asterisk with no numeric
values means all types from 1 to M. A leading asterisk means all types
from 1 to n (inclusive). A trailing asterisk means all types from n to M
(inclusive). A middle asterisk means all types from m to n (inclusive).
Note that all atom types must be included in exactly one of the N collections.
The *collection/interval* option provides a similar capability.
This command allows a user to define collections by specifying a
series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals
based on their type-dependent cutoffs or their finite size.
You must first specify the number of collections N to be
defined followed by N values representing the upper cutoff of each interval.
This command is particularly useful for granular pairstyles where the interaction distance
of particles depends on their radius and may not depend on their atom type.
Restrictions
""""""""""""

39
doc/src/neighbor.rst
View File

@ -11,7 +11,7 @@ Syntax
neighbor skin style
* skin = extra distance beyond force cutoff (distance units)
* style = *bin* or *nsq* or *multi*
* style = *bin* or *nsq* or *multi* or *multi/old*
Examples
""""""""
@ -55,14 +55,31 @@ For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
other type pairs have a much shorter cutoff. For style *multi* the
bin size is set to 1/2 of the shortest cutoff distance and multiple
sets of bins are defined to search over for different atom types.
other type pairs have a much shorter cutoff. The *multi* style uses
different sized bins for collections of different sized particles, where
"size" may mean the physical size of the particle or its cutoff
distance for interacting with other particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves
may be much faster for the short-cutoff cases.
See the :doc:`comm_modify mode multi <comm_modify>` command for a
communication option that may also be beneficial for simulations of
this kind.
may be much faster. By default, each atom type defines a separate
collection of particles. For systems where two or more atom types
have the same size (either physical size or cutoff distance), the
definition of collections can be customized, which can result in less
overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
command for how to define custom collections. Whether the collection
definition is customized or not, also see the
:doc:`comm_modify mode multi <comm_modify>` command for communication
options that further improve performance in a manner consistent with
neighbor style multi.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
different atom types. This algorithm used to be the default *multi*
algorithm in LAMMPS but was found to be significantly slower than the new
approach. For now we are keeping the old option in case there are use cases
where multi/old outperforms the new multi style.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are
@ -90,3 +107,9 @@ Default
| 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
|
----------
.. _bytype-Shire:
**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020).

1
doc/src/pair_coul_tt.rst
View File

@ -29,6 +29,7 @@ Examples
pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0
pair_coeff 1 3* coul/tt 4.5 1.0 4
Example input scripts available: examples/USER/drude
Description
"""""""""""

138
doc/src/pair_dpd_ext.rst Normal file
View File

@ -0,0 +1,138 @@
.. index:: pair_style dpd/ext
.. index:: pair_style dpd/ext/tstat
pair_style dpd/ext command
==========================
pair_style dpd/ext/tstat command
================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style dpd/ext T cutoff seed
pair_style dpd/ext/tstat Tstart Tstop cutoff seed
* T = temperature (temperature units)
* Tstart,Tstop = desired temperature at start/end of run (temperature units)
* cutoff = global cutoff for DPD interactions (distance units)
* seed = random # seed (positive integer)
Examples
""""""""
.. code-block:: LAMMPS
pair_style dpd/ext 1.0 2.5 34387
pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2
pair_style dpd/ext/tstat 1.0 1.0 2.5 34387
pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2
Description
"""""""""""
The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) <Groot>`, :ref:`(Junghans) <Junghans>`.
Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired pair interaction and the thermostat for each pair of particles.
For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum
of 3 terms
.. math::
\mathbf{f} = & f^C + f^D + f^R \qquad \qquad r < r_c \\
f^C = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
f^D = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij} - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
w(r) = & 1 - r/r_c \\
where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command.
For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above:
* A (force units)
* :math:`\gamma_{\perp}` (force/velocity units)
* :math:`\gamma_{\parallel}` (force/velocity units)
* :math:`s_{\perp}` (unitless)
* :math:`s_{\parallel}` (unitless)
* :math:`r_c` (distance units)
The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style <pair_style>` command so it does not need to be specified.
For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command is the same, except that A is not included.
.. note::
If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp <pair_srp>` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other.
.. note::
The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
The pair styles do not support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`.
The :doc:`pair_modify <pair_modify>` table option is not relevant for the style *dpd/ext*.
The style *dpd/ext* does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
The pair styles can only be used via the pair keyword of the :doc:`run_style respa <run_style>` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords.
The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run <run>` command. See the :doc:`run <run>` command for details of how to do this.
----------
Restrictions
""""""""""""
The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify <neigh_modify>` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change.
The pair styles require to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost atoms.
The pair styles will not restart exactly when using the :doc:`read_restart <read_restart>` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart <read_restart>` command for more details.
Related commands
""""""""""""""""
:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`pair_style srp <pair_srp>`
**Default:** none
----------
.. _Groot:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
.. _Junghans:
**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008).

2
doc/src/pair_fep_soft.rst
View File

@ -182,6 +182,8 @@ Examples
pair_coeff * * 100.0 2.0 1.5 1.0
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
Example input scripts available: examples/USER/fep
Description
"""""""""""

12
doc/src/pair_hybrid.rst
View File

@ -257,7 +257,7 @@ then overrides them with 0.0 only for CHARMM:
.. code-block:: LAMMPS
special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
The this input achieves the same effect:
@ -265,7 +265,7 @@ The this input achieves the same effect:
.. code-block:: LAMMPS
special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
@ -279,7 +279,7 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
.. code-block:: LAMMPS
special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_style hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
For use with the various :doc:`compute \*/tally <compute_tally>`
@ -417,7 +417,11 @@ assigned automatically to the sub-style defined for both I,I and J,J and
its coefficients generated by the mixing rule used by that sub-style.
For the *hybrid/overlay* and *hybrid/scaled* style, there is an
additional requirement that both the I,I and J,J pairs are assigned to a
single sub-style. See the :doc:`pair_modify <pair_modify>` command for
single sub-style. If this requirement is not met, no I,J coeffs will be
generated, even if the sub-styles support mixing, and I,J pair
coefficients must be explicitly defined.
See the :doc:`pair_modify <pair_modify>` command for
details of mixing rules. See the See the doc page for the sub-style to
see if allows for mixing.

3
doc/src/pair_lj_smooth.rst
View File

@ -1,10 +1,11 @@
.. index:: pair_style lj/smooth
.. index:: pair_style lj/smooth/gpu
.. index:: pair_style lj/smooth/omp
pair_style lj/smooth command
============================
Accelerator Variants: *lj/smooth/omp*
Accelerator Variants: *lj/smooth/gpu*, *lj/smooth/omp*
Syntax
""""""

2
doc/src/pair_style.rst
View File

@ -150,6 +150,8 @@ accelerated styles exist.
* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting

2
doc/src/pair_thole.rst
View File

@ -42,6 +42,8 @@ Examples
pair_style lj/cut/thole/long 2.6 12.0
Example input scripts available: examples/USER/drude
Description
"""""""""""

3
doc/src/read_data.rst
View File

@ -223,6 +223,9 @@ The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
The file will be read line by line, but there is a limit of 254
characters per line and characters beyond that limit will be ignored.
A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a
description of the file. Then lines are read one at a time. Lines

46
doc/src/thermo_modify.rst
View File

@ -11,12 +11,13 @@ Syntax
thermo_modify keyword value ...
* one or more keyword/value pairs may be listed
* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*
* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press*
.. parsed-literal::
*lost* value = *error* or *warn* or *ignore*
*lost/bond* value = *error* or *warn* or *ignore*
*warn* value = *ignore* or *reset* or *default* or a number
*norm* value = *yes* or *no*
*flush* value = *yes* or *no*
*line* value = *one* or *multi*
@ -75,6 +76,43 @@ are drifting out of the box through a fixed boundary condition (see
the :doc:`boundary <boundary>` command). In this case one atom may be
deleted before the rest of the molecule is, on a later timestep.
The *warn* keyword allows you to control whether LAMMPS will print
warning messages and how many of them. Most warning messages are only
printed by MPI rank 0. They are usually pointing out important issues
that should be investigated, but LAMMPS cannot determine for
certain whether they are an indication of an error.
Some warning messages are printed during a run (or immediately before)
each time a specific MPI rank encounters the issue, e.g. bonds that are
stretched too far or dihedrals in extreme configurations. These number
of these can quickly blow up the size of the log file and screen output.
Thus a limit of 100 warning messages is applied by default. The warning
count is applied to the entire input unless reset with a ``thermo_modify
warn reset`` command. If there are more warnings than the limit, LAMMPS
will print one final warning that it will not print any additional
warning messages.
.. note::
The warning limit is enforced on either the per-processor count or
the total count across all processors. For efficiency reasons,
however, the total count is only updated at steps with thermodynamic
output. Thus when running on a large number of processors in
parallel, the total number of warnings printed can be significantly
larger than the given limit.
Any number after the keyword *warn* will change the warning limit
accordingly. With the value *ignore* all warnings will be suppressed,
with the value *always* no limit will be applied and warnings will
always be printed, with the value *reset* the internal warning counter
will be reset to zero, and with the value *default*, the counter is
reset and the limit set to 100. An example usage of either *reset* or
*default* would be to re-enable warnings that were disabled or have
reached the limit during equilibration, where the warnings would be
acceptable while the system is still adjusting, but then change
to all warnings for the production run, where they would indicate
problems that would require a closer look at what is causing them.
The *norm* keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to *yes* or *no*\ . Different unit styles have
@ -183,9 +221,9 @@ Related commands
Default
"""""""
The option defaults are lost = error, norm = yes for unit style of
*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no,
and temp/press = compute IDs defined by thermo_style.
The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*\ , norm = no for unit style of *real* and *metal*\ ,
flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults

14
doc/src/variable.rst
View File

@ -363,12 +363,14 @@ variable, as discussed below.
The rules for formatting the file are as follows. Each time a set of
per-atom values is read, a non-blank line is searched for in the file.
A comment character "#" can be used anywhere on a line; text starting
with the comment character is stripped. Blank lines are skipped. The
first "word" of a non-blank line, delimited by white-space, is read as
the count N of per-atom lines to immediately follow. N can be the
total number of atoms in the system, or only a subset. The next N
lines have the following format
The file is read line by line but only up to 254 characters are used.
The rest are ignored. A comment character "#" can be used anywhere
on a line and all text following and the "#" character are ignored;
text starting with the comment character is stripped. Blank lines
are skipped. The first "word" of a non-blank line, delimited by
white-space, is read as the count N of per-atom lines to immediately
follow. N can be the total number of atoms in the system, or only a
subset. The next N lines have the following format
.. parsed-literal::

1
doc/utils/requirements.txt
View File

@ -4,3 +4,4 @@ git+git://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs
breathe
Pygments
six

19
doc/utils/sphinx-config/false_positives.txt
View File

@ -101,6 +101,7 @@ anisotropic
anisotropies
anisotropy
ansi
antiferromagnetic
antiquewhite
Antisymmetrized
antisymmetry
@ -311,6 +312,7 @@ br
Branduardi
Branicio
brennan
Briels
Brien
Brilliantov
Broadwell
@ -625,6 +627,7 @@ delflag
Dellago
delocalization
delocalized
Delong
delr
deltaHf
Dendrimer
@ -708,6 +711,7 @@ dodgerblue
dof
doi
Donadio
Donev
dotc
Doty
doxygen
@ -1023,6 +1027,7 @@ fmag
fmass
fmm
fmt
fmtlib
fmx
fmy
fmz
@ -1141,6 +1146,7 @@ GMock
gneb
GNEB
Goldfarb
Gompper
Gonzalez-Melchor
googlemail
googletest
@ -1319,6 +1325,7 @@ ijk
ijkl
ik
Ikeshoji
Ilie
ilmenau
Ilmenau
ilp
@ -2177,6 +2184,7 @@ nimpropers
nimpropertypes
Nimpropertype
Ninteger
NiO
Nissila
nist
nitride
@ -2188,6 +2196,7 @@ nl
nlayers
nlen
Nlines
nlines
nlo
nlocal
Nlocal
@ -2279,6 +2288,7 @@ Ntype
ntypes
Ntypes
nucleotides
nullptr
num
numa
numactl
@ -2538,6 +2548,7 @@ ppn
pppm
prd
Prakash
Praprotnik
pre
Pre
prec
@ -3103,6 +3114,7 @@ Swinburne
Swol
Swope
Sx
sx
sy
Sy
symplectic
@ -3112,6 +3124,7 @@ sysdim
Syst
systemd
Sz
sz
Tabbernor
tabinner
Tadmor
@ -3163,6 +3176,7 @@ th
thb
thei
Theodorou
Theophile
Theor
thermalization
thermalize
@ -3315,6 +3329,7 @@ Uleft
uloop
Ulomek
ulsph
Ultrafast
uMech
umin
Umin
@ -3350,6 +3365,7 @@ upenn
upto
Urbakh
Urbana
Usabiaga
usec
uSemiParallel
userguide
@ -3494,6 +3510,7 @@ Wikipedia
Wildcard
wildcard
wildcards
Winkler
Wirnsberger
wirtes
witin
@ -3505,6 +3522,7 @@ Worley
Wriggers
Wuppertal
Wurtzite
Wysocki
www
wx
Wx
@ -3595,6 +3613,7 @@ ZBL
Zc
zcm
Zeeman
zeeman
Zemer
Zepeda
zflag

53
examples/USER/brownian/2d_velocity/in2d.velocity Normal file
View File

@ -0,0 +1,53 @@
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
units lj
dimension 2
newton off
lattice sq 0.4
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix vel all propel/self velocity ${fp}
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
variable params string 1_${temp}_${fp}
variable params string 1_1_${fp}
variable params string 1_1_4
units lj
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t 1
fix vel all propel/self velocity ${fp}
fix vel all propel/self velocity 4
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
Step Temp E_pair c_press
0 1 0 -0.18336111
500 2.0519273e+10 0 -0.048238222
1000 1.9821717e+10 0 -0.4711053
1500 1.9697609e+10 0 -0.13539588
2000 2.0209443e+10 0 0.0094958039
2500 1.9591299e+10 0 0.40117118
3000 2.089566e+10 0 -0.036548251
3500 1.978692e+10 0 0.28282578
4000 2.0657848e+10 0 0.17618064
4500 2.0837353e+10 0 -0.080724651
5000 2.0348316e+10 0 -0.17471195
Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms
Performance: 0.075 tau/day, 8693.168 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41
Other | | 0.05121 | | | 8.90
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 65.0000 ave 65 max 65 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 2.0328444e+10 0 0 0 0 0 -0.17471195
1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807
2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929
3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039
4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117
5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406
6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034
7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674
8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569
9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407
10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211
11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437
12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034
Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms
Performance: 7542.303 tau/day, 8729.517 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01
Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18
Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05
Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78
Other | | 0.1235 | | | 8.98
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
variable gamma_t equal 1.0
variable temp equal 1.0
variable seed equal 1974019
variable fp equal 4.0
variable params string ${gamma_t}_${temp}_${fp}
variable params string 1_${temp}_${fp}
variable params string 1_1_${fp}
variable params string 1_1_4
units lj
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t ${gamma_t}
fix step all brownian 1 1974019 gamma_t 1
fix vel all propel/self velocity ${fp}
fix vel all propel/self velocity 4
fix 2 all enforce2d
fix_modify vel virial yes
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 500
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
Step Temp E_pair c_press
0 1 0 -0.18336111
500 1.9862591e+10 0 -0.32013566
1000 2.0093184e+10 0 -0.36609742
1500 1.9562283e+10 0 -0.53349351
2000 1.9903977e+10 0 0.63783249
2500 2.0260128e+10 0 0.30046413
3000 1.9948065e+10 0 -0.63093105
3500 1.9507486e+10 0 0.48762848
4000 2.0049087e+10 0 0.40289309
4500 1.9975813e+10 0 0.57649363
5000 2.0129291e+10 0 -0.41288352
Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
Performance: 0.181 tau/day, 20924.952 timesteps/s
92.6% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
Other | | 0.06992 | | | 29.26
Nlocal: 256.000 ave 256 max 256 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 33.0000 ave 33 max 33 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 2.0109634e+10 0 0 0 0 0 -0.41288352
1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031
12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052
Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms
Performance: 23402.683 tau/day, 27086.439 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01
Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69
Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12
Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33
Other | | 0.1057 | | | 23.86
Nlocal: 256.000 ave 259 max 253 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

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##### overdamped dynamics of non-interacting ellipsoids in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string inf
variable gamma_r_2 string inf
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string inf
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
units lj
atom_style hybrid dipole ellipsoid
dimension 2
newton off
lattice sq 0.4
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * shape 3.0 1.0 1.0
set type * quat/random ${seed}
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
# x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

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##### overdamped dynamics of non-interacting ellipsoids in 3D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string 2.0
variable gamma_r_2 string 0.25
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string 9.0
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
units lj
atom_style hybrid dipole ellipsoid
dimension 3
newton off
lattice sc 0.4
region box block -8 8 -8 8 -8 8
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * shape 3.0 1.0 1.0
set type * quat/random ${seed}
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
# x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string inf
variable gamma_r_2 string inf
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string inf
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
units lj
atom_style hybrid dipole ellipsoid
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.005 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
3600 settings made for dipole/random
set type * shape 3.0 1.0 1.0
Setting atom values ...
3600 settings made for shape
set type * quat/random ${seed}
set type * quat/random 198098
Setting atom values ...
3600 settings made for quat/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 34376.187 0 0.00034728749 0.00034318997 0 0.00069047747
200 36135.708 0 0.00067452936 0.0006818928 0 0.0013564222
300 34444.929 0 0.0010189319 0.00099849203 0 0.002017424
400 35668.312 0 0.0013648699 0.0013311884 0 0.0026960583
500 35388.615 0 0.0017330203 0.0016077184 0 0.0033407387
600 35180.065 0 0.002052223 0.0019394635 0 0.0039916865
700 34035.38 0 0.0024329956 0.0022664905 0 0.0046994861
800 34581.664 0 0.002783885 0.0025794872 0 0.0053633723
900 34579.945 0 0.003163442 0.0029351952 0 0.0060986372
1000 34158.066 0 0.0035589034 0.0032627605 0 0.0068216639
1100 33453.827 0 0.0038861895 0.003565372 0 0.0074515615
1200 33608.06 0 0.0041325698 0.0038943268 0 0.0080268966
1300 34381.633 0 0.004405682 0.0043294156 0 0.0087350976
1400 32925.746 0 0.0047383547 0.0046803517 0 0.0094187065
1500 34809.764 0 0.0051149571 0.0049309746 0 0.010045932
1600 33580.096 0 0.0054893472 0.0052465377 0 0.010735885
1700 34596.275 0 0.00581894 0.0056500316 0 0.011468972
1800 33926.736 0 0.0062129617 0.0059796125 0 0.012192574
1900 35577.131 0 0.0065668637 0.0062530163 0 0.01281988
2000 34224.967 0 0.0070005917 0.006598912 0 0.013599504
2100 33991.406 0 0.0073134826 0.0069119252 0 0.014225408
2200 34647.054 0 0.007659301 0.0073434715 0 0.015002772
2300 33956.835 0 0.007965191 0.0076318537 0 0.015597045
2400 35272.549 0 0.0082467116 0.007929202 0 0.016175914
2500 33901.494 0 0.0086251299 0.0082790757 0 0.016904206
2600 34138.227 0 0.0089419364 0.0086639744 0 0.017605911
2700 33691.013 0 0.0093083376 0.0090219118 0 0.018330249
2800 34716.817 0 0.0095840095 0.0094118945 0 0.018995904
2900 34473.982 0 0.0099773501 0.0098167668 0 0.019794117
3000 33406.776 0 0.010391969 0.010098625 0 0.020490594
Loop time of 3.67112 on 1 procs for 3000 steps with 3600 atoms
Performance: 706.051 tau/day, 817.189 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.037973 | 0.037973 | 0.037973 | 0.0 | 1.03
Output | 0.0040674 | 0.0040674 | 0.0040674 | 0.0 | 0.11
Modify | 3.515 | 3.515 | 3.515 | 0.0 | 95.75
Other | | 0.1141 | | | 3.11
Nlocal: 3600.00 ave 3600 max 3600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 121.000 ave 121 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string inf
variable gamma_r_2 string inf
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string inf
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
units lj
atom_style hybrid dipole ellipsoid
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.007 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
3600 settings made for dipole/random
set type * shape 3.0 1.0 1.0
Setting atom values ...
3600 settings made for shape
set type * quat/random ${seed}
set type * quat/random 198098
Setting atom values ...
3600 settings made for quat/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 5.102 | 5.102 | 5.102 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 33874.438 0 0.0003458147 0.00033165629 0 0.00067747099
200 34893.188 0 0.00066290209 0.00068146332 0 0.0013443654
300 34494.226 0 0.0010064902 0.0010276646 0 0.0020341548
400 34537.887 0 0.0013457339 0.0014057042 0 0.0027514381
500 34458.46 0 0.0017006949 0.0017120083 0 0.0034127033
600 33229.977 0 0.0020841613 0.0020485346 0 0.0041326959
700 33288.631 0 0.0024270272 0.0023673304 0 0.0047943576
800 35317.512 0 0.0027924435 0.0026950912 0 0.0054875347
900 33094.299 0 0.0031503627 0.0030789319 0 0.0062292946
1000 35801.751 0 0.003489398 0.0034594626 0 0.0069488607
1100 33427.701 0 0.0038547506 0.0038375809 0 0.0076923316
1200 34675.07 0 0.0041824195 0.0042017298 0 0.0083841493
1300 33080.294 0 0.0045258945 0.0045816356 0 0.0091075301
1400 34927.288 0 0.0048252992 0.0049215701 0 0.0097468693
1500 34338.558 0 0.0051959155 0.0053020102 0 0.010497926
1600 34686.248 0 0.0055111463 0.0056220225 0 0.011133169
1700 34336.158 0 0.0059240394 0.0059060319 0 0.011830071
1800 34315.859 0 0.0063027944 0.0063004467 0 0.012603241
1900 35096.721 0 0.0066098525 0.00672222 0 0.013332073
2000 33544.18 0 0.0069401261 0.007074124 0 0.01401425
2100 33863.219 0 0.0072726502 0.0074175954 0 0.014690246
2200 34705.892 0 0.0075586722 0.0077552683 0 0.015313941
2300 34025.357 0 0.0079046728 0.0081760519 0 0.016080725
2400 34741.849 0 0.008252969 0.0085203087 0 0.016773278
2500 34406.959 0 0.0085370091 0.0088556377 0 0.017392647
2600 34062.63 0 0.0088134153 0.0092536326 0 0.018067048
2700 34677.666 0 0.0090592854 0.0096225881 0 0.018681874
2800 33464.216 0 0.0093984162 0.0099647695 0 0.019363186
2900 32920.721 0 0.0098222985 0.010366517 0 0.020188816
3000 34539.66 0 0.010133317 0.01068102 0 0.020814337
Loop time of 1.12143 on 4 procs for 3000 steps with 3600 atoms
Performance: 2311.341 tau/day, 2675.163 timesteps/s
96.1% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.036017 | 0.042828 | 0.051558 | 2.7 | 3.82
Output | 0.0012608 | 0.0025993 | 0.0063775 | 4.3 | 0.23
Modify | 0.9002 | 0.93095 | 0.99546 | 3.9 | 83.01
Other | | 0.1451 | | | 12.93
Nlocal: 900.000 ave 900 max 900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 61.0000 ave 61 max 61 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string 2.0
variable gamma_r_2 string 0.25
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string 9.0
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
units lj
atom_style hybrid dipole ellipsoid
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.005 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
4096 settings made for dipole/random
set type * shape 3.0 1.0 1.0
Setting atom values ...
4096 settings made for shape
set type * quat/random ${seed}
set type * quat/random 198098
Setting atom values ...
4096 settings made for quat/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 45690.838 0 0.00029994317 0.00029953902 0.00030002809 0.00089951027
200 45571.166 0 0.00061376797 0.00060955238 0.00061153551 0.0018348559
300 44693.418 0 0.00093058034 0.00089383536 0.00091554588 0.0027399616
400 44831.846 0 0.001250227 0.0012230128 0.0012120517 0.0036852914
500 45028.015 0 0.0015448869 0.0015339549 0.0014978843 0.0045767262
600 45895.442 0 0.0018621952 0.0018169905 0.0018352784 0.0055144641
700 45858.744 0 0.0021617097 0.0021137714 0.0021360394 0.0064115206
800 45155.215 0 0.002428445 0.0024288837 0.0024516737 0.0073090023
900 45427.427 0 0.0027265978 0.0027662531 0.0027329878 0.0082258387
1000 45398.166 0 0.0030685345 0.0030805014 0.0029765916 0.0091256275
1100 44622.428 0 0.0033766954 0.0033976168 0.0032745406 0.010048853
1200 45500.277 0 0.0036410565 0.0036840528 0.0035831659 0.010908275
1300 45265.8 0 0.0039143146 0.0039419334 0.0038761633 0.011732411
1400 45482.435 0 0.0042006542 0.0043373651 0.004164002 0.012702021
1500 45126.629 0 0.0044647379 0.0046021855 0.004487041 0.013553965
1600 45178.172 0 0.0047726618 0.0049110287 0.0048012671 0.014484958
1700 44918.685 0 0.005104787 0.0052522662 0.0050844375 0.015441491
1800 44776.678 0 0.0054395368 0.0056092038 0.0054623875 0.016511128
1900 46035.987 0 0.0057735872 0.0059357043 0.0057296009 0.017438892
2000 45436.517 0 0.0060837459 0.0063485717 0.0059769119 0.018409229
2100 45871.502 0 0.0063736337 0.0066551978 0.0063077439 0.019336575
2200 45511.847 0 0.0066419141 0.0069700452 0.0065553318 0.020167291
2300 45597.047 0 0.0069251517 0.0073015716 0.0068945654 0.021121289
2400 44832.007 0 0.0071894253 0.0076238221 0.0071638554 0.021977103
2500 45668.42 0 0.0074351304 0.0079594991 0.0075390719 0.022933701
2600 45248.483 0 0.007781496 0.008293944 0.0077956068 0.023871047
2700 45308.515 0 0.0080302993 0.0086329679 0.0081457335 0.024809001
2800 45637.72 0 0.0083889026 0.0089173198 0.0086032427 0.025909465
2900 45909.343 0 0.0087169392 0.009181179 0.0088778569 0.026775975
3000 45213.613 0 0.0090508891 0.0094253485 0.0092660321 0.02774227
Loop time of 4.13937 on 1 procs for 3000 steps with 4096 atoms
Performance: 626.183 tau/day, 724.749 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.24709 | 0.24709 | 0.24709 | 0.0 | 5.97
Output | 0.004636 | 0.004636 | 0.004636 | 0.0 | 0.11
Modify | 3.7604 | 3.7604 | 3.7604 | 0.0 | 90.85
Other | | 0.1272 | | | 3.07
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 817.000 ave 817 max 817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_r_1 string 2.0
variable gamma_r_2 string 0.25
variable gamma_r_3 string 0.1
variable gamma_t_1 string 5.0
variable gamma_t_2 string 7.0
variable gamma_t_3 string 9.0
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
units lj
atom_style hybrid dipole ellipsoid
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
2 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.002 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
4096 settings made for dipole/random
set type * shape 3.0 1.0 1.0
Setting atom values ...
4096 settings made for shape
set type * quat/random ${seed}
set type * quat/random 198098
Setting atom values ...
4096 settings made for quat/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 45236.508 0 0.00030817418 0.00030717742 0.0003019227 0.0009172743
200 45564.566 0 0.00062027526 0.00062110132 0.0006080391 0.0018494157
300 46232.801 0 0.00091155216 0.00094473459 0.00093009391 0.0027863807
400 45250.414 0 0.0011980791 0.0012538262 0.0012201461 0.0036720513
500 45217.133 0 0.0015186813 0.0015752994 0.001509437 0.0046034177
600 45531.276 0 0.0018194588 0.0019243758 0.0018209246 0.0055647592
700 44834.624 0 0.0021277747 0.0022417115 0.0021352036 0.0065046898
800 45413.998 0 0.0024558838 0.0025741787 0.0024088704 0.0074389329
900 45668.624 0 0.0027366171 0.002858242 0.0027580782 0.0083529374
1000 45809.223 0 0.0030331425 0.003186293 0.0030414906 0.0092609261
1100 45193.019 0 0.0033199824 0.0034668659 0.003298885 0.010085733
1200 44522.927 0 0.0036503132 0.0037490684 0.0036089852 0.011008367
1300 45214.567 0 0.0039958617 0.0040881934 0.0038709079 0.011954963
1400 45217.997 0 0.004276499 0.0044624985 0.0041104891 0.012849487
1500 45497.171 0 0.0045943272 0.0047116875 0.0044113504 0.013717365
1600 45905.187 0 0.0049004996 0.0049982014 0.0047394999 0.014638201
1700 45551.346 0 0.0051540939 0.0053187249 0.0050861052 0.015558924
1800 45347.782 0 0.0054101891 0.0056306 0.0053515873 0.016392376
1900 45107.895 0 0.005743705 0.0059584896 0.0056220384 0.017324233
2000 45043.389 0 0.0059803588 0.006230449 0.005911555 0.018122363
2100 45433.293 0 0.0062610364 0.0066140744 0.0062152977 0.019090408
2200 45804.217 0 0.0064995183 0.0068831274 0.0064971789 0.019879825
2300 45697.516 0 0.0067910846 0.0071845673 0.0068046192 0.020780271
2400 45447.422 0 0.0071022706 0.0074743709 0.0070983185 0.02167496
2500 45395.18 0 0.0073817023 0.0077467991 0.0074263196 0.022554821
2600 45943.044 0 0.0075953233 0.007997707 0.0076508583 0.023243889
2700 45859.978 0 0.0079082128 0.0082090043 0.0078853376 0.024002555
2800 45822.007 0 0.0082607534 0.0084510061 0.0081985549 0.024910314
2900 45438.456 0 0.0085958203 0.0088807705 0.0084755353 0.025952126
3000 45060.957 0 0.0089017992 0.0090966159 0.0086718875 0.026670303
Loop time of 1.23282 on 4 procs for 3000 steps with 4096 atoms
Performance: 2102.502 tau/day, 2433.452 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.00
Comm | 0.10931 | 0.11473 | 0.11748 | 0.9 | 9.31
Output | 0.001375 | 0.0018924 | 0.0034099 | 2.0 | 0.15
Modify | 0.97744 | 0.99158 | 1.0089 | 1.3 | 80.43
Other | | 0.1246 | | | 10.11
Nlocal: 1024.00 ave 1035 max 1016 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

43
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##### dynamics of non-interacting point particles in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
units lj
atom_style atomic
dimension 2
newton off
lattice sq 0.4
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
# x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

44
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##### overdamped dynamics of non-interacting point particles in 3D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
units lj
atom_style atomic
dimension 3
newton off
lattice sc 0.4
region box block -8 8 -8 8 -8 8
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
# x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### dynamics of non-interacting point particles in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
variable params string gaussian_${temp}_${gamma_t}
variable params string gaussian_5.0_${gamma_t}
variable params string gaussian_5.0_1.0
units lj
atom_style atomic
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.003 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 1022861.2 0 0.010252464 0.0095481044 0 0.019800568
200 986781.19 0 0.020552091 0.019485252 0 0.040037343
300 1030219 0 0.030642552 0.028377678 0 0.05902023
400 1003322.5 0 0.040610693 0.038179284 0 0.078789978
500 989343.12 0 0.049978908 0.047445856 0 0.097424764
600 1029781.3 0 0.059551719 0.057941149 0 0.11749287
700 999447.72 0 0.06979546 0.067552325 0 0.13734778
800 995373.97 0 0.080049251 0.078006344 0 0.1580556
900 1011991.4 0 0.089753134 0.087065214 0 0.17681835
1000 1006017.1 0 0.10041092 0.097934217 0 0.19834514
1100 997762.63 0 0.11229742 0.10841547 0 0.22071289
1200 1011707.8 0 0.12006388 0.1190115 0 0.23907538
1300 1012099.1 0 0.13097486 0.12996632 0 0.26094117
1400 997602.43 0 0.14345778 0.13830585 0 0.28176362
1500 1005358.1 0 0.15441686 0.14927539 0 0.30369225
1600 1007081.8 0 0.16496828 0.15936363 0 0.3243319
1700 990284.9 0 0.1747286 0.16818246 0 0.34291106
1800 969006.97 0 0.18228778 0.17972813 0 0.3620159
1900 998066.69 0 0.19338277 0.19226121 0 0.38564397
2000 972300.66 0 0.20352485 0.20145928 0 0.40498413
2100 985025.88 0 0.21283854 0.21090075 0 0.42373929
2200 1010964.6 0 0.22279055 0.22110734 0 0.44389789
2300 975819.44 0 0.23128131 0.23226488 0 0.46354619
2400 977043.53 0 0.24284105 0.24301689 0 0.48585794
2500 969708.21 0 0.25415238 0.25354284 0 0.50769522
2600 981969.5 0 0.26457173 0.26318018 0 0.52775192
2700 987261.1 0 0.27497004 0.27761213 0 0.55258218
2800 1005751.1 0 0.28530448 0.28715428 0 0.57245876
2900 975930.11 0 0.29394811 0.29896948 0 0.59291759
3000 997388.08 0 0.30674701 0.31193573 0 0.61868274
Loop time of 1.501 on 1 procs for 3000 steps with 3600 atoms
Performance: 1726.852 tau/day, 1998.672 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00059271 | 0.00059271 | 0.00059271 | 0.0 | 0.04
Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.37
Output | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 0.27
Modify | 1.3852 | 1.3852 | 1.3852 | 0.0 | 92.28
Other | | 0.1057 | | | 7.04
Nlocal: 3600.00 ave 3600 max 3600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 21
Dangerous builds = 0
Total wall time: 0:00:01

119
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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### dynamics of non-interacting point particles in 2D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
variable params string gaussian_${temp}_${gamma_t}
variable params string gaussian_5.0_${gamma_t}
variable params string gaussian_5.0_1.0
units lj
atom_style atomic
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 1017972.1 0 0.010094052 0.0097502899 0 0.019844342
200 1004552.1 0 0.020125116 0.01957629 0 0.039701406
300 1017712.9 0 0.030271373 0.029411656 0 0.059683029
400 1016693.8 0 0.040610061 0.038605869 0 0.07921593
500 999527.84 0 0.049451389 0.049042225 0 0.098493614
600 961157.92 0 0.059691948 0.059033176 0 0.11872512
700 1006804.9 0 0.071205977 0.069972106 0 0.14117808
800 1007321.8 0 0.081136977 0.079825976 0 0.16096295
900 1002801.7 0 0.091236148 0.090833816 0 0.18206996
1000 1010134.7 0 0.10091362 0.10023906 0 0.20115269
1100 990246.55 0 0.1118367 0.11141049 0 0.22324719
1200 1010555.5 0 0.12091736 0.12355456 0 0.24447192
1300 997117.19 0 0.13099592 0.13292775 0 0.26392367
1400 1020817.1 0 0.14167961 0.14172898 0 0.28340859
1500 1015048.1 0 0.15225884 0.15162948 0 0.30388833
1600 990291.98 0 0.16460973 0.16251919 0 0.32712891
1700 980848.58 0 0.17380313 0.17351201 0 0.34731513
1800 1000673.8 0 0.18383991 0.18175453 0 0.36559445
1900 1009388.9 0 0.19411523 0.19367453 0 0.38778976
2000 1005935.9 0 0.2015342 0.20585359 0 0.40738779
2100 985500.56 0 0.21161056 0.21238463 0 0.42399519
2200 997241.34 0 0.21841986 0.22117922 0 0.43959908
2300 1011672.3 0 0.22688099 0.23155741 0 0.4584384
2400 989837.68 0 0.23849839 0.24219 0 0.48068839
2500 1035706.8 0 0.24541408 0.24947563 0 0.49488971
2600 992370.08 0 0.25537803 0.25758332 0 0.51296135
2700 990586.56 0 0.26542605 0.26762286 0 0.53304892
2800 1002767.3 0 0.27570392 0.27874972 0 0.55445363
2900 995307.27 0 0.28580946 0.29115624 0 0.5769657
3000 1024317.7 0 0.29493208 0.30208924 0 0.59702132
Loop time of 0.413047 on 4 procs for 3000 steps with 3600 atoms
Performance: 6275.312 tau/day, 7263.093 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00016236 | 0.00016338 | 0.00016403 | 0.0 | 0.04
Comm | 0.0026367 | 0.0030084 | 0.0031497 | 0.4 | 0.73
Output | 0.0011849 | 0.0013574 | 0.0018065 | 0.7 | 0.33
Modify | 0.34447 | 0.35223 | 0.36357 | 1.2 | 85.28
Other | | 0.05629 | | | 13.63
Nlocal: 900.000 ave 906 max 891 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 22
Dangerous builds = 0
Total wall time: 0:00:00

119
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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting point particles in 3D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
variable params string gaussian_${temp}_${gamma_t}
variable params string gaussian_5.0_${gamma_t}
variable params string gaussian_5.0_1.0
units lj
atom_style atomic
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.002 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.694 | 2.694 | 2.694 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 1500286.3 0 0.0098123603 0.010352169 0.010242435 0.030406964
200 1488308 0 0.019934427 0.019968198 0.020471735 0.06037436
300 1484472.4 0 0.029397156 0.030749312 0.030121294 0.090267762
400 1517938.7 0 0.039217504 0.041440617 0.040512943 0.12117106
500 1492769.5 0 0.04890343 0.051561801 0.050614941 0.15108017
600 1510159.6 0 0.059770181 0.061650364 0.061298117 0.18271866
700 1485424.1 0 0.070537955 0.071144877 0.071141546 0.21282438
800 1496377.2 0 0.081291995 0.082546059 0.080653381 0.24449144
900 1484409.1 0 0.090940427 0.093298981 0.091328056 0.27556746
1000 1503322.4 0 0.10176921 0.10246052 0.10151773 0.30574747
1100 1503322.4 0 0.11295993 0.11052632 0.11053406 0.33402031
1200 1489236.2 0 0.12509723 0.11961982 0.12146498 0.36618203
1300 1476050.3 0 0.13449034 0.12941323 0.1309765 0.39488007
1400 1520818.7 0 0.14613571 0.13788044 0.14083944 0.42485558
1500 1498936.4 0 0.15752286 0.15057712 0.15063399 0.45873397
1600 1507524.1 0 0.16793678 0.16095681 0.16063531 0.4895289
1700 1480581.2 0 0.17748019 0.172614 0.16922383 0.51931802
1800 1505353.6 0 0.18850931 0.18304171 0.18063119 0.55218221
1900 1491234.7 0 0.19836402 0.19306339 0.1929707 0.58439811
2000 1519868.8 0 0.20698191 0.20211344 0.20328302 0.61237838
2100 1493919.5 0 0.21453524 0.21186097 0.21423293 0.64062914
2200 1517098.6 0 0.2257338 0.22381647 0.22474081 0.67429108
2300 1481270.7 0 0.23499747 0.23348379 0.23498244 0.70346369
2400 1495445.1 0 0.24535894 0.24290239 0.24229161 0.73055293
2500 1522839.3 0 0.25695938 0.25109669 0.25214541 0.76020148
2600 1518697.4 0 0.26680819 0.26120216 0.2604112 0.78842155
2700 1529283.1 0 0.27524422 0.26942681 0.27148042 0.81615146
2800 1500557.5 0 0.28436226 0.27957592 0.27935619 0.84329437
2900 1509711.1 0 0.2948528 0.28562401 0.29055956 0.87103637
3000 1522712.8 0 0.30347033 0.2975063 0.30121685 0.90219348
Loop time of 2.35056 on 1 procs for 3000 steps with 4096 atoms
Performance: 1102.718 tau/day, 1276.293 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00077772 | 0.00077772 | 0.00077772 | 0.0 | 0.03
Comm | 0.010985 | 0.010985 | 0.010985 | 0.0 | 0.47
Output | 0.0045807 | 0.0045807 | 0.0045807 | 0.0 | 0.19
Modify | 2.2116 | 2.2116 | 2.2116 | 0.0 | 94.09
Other | | 0.1226 | | | 5.22
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of non-interacting point particles in 3D #####
variable rng string gaussian
variable seed string 198098
variable temp string 5.0
variable gamma_t string 1.0
variable params string ${rng}_${temp}_${gamma_t}
variable params string gaussian_${temp}_${gamma_t}
variable params string gaussian_5.0_${gamma_t}
variable params string gaussian_5.0_1.0
units lj
atom_style atomic
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
2 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 2.672 | 2.672 | 2.672 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 1515328.2 0 0.010465453 0.010044629 0.0097242319 0.030234314
200 1510820.8 0 0.020658886 0.019954762 0.020008864 0.060622512
300 1482006.5 0 0.030402195 0.029802874 0.030047586 0.090252655
400 1492228.5 0 0.039622543 0.038899144 0.040381854 0.11890354
500 1494985.5 0 0.050523465 0.050022913 0.050186478 0.15073286
600 1516047.4 0 0.061111845 0.061433818 0.059195364 0.18174103
700 1510021.8 0 0.071636778 0.072829755 0.06946406 0.21393059
800 1505964.7 0 0.08240965 0.08433785 0.078799851 0.24554735
900 1491035.9 0 0.093659937 0.094517749 0.08812559 0.27630328
1000 1516599.6 0 0.10436496 0.10431759 0.097480868 0.30616342
1100 1495170.3 0 0.11468757 0.111397 0.1069763 0.33306087
1200 1500630.6 0 0.12360977 0.12264534 0.11583999 0.3620951
1300 1474889.5 0 0.13432447 0.13471694 0.12702491 0.39606632
1400 1487145.8 0 0.14573239 0.14431493 0.13669403 0.42674135
1500 1519496.7 0 0.15610742 0.15505416 0.14600182 0.4571634
1600 1525674.1 0 0.16728653 0.1649354 0.15562133 0.48784325
1700 1540725.4 0 0.17846447 0.17666562 0.16531781 0.52044791
1800 1512334.8 0 0.18872753 0.18538847 0.17450009 0.54861609
1900 1498371.4 0 0.19688928 0.19333299 0.18581712 0.5760394
2000 1546459.4 0 0.20955053 0.20243854 0.19613897 0.60812803
2100 1509712.9 0 0.21922567 0.20940597 0.20567239 0.63430404
2200 1509630.4 0 0.23067999 0.21856734 0.21619911 0.66544645
2300 1483929.1 0 0.24160803 0.231048 0.22617193 0.69882797
2400 1488492.1 0 0.25399491 0.24082678 0.23972356 0.73454526
2500 1508107.9 0 0.26608734 0.25316913 0.2486814 0.76793787
2600 1511952.1 0 0.27523956 0.2623673 0.25706539 0.79467225
2700 1488888.8 0 0.28518299 0.27425585 0.26728622 0.82672506
2800 1515428.4 0 0.29595429 0.28589969 0.27781327 0.85966725
2900 1504312.1 0 0.30393798 0.29533034 0.28725362 0.88652194
3000 1521521.3 0 0.31445132 0.30117607 0.29959324 0.91522062
Loop time of 0.708196 on 4 procs for 3000 steps with 4096 atoms
Performance: 3660.004 tau/day, 4236.115 timesteps/s
97.2% 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 | 0.00020647 | 0.00021023 | 0.0002141 | 0.0 | 0.03
Comm | 0.0045607 | 0.0050649 | 0.0053098 | 0.4 | 0.72
Output | 0.0013759 | 0.002265 | 0.0037355 | 1.9 | 0.32
Modify | 0.57353 | 0.58931 | 0.6109 | 1.8 | 83.21
Other | | 0.1113 | | | 15.72
Nlocal: 1024.00 ave 1043 max 1001 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:00

45
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##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
units lj
atom_style hybrid dipole sphere
dimension 2
newton off
lattice sq 0.4
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
# x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

45
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##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
units lj
atom_style hybrid dipole sphere
dimension 3
newton off
lattice sc 0.4
region box block -8 8 -8 8 -8 8
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
# x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_1.0_${gamma_r}_${gamma_t}
variable params string uniform_1.0_0.7_${gamma_t}
variable params string uniform_1.0_0.7_5.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.005 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
3600 settings made for dipole/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 20867.136 0 0.00040006704 0.00039570887 0 0.00079577592
200 20835.491 0 0.00077560901 0.00080455484 0 0.0015801638
300 20813.122 0 0.0011737739 0.0012172689 0 0.0023910428
400 21137.397 0 0.0015587675 0.0016096093 0 0.0031683768
500 21167.188 0 0.0019294105 0.0020251322 0 0.0039545428
600 21345.908 0 0.0023105313 0.0024111742 0 0.0047217054
700 21086.272 0 0.0027236116 0.0027846006 0 0.0055082122
800 20840.906 0 0.0031505299 0.0031810732 0 0.0063316031
900 20916.456 0 0.0035525852 0.0035981301 0 0.0071507153
1000 20752.249 0 0.0039147929 0.0039791172 0 0.0078939101
1100 20643.612 0 0.0042977921 0.0043701484 0 0.0086679405
1200 21085.63 0 0.0045584242 0.0047475091 0 0.0093059332
1300 20900.794 0 0.0049718803 0.0051481706 0 0.010120051
1400 20980.731 0 0.0054234603 0.0054230724 0 0.010846533
1500 20916.308 0 0.0058502946 0.0058114313 0 0.011661726
1600 20949.786 0 0.0062258463 0.006208129 0 0.012433975
1700 20531.205 0 0.0066276219 0.006595921 0 0.013223543
1800 21418.472 0 0.0070077409 0.007030461 0 0.014038202
1900 21291.928 0 0.0074052208 0.0074333041 0 0.014838525
2000 20893.895 0 0.0077407477 0.007901402 0 0.01564215
2100 21218.001 0 0.0080384756 0.0082611258 0 0.016299601
2200 21116.189 0 0.0084325164 0.008617977 0 0.017050493
2300 20718.83 0 0.0089455345 0.0091768161 0 0.018122351
2400 20719.164 0 0.0093666455 0.0095272546 0 0.0188939
2500 20991.382 0 0.009706795 0.0098256506 0 0.019532446
2600 20515.74 0 0.0099247069 0.010329841 0 0.020254548
2700 21001.55 0 0.010448354 0.010693502 0 0.021141855
2800 21363.824 0 0.010990971 0.011142092 0 0.022133063
2900 20497.025 0 0.011399704 0.011504868 0 0.022904573
3000 20726.572 0 0.011785354 0.01187482 0 0.023660175
Loop time of 1.76023 on 1 procs for 3000 steps with 3600 atoms
Performance: 1472.538 tau/day, 1704.326 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026518 | 0.026518 | 0.026518 | 0.0 | 1.51
Output | 0.0040107 | 0.0040107 | 0.0040107 | 0.0 | 0.23
Modify | 1.6194 | 1.6194 | 1.6194 | 0.0 | 92.00
Other | | 0.1103 | | | 6.27
Nlocal: 3600.00 ave 3600 max 3600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 121.000 ave 121 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

126
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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_1.0_${gamma_r}_${gamma_t}
variable params string uniform_1.0_0.7_${gamma_t}
variable params string uniform_1.0_0.7_5.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -30 30 -30 30 -0.2 0.2
create_box 1 box
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.002 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
3600 settings made for dipole/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 0.99972222 0 0 0 0 0
100 21085.797 0 0.00042014118 0.00040399828 0 0.00082413946
200 20598.717 0 0.00081715618 0.00082613236 0 0.0016432885
300 21040.226 0 0.0012412527 0.0012520475 0 0.0024933002
400 21289.734 0 0.0016129899 0.001634482 0 0.003247472
500 20951.595 0 0.0020104279 0.0020197694 0 0.0040301973
600 20984.974 0 0.0023965593 0.0024277086 0 0.0048242679
700 21252.602 0 0.0028349303 0.0028407812 0 0.0056757114
800 20951.95 0 0.0032674595 0.0032573476 0 0.0065248071
900 20828.611 0 0.003647953 0.0036650963 0 0.0073130493
1000 21073.256 0 0.0040238604 0.0040103537 0 0.0080342142
1100 21104.396 0 0.0043694059 0.0044146515 0 0.0087840574
1200 20580.591 0 0.0047638237 0.0047646659 0 0.0095284896
1300 20667.623 0 0.0051512568 0.0051134445 0 0.010264701
1400 20466.72 0 0.0055921578 0.005517863 0 0.011110021
1500 20842.366 0 0.0059747304 0.0059374031 0 0.011912134
1600 20867.02 0 0.0065493697 0.0064163066 0 0.012965676
1700 21021.077 0 0.0070208005 0.0068164842 0 0.013837285
1800 21191.183 0 0.0073708939 0.0073226521 0 0.014693546
1900 20792.8 0 0.0076984189 0.0077400043 0 0.015438423
2000 21296.326 0 0.0081882545 0.0081503672 0 0.016338622
2100 21085.097 0 0.008596146 0.0086041272 0 0.017200273
2200 20506.523 0 0.0089905439 0.0091045462 0 0.01809509
2300 21068.555 0 0.0094163509 0.0094703314 0 0.018886682
2400 21128.867 0 0.0097349212 0.0098535832 0 0.019588504
2500 21009.514 0 0.010218059 0.010244621 0 0.020462679
2600 21177.52 0 0.01060437 0.010642719 0 0.021247089
2700 20832.56 0 0.011052623 0.011078899 0 0.022131522
2800 21298.053 0 0.011439708 0.011587702 0 0.023027411
2900 21002.28 0 0.011863624 0.01199682 0 0.023860443
3000 20737.939 0 0.012229608 0.012324579 0 0.024554186
Loop time of 0.492798 on 4 procs for 3000 steps with 3600 atoms
Performance: 5259.763 tau/day, 6087.689 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.018005 | 0.021524 | 0.025207 | 2.2 | 4.37
Output | 0.0013187 | 0.0018334 | 0.0032332 | 1.9 | 0.37
Modify | 0.37545 | 0.38775 | 0.40664 | 1.9 | 78.68
Other | | 0.08169 | | | 16.58
Nlocal: 900.000 ave 900 max 900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 61.0000 ave 61 max 61 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_1.0_${gamma_r}_${gamma_t}
variable params string uniform_1.0_0.7_${gamma_t}
variable params string uniform_1.0_0.7_5.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.005 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
4096 settings made for dipole/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 32032.279 0 0.00040227568 0.00039159837 0.00040147813 0.0011953522
200 31673.093 0 0.00077657885 0.00077292327 0.00079963705 0.0023491392
300 31476.164 0 0.0011712083 0.0011606723 0.0012089537 0.0035408343
400 31911.374 0 0.0015803424 0.001562091 0.0016042321 0.0047466655
500 31182.011 0 0.0019677217 0.0019269105 0.0020015977 0.0058962298
600 31206.05 0 0.0023360975 0.0023134398 0.0024213372 0.0070708745
700 31278.057 0 0.0026966955 0.0027129858 0.0028721373 0.0082818187
800 31677.724 0 0.0031197964 0.003134834 0.0032726303 0.0095272607
900 31312.741 0 0.0035636612 0.0035573653 0.0037328373 0.010853864
1000 31426.075 0 0.0039774626 0.003952159 0.0041879386 0.01211756
1100 31361.699 0 0.0044256852 0.004320566 0.004638132 0.013384383
1200 31559.778 0 0.0048338539 0.0047210601 0.0050296056 0.01458452
1300 31716.797 0 0.0052239651 0.0050796723 0.0054794684 0.015783106
1400 31231.077 0 0.0055890568 0.005472377 0.0059264123 0.016987846
1500 31605.513 0 0.0059876582 0.0058974054 0.0063452478 0.018230311
1600 31551.402 0 0.006413094 0.0062665632 0.0067442106 0.019423868
1700 31725.868 0 0.0068244611 0.0067189707 0.0071424779 0.02068591
1800 31385.794 0 0.0071570297 0.0070502303 0.0075240296 0.02173129
1900 31754.094 0 0.0075638662 0.0074243015 0.0079935325 0.0229817
2000 31668.959 0 0.0080059944 0.0079019753 0.0084000614 0.024308031
2100 31781.994 0 0.0084108141 0.0082719077 0.0088004977 0.02548322
2200 31455.021 0 0.0088844434 0.0086931769 0.0091916929 0.026769313
2300 31273.079 0 0.0093155639 0.0091027782 0.0095364621 0.027954804
2400 31283.781 0 0.0098441686 0.0094496218 0.0099279073 0.029221698
2500 31758.315 0 0.010372129 0.0097843406 0.010334653 0.030491123
2600 31780.442 0 0.010770862 0.010313119 0.010637545 0.031721525
2700 31552.277 0 0.011268703 0.010693437 0.01110762 0.033069759
2800 31124.693 0 0.011661333 0.011100115 0.011480624 0.034242072
2900 31438.795 0 0.012068847 0.011346633 0.011842006 0.035257486
3000 31574.258 0 0.012482632 0.011691477 0.012210207 0.036384317
Loop time of 2.8531 on 1 procs for 3000 steps with 4096 atoms
Performance: 908.486 tau/day, 1051.488 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.2425e-05 | 3.2425e-05 | 3.2425e-05 | 0.0 | 0.00
Comm | 0.13219 | 0.13219 | 0.13219 | 0.0 | 4.63
Output | 0.0045686 | 0.0045686 | 0.0045686 | 0.0 | 0.16
Modify | 2.5857 | 2.5857 | 2.5857 | 0.0 | 90.63
Other | | 0.1307 | | | 4.58
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
variable rng string uniform
variable seed string 198098
variable temp string 1.0
variable gamma_t string 5.0
variable gamma_r string 0.7
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
variable params string uniform_1.0_${gamma_r}_${gamma_t}
variable params string uniform_1.0_0.7_${gamma_t}
variable params string uniform_1.0_0.7_5.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
2 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.006 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 198098 1.0
Setting atom values ...
4096 settings made for dipole/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step ke pe c_msd[*]
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 100
# main run
run 3000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
0 1.4996338 0 0 0 0 0
100 30882.707 0 0.00040787161 0.00039391576 0.00040796913 0.0012097565
200 31370.751 0 0.00081742036 0.00078240455 0.0008195167 0.0024193416
300 31469.51 0 0.0012118299 0.0011819412 0.0012477119 0.003641483
400 31696.58 0 0.0015540547 0.0015849689 0.0015836091 0.0047226327
500 31488.269 0 0.0019638041 0.0019659637 0.0020547832 0.005984551
600 30942.589 0 0.0023273784 0.0023572171 0.0024715245 0.00715612
700 31228.473 0 0.0027821732 0.002735338 0.0028734675 0.0083909787
800 31426.92 0 0.0031663838 0.0031092782 0.0033231014 0.0095987634
900 31447.595 0 0.003539588 0.003564381 0.003753036 0.010857005
1000 31363.911 0 0.0039854308 0.003937555 0.0041203919 0.012043378
1100 31522.958 0 0.0043009285 0.0043676491 0.0044799414 0.013148519
1200 31403.033 0 0.0046361199 0.0047513598 0.0049014974 0.014288977
1300 31752.182 0 0.0049824718 0.0051327113 0.0053130614 0.015428244
1400 31336.955 0 0.0054251445 0.0055442325 0.0057472998 0.016716677
1500 31224.306 0 0.0059295596 0.0059920697 0.0061375228 0.018059152
1600 31744.535 0 0.0063845142 0.0063600989 0.0064833215 0.019227935
1700 31472.081 0 0.0068360092 0.0067985824 0.0069464303 0.020581022
1800 31577.334 0 0.0073001079 0.0071355564 0.0073400543 0.021775719
1900 31521.234 0 0.0077178677 0.0074371106 0.007708008 0.022862986
2000 31045.148 0 0.0080515968 0.0078583776 0.0081000219 0.024009996
2100 31289.809 0 0.0084280175 0.0082322226 0.0084475904 0.02510783
2200 31505.455 0 0.008802925 0.0085708943 0.0087648194 0.026138639
2300 31882.722 0 0.0092223105 0.0089242925 0.0092643028 0.027410906
2400 31028.15 0 0.0095737559 0.0093585981 0.0096771837 0.028609538
2500 31581.041 0 0.0099316284 0.009785264 0.010100235 0.029817127
2600 31272.119 0 0.010332986 0.01007291 0.010474606 0.030880502
2700 31537.8 0 0.010751592 0.010565273 0.01093107 0.032247935
2800 31060.697 0 0.011156729 0.011010751 0.011260025 0.033427506
2900 31541.612 0 0.011542003 0.011499419 0.011642873 0.034684295
3000 31305.382 0 0.011876832 0.011866445 0.012052577 0.035795854
Loop time of 1.00142 on 4 procs for 3000 steps with 4096 atoms
Performance: 2588.329 tau/day, 2995.751 timesteps/s
95.2% 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 | 0.084416 | 0.10685 | 0.12695 | 5.7 | 10.67
Output | 0.001471 | 0.0019466 | 0.0033245 | 1.8 | 0.19
Modify | 0.66585 | 0.70645 | 0.78995 | 6.0 | 70.54
Other | | 0.1862 | | | 18.59
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 353.000 ave 353 max 353 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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# 2D overdamped active brownian particle dynamics (ABP)
# with WCA potential
variable gamma_t string 1.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
units lj
atom_style hybrid dipole sphere
dimension 2
newton off
lattice sq 0.4
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
velocity all create 1.0 1 loop geom
# more careful with neighbors since higher diffusion in abps
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
# WCA potential (purely repulsive)
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.1224
pair_modify shift yes
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
fix 2 all enforce2d
compute press all pressure NULL virial
thermo_style custom step pe ke c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
reset_timestep 0
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 20000

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# 3D overdamped active brownian dynamics with no interactions
variable gamma_t string 3.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
units lj
atom_style hybrid dipole sphere
dimension 3
newton off
lattice sc 0.4
region box block -8 8 -8 8 -8 8
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
velocity all create 1.0 1 loop geom
pair_style none
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
compute press all pressure NULL virial
thermo_style custom step ke pe c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
reset_timestep 0
# MSD to demonstrate expected diffusive behaviour for ideal active
# brownian motion, which is
#
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
#
# with d being simulation dimension
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
# if you want to check that rotational diffusion is behaving as expected,
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
# which should decay exponentially with timescale (d-1)*D_r (with d
# being simulation dimension)
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
# x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
#run 120000

221
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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 2D overdamped active brownian particle dynamics (ABP)
# with WCA potential
variable gamma_t string 1.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_1.0_${gamma_r}_${fp}
variable params string 1.0_1.0_1.0_${fp}
variable params string 1.0_1.0_1.0_4.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.002 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
1024 settings made for dipole/random
velocity all create 1.0 1 loop geom
# more careful with neighbors since higher diffusion in abps
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
# WCA potential (purely repulsive)
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.1224
pair_modify shift yes
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
fix activity all propel/self dipole 4.0
fix 2 all enforce2d
compute press all pressure NULL virial
thermo_style custom step pe ke c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.1224
ghost atom cutoff = 2.1224
binsize = 1.0612, bins = 48 48 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes
Step PotEng KinEng c_press
0 0 0.99902344 -0.53979198
100 0 1.026585e+10 -0.5398101
200 0 1.0630628e+10 -0.53977393
300 0 1.03483e+10 -0.53977041
400 0 1.049279e+10 -0.53974314
500 0 1.0832067e+10 -0.53979451
600 0 1.0403632e+10 -0.53976233
700 0 1.0334726e+10 -0.53976174
800 0 1.0119596e+10 -0.53969338
900 0 1.0786136e+10 -0.53970415
1000 0 1.0539036e+10 -0.53974577
1100 0 1.0643695e+10 -0.53982431
1200 0 1.0234642e+10 -0.53976823
1300 0 1.036268e+10 -0.53981454
1400 0 1.0605702e+10 -0.53988117
1500 0 1.0517916e+10 -0.53989207
1600 0 1.0564482e+10 -0.53993016
1700 0 1.0460152e+10 -0.53984454
1800 0 1.0468566e+10 -0.53985574
1900 0 1.0474075e+10 -0.53985439
2000 0 1.0683568e+10 -0.53987349
2100 0 1.0269077e+10 -0.53990709
2200 0 1.0386943e+10 -0.53990068
2300 0 1.0406078e+10 -0.53978402
2400 0 1.0482072e+10 -0.53980757
2500 0 1.0442975e+10 -0.53982657
2600 0 1.0292103e+10 -0.53985533
2700 0 1.1106453e+10 -0.53991861
2800 0 1.0395289e+10 -0.53990138
2900 0 1.034021e+10 -0.53992375
3000 0 1.0434718e+10 -0.53995566
3100 0 1.0194094e+10 -0.53993997
3200 0 1.0411552e+10 -0.54000097
3300 0 1.0214175e+10 -0.53999884
3400 0 1.0434719e+10 -0.54000005
3500 0 1.0529638e+10 -0.53998281
3600 0 1.0406541e+10 -0.54000141
3700 0 1.0577151e+10 -0.54002354
3800 0 1.0488249e+10 -0.53996003
3900 0 1.0316153e+10 -0.54002024
4000 0 1.0491289e+10 -0.5400259
4100 0 1.0587981e+10 -0.5399811
4200 0 1.0332035e+10 -0.53997951
4300 0 1.0776469e+10 -0.53994151
4400 0 1.0982142e+10 -0.53983842
4500 0 1.0796919e+10 -0.5398414
4600 0 1.0324249e+10 -0.53979712
4700 0 1.0420899e+10 -0.53981967
4800 0 1.0274188e+10 -0.53976759
4900 0 1.0411535e+10 -0.5397757
5000 0 1.0399215e+10 -0.53980199
Loop time of 1.34285 on 1 procs for 5000 steps with 1024 atoms
Performance: 0.032 tau/day, 3723.422 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25309 | 0.25309 | 0.25309 | 0.0 | 18.85
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.068734 | 0.068734 | 0.068734 | 0.0 | 5.12
Output | 0.0012887 | 0.0012887 | 0.0012887 | 0.0 | 0.10
Modify | 0.96552 | 0.96552 | 0.96552 | 0.0 | 71.90
Other | | 0.05422 | | | 4.04
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 201.000 ave 201 max 201 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2112.00 ave 2112 max 2112 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2112
Ave neighs/atom = 2.0625000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 20000
Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 1.0409381e+10 0 0 0 0 0 -0.53980199
1000 107022.73 0.0080050427 0.020451432 0.021388798 0 0.04184023 -0.54900967
2000 107475.82 0.017262846 0.040669645 0.044251149 0 0.084920794 -0.42740968
3000 105388.35 0.042257875 0.062828995 0.05845782 0 0.12128682 -0.31792184
4000 106238.38 0.052733384 0.079036841 0.079396453 0 0.15843329 -0.24243699
5000 102904.54 0.088524456 0.095977642 0.099533961 0 0.1955116 -0.093468615
6000 105274.15 0.065334999 0.11591691 0.11675531 0 0.23267222 -0.21904478
7000 108903.41 0.06724271 0.13694218 0.13914947 0 0.27609164 -0.15913012
8000 101451.44 0.097201152 0.15704893 0.16178845 0 0.31883738 -0.055786965
9000 106808.72 0.084301668 0.18029391 0.175753 0 0.3560469 0.014898739
10000 107381.19 0.088583354 0.2000753 0.19569789 0 0.39577319 0.19417596
11000 102105.78 0.081066654 0.22042599 0.21914042 0 0.43956641 0.060574143
12000 105384.94 0.098716908 0.24382064 0.24673594 0 0.49055657 0.17067875
13000 107479.53 0.099989043 0.26942088 0.27207566 0 0.54149654 0.25514896
14000 102938.12 0.093252916 0.28529564 0.28698837 0 0.57228401 0.19976355
15000 104408.02 0.11900926 0.31291315 0.31195058 0 0.62486373 0.36956014
16000 103447.68 0.09627777 0.34145225 0.33159885 0 0.6730511 0.29857404
17000 108400.05 0.11433561 0.36561966 0.36068301 0 0.72630267 0.41922801
18000 103363.68 0.11040153 0.38709746 0.39228677 0 0.77938423 0.38111686
19000 103310.43 0.10660536 0.41406235 0.40975085 0 0.8238132 0.36022184
20000 102692.1 0.13517651 0.43870812 0.44138776 0 0.88009588 0.51144366
Loop time of 5.66207 on 1 procs for 20000 steps with 1024 atoms
Performance: 3051.889 tau/day, 3532.279 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3123 | 1.3123 | 1.3123 | 0.0 | 23.18
Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.21
Comm | 0.2747 | 0.2747 | 0.2747 | 0.0 | 4.85
Output | 0.0011516 | 0.0011516 | 0.0011516 | 0.0 | 0.02
Modify | 3.8451 | 3.8451 | 3.8451 | 0.0 | 67.91
Other | | 0.2169 | | | 3.83
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 184.000 ave 184 max 184 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2558.00 ave 2558 max 2558 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2558
Ave neighs/atom = 2.4980469
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:07

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 2D overdamped active brownian particle dynamics (ABP)
# with WCA potential
variable gamma_t string 1.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_1.0_${gamma_r}_${fp}
variable params string 1.0_1.0_1.0_${fp}
variable params string 1.0_1.0_1.0_4.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 2
newton off
lattice sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region box block -16 16 -16 16 -0.2 0.2
create_box 1 box
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 1024 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
1024 settings made for dipole/random
velocity all create 1.0 1 loop geom
# more careful with neighbors since higher diffusion in abps
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
# WCA potential (purely repulsive)
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.1224
pair_modify shift yes
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
fix activity all propel/self dipole 4.0
fix 2 all enforce2d
compute press all pressure NULL virial
thermo_style custom step pe ke c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.1224
ghost atom cutoff = 2.1224
binsize = 1.0612, bins = 48 48 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes
Step PotEng KinEng c_press
0 0 0.99902344 -0.53979198
100 0 1.0503521e+10 -0.53983092
200 0 1.0390343e+10 -0.5398287
300 0 1.0493441e+10 -0.53979247
400 0 1.0545991e+10 -0.53978678
500 0 1.0266398e+10 -0.53986297
600 0 1.0484775e+10 -0.53978746
700 0 1.0583596e+10 -0.53969114
800 0 1.0521919e+10 -0.53968754
900 0 1.0492019e+10 -0.53958643
1000 0 1.0298052e+10 -0.53949872
1100 0 1.0531424e+10 -0.53955431
1200 0 1.0635635e+10 -0.53960048
1300 0 1.0633405e+10 -0.53966331
1400 0 1.0195401e+10 -0.53968849
1500 0 1.0593758e+10 -0.53969763
1600 0 1.0425238e+10 -0.53971936
1700 0 1.0470017e+10 -0.53981957
1800 0 1.0545953e+10 -0.53987747
1900 0 1.0425015e+10 -0.53990412
2000 0 1.0655092e+10 -0.5399511
2100 0 1.0197224e+10 -0.53988687
2200 0 1.0448012e+10 -0.53986066
2300 0 1.0355268e+10 -0.53980415
2400 0 1.0246979e+10 -0.53979737
2500 0 1.0021539e+10 -0.5397919
2600 0 1.0200824e+10 -0.5397575
2700 0 1.0721591e+10 -0.53973512
2800 0 1.0354562e+10 -0.5397127
2900 0 1.0306795e+10 -0.5396946
3000 0 1.0301339e+10 -0.53968642
3100 0 1.0435826e+10 -0.53970945
3200 0 1.019524e+10 -0.53969746
3300 0 1.0550481e+10 -0.53967977
3400 0 1.0283446e+10 -0.53971102
3500 0 1.0956695e+10 -0.53976173
3600 0 1.0271033e+10 -0.53983632
3700 0 1.0389461e+10 -0.53977293
3800 0 1.0680515e+10 -0.53977425
3900 0 1.0072183e+10 -0.53982922
4000 0 1.0458036e+10 -0.53980042
4100 0 1.0588689e+10 -0.53971405
4200 0 1.0068308e+10 -0.5398033
4300 0 1.0502064e+10 -0.53981291
4400 0 1.0590544e+10 -0.5398346
4500 0 1.0411612e+10 -0.5397916
4600 0 1.0518596e+10 -0.53984868
4700 0 1.0386105e+10 -0.53977803
4800 0 1.029525e+10 -0.53970882
4900 0 1.0519112e+10 -0.53969616
5000 0 1.0335841e+10 -0.53976477
Loop time of 0.471663 on 4 procs for 5000 steps with 1024 atoms
Performance: 0.092 tau/day, 10600.781 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.067099 | 0.07105 | 0.077898 | 1.6 | 15.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0581 | 0.066084 | 0.072322 | 2.0 | 14.01
Output | 0.0014644 | 0.002618 | 0.0037239 | 1.6 | 0.56
Modify | 0.24817 | 0.25719 | 0.26697 | 1.3 | 54.53
Other | | 0.07472 | | | 15.84
Nlocal: 256.000 ave 256 max 256 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 105.000 ave 105 max 105 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 544.000 ave 544 max 544 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2176
Ave neighs/atom = 2.1250000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 20000
Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 1.0345945e+10 0 0 0 0 0 -0.53976477
1000 100114.28 0.0029703577 0.020320684 0.020950989 0 0.041271673 -0.43948247
2000 106825.83 0.020969054 0.039616412 0.039459167 0 0.079075578 -0.22765541
3000 105287.4 0.037343571 0.056828177 0.058639835 0 0.11546801 -0.11728136
4000 104522.23 0.052237136 0.080264931 0.080863543 0 0.16112847 0.033230576
5000 103277.94 0.053791862 0.099188864 0.10141444 0 0.20060331 0.073591503
6000 104252.87 0.073304776 0.11964238 0.1215576 0 0.24119999 0.22062305
7000 105184.19 0.089054043 0.13691291 0.14216478 0 0.27907769 0.29015692
8000 104211.82 0.072577918 0.15820522 0.15658491 0 0.31479013 0.25908291
9000 99242.172 0.071616004 0.17658708 0.17479704 0 0.35138412 0.26305532
10000 105070.83 0.077009979 0.20175025 0.19871513 0 0.40046538 0.34120567
11000 106421.07 0.098623061 0.22472634 0.22671582 0 0.45144216 0.44021335
12000 103209.85 0.12032847 0.25004966 0.25368441 0 0.50373406 0.57344873
13000 107156.89 0.1058386 0.27283231 0.2744873 0 0.54731961 0.47957408
14000 108119.3 0.1204768 0.29333677 0.30054535 0 0.59388213 0.51832639
15000 105477.62 0.12510026 0.32217621 0.32806599 0 0.6502422 0.50174158
16000 106676.27 0.10893618 0.34980866 0.36031184 0 0.7101205 0.44769198
17000 103048.41 0.10625673 0.3781797 0.37970499 0 0.75788468 0.42803898
18000 109454.8 0.10555778 0.40997694 0.41396777 0 0.82394471 0.41380982
19000 107459.73 0.11267582 0.43757738 0.43577856 0 0.87335594 0.4917748
20000 101991.9 0.084279008 0.45363612 0.46278076 0 0.91641688 0.41707912
Loop time of 1.80877 on 4 procs for 20000 steps with 1024 atoms
Performance: 9553.439 tau/day, 11057.221 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34461 | 0.36424 | 0.40948 | 4.4 | 20.14
Neigh | 0.0031493 | 0.003215 | 0.0032432 | 0.1 | 0.18
Comm | 0.19538 | 0.20419 | 0.2104 | 1.2 | 11.29
Output | 0.00054121 | 0.00087297 | 0.0018425 | 0.0 | 0.05
Modify | 0.98335 | 1.0156 | 1.0791 | 3.8 | 56.15
Other | | 0.2207 | | | 12.20
Nlocal: 256.000 ave 261 max 252 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 93.0000 ave 100 max 83 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 662.250 ave 693 max 635 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 2649
Ave neighs/atom = 2.5869141
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 3D overdamped active brownian dynamics with no interactions
variable gamma_t string 3.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_3.0_${gamma_r}_${fp}
variable params string 1.0_3.0_1.0_${fp}
variable params string 1.0_3.0_1.0_4.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.004 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
4096 settings made for dipole/random
velocity all create 1.0 1 loop geom
pair_style none
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
fix activity all propel/self dipole 4.0
compute press all pressure NULL virial
thermo_style custom step ke pe c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes
Step KinEng PotEng c_press
0 1.4996338 0 0.068021726
100 5.184227e+09 0 0.06801544
200 5.2165482e+09 0 0.068010729
300 5.2782092e+09 0 0.068009058
400 5.3244927e+09 0 0.068003481
500 5.2376606e+09 0 0.067998237
600 5.2735634e+09 0 0.067998037
700 5.2692439e+09 0 0.068025402
800 5.2667984e+09 0 0.068030143
900 5.242057e+09 0 0.0680246
1000 5.2557468e+09 0 0.068028348
1100 5.2975687e+09 0 0.068029528
1200 5.2081927e+09 0 0.068017542
1300 5.2636873e+09 0 0.068012572
1400 5.2187907e+09 0 0.06802049
1500 5.2349541e+09 0 0.0680373
1600 5.216092e+09 0 0.068056885
1700 5.2598019e+09 0 0.068069504
1800 5.2569065e+09 0 0.068065306
1900 5.2072055e+09 0 0.068074863
2000 5.2092961e+09 0 0.068061619
2100 5.2918572e+09 0 0.068076418
2200 5.2680626e+09 0 0.068072149
2300 5.242958e+09 0 0.06806486
2400 5.2494099e+09 0 0.06805038
2500 5.2055798e+09 0 0.068072194
2600 5.2264829e+09 0 0.068069312
2700 5.3557342e+09 0 0.068064812
2800 5.2186177e+09 0 0.068042942
2900 5.2652497e+09 0 0.068044214
3000 5.1894899e+09 0 0.068044801
3100 5.241524e+09 0 0.068056675
3200 5.1915006e+09 0 0.06805641
3300 5.2367825e+09 0 0.068049946
3400 5.2288011e+09 0 0.068060182
3500 5.2704335e+09 0 0.068070881
3600 5.2886558e+09 0 0.068050439
3700 5.1976022e+09 0 0.068045927
3800 5.1525512e+09 0 0.068054494
3900 5.2212395e+09 0 0.068061432
4000 5.2309575e+09 0 0.068070842
4100 5.2260184e+09 0 0.068078378
4200 5.2829349e+09 0 0.068071652
4300 5.2204917e+09 0 0.068083072
4400 5.255242e+09 0 0.068066175
4500 5.2435681e+09 0 0.068050802
4600 5.2483356e+09 0 0.06805658
4700 5.2365098e+09 0 0.068041845
4800 5.2254325e+09 0 0.068038583
4900 5.1842852e+09 0 0.068028401
5000 5.2240722e+09 0 0.068031544
Loop time of 5.14275 on 1 procs for 5000 steps with 4096 atoms
Performance: 0.008 tau/day, 972.242 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.26842 | 0.26842 | 0.26842 | 0.0 | 5.22
Output | 0.0035088 | 0.0035088 | 0.0035088 | 0.0 | 0.07
Modify | 4.6588 | 4.6588 | 4.6588 | 0.0 | 90.59
Other | | 0.212 | | | 4.12
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 817.000 ave 817 max 817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# MSD to demonstrate expected diffusive behaviour for ideal active
# brownian motion, which is
#
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
#
# with d being simulation dimension
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 5.2240722e+09 0 0 0 0 0 0.068031544
1000 52651.581 0 0.0066842466 0.0067977045 0.0066831353 0.020165086 0.060774985
2000 52835.806 0 0.013693443 0.014008773 0.013518945 0.041221161 0.094748037
3000 52097.629 0 0.020666918 0.021696789 0.020665685 0.063029392 0.10673866
4000 52579.452 0 0.028145318 0.028504548 0.02830967 0.084959536 0.13358122
5000 51255.456 0 0.035019271 0.034644123 0.03638843 0.10605182 0.13507609
6000 52730.035 0 0.041412307 0.042689213 0.043339117 0.12744064 0.16497663
7000 52247.642 0 0.048119396 0.050556395 0.050706527 0.14938232 0.16360301
8000 52169.849 0 0.055241196 0.058678631 0.059373122 0.17329295 0.1676169
9000 52520.526 0 0.063519587 0.066592779 0.066988842 0.19710121 0.17142694
10000 53519.297 0 0.07164814 0.074576535 0.075619236 0.22184391 0.15619444
11000 52937.293 0 0.077992504 0.083184462 0.082988794 0.24416576 0.15257327
12000 51762.283 0 0.085959749 0.090992292 0.08984213 0.26679417 0.15996211
Loop time of 11.6748 on 1 procs for 12000 steps with 4096 atoms
Performance: 888.063 tau/day, 1027.851 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.0024164 | 0.0024164 | 0.0024164 | 0.0 | 0.02
Comm | 0.048127 | 0.048127 | 0.048127 | 0.0 | 0.41
Output | 0.0019393 | 0.0019393 | 0.0019393 | 0.0 | 0.02
Modify | 11.12 | 11.12 | 11.12 | 0.0 | 95.24
Other | | 0.5027 | | | 4.31
Nlocal: 4096.00 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 75
Dangerous builds = 0
# if you want to check that rotational diffusion is behaving as expected,
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
# which should decay exponentially with timescale (d-1)*D_r (with d
# being simulation dimension)
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
#run 120000
Total wall time: 0:00:16

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LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 3D overdamped active brownian dynamics with no interactions
variable gamma_t string 3.0
variable gamma_r string 1.0
variable temp string 1.0
variable seed equal 1974019
variable fp string 4.0
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
variable params string 1.0_3.0_${gamma_r}_${fp}
variable params string 1.0_3.0_1.0_${fp}
variable params string 1.0_3.0_1.0_4.0
units lj
atom_style hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -8 8 -8 8 -8 8
create_box 1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
2 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 4096 atoms
create_atoms CPU = 0.002 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
4096 settings made for dipole/random
velocity all create 1.0 1 loop geom
pair_style none
# overdamped brownian dynamics time-step
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
# self-propulsion force along the dipole direction
fix activity all propel/self dipole ${fp}
fix activity all propel/self dipole 4.0
compute press all pressure NULL virial
thermo_style custom step ke pe c_press
#equilibration
timestep 0.0000000001
thermo 100
run 5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes
Step KinEng PotEng c_press
0 1.4996338 0 0.068021726
100 5.2484581e+09 0 0.068010768
200 5.277936e+09 0 0.068024039
300 5.2651427e+09 0 0.068014821
400 5.2066432e+09 0 0.068027583
500 5.2250276e+09 0 0.068030242
600 5.239771e+09 0 0.068018406
700 5.1953674e+09 0 0.068017081
800 5.2097107e+09 0 0.068010167
900 5.2559863e+09 0 0.068012923
1000 5.2743197e+09 0 0.068017855
1100 5.1999741e+09 0 0.068014189
1200 5.3216344e+09 0 0.068005604
1300 5.2839264e+09 0 0.067982558
1400 5.2462761e+09 0 0.067977843
1500 5.2208208e+09 0 0.067979594
1600 5.2740284e+09 0 0.067972573
1700 5.1919692e+09 0 0.067974452
1800 5.2497614e+09 0 0.067966417
1900 5.2910442e+09 0 0.067976096
2000 5.27238e+09 0 0.067963979
2100 5.3305398e+09 0 0.06795661
2200 5.205471e+09 0 0.067970212
2300 5.1803713e+09 0 0.067931775
2400 5.2134311e+09 0 0.067941825
2500 5.2367424e+09 0 0.067963456
2600 5.2246738e+09 0 0.067957556
2700 5.2514573e+09 0 0.067960724
2800 5.2601577e+09 0 0.067965167
2900 5.2422855e+09 0 0.067956561
3000 5.1796674e+09 0 0.067946764
3100 5.2308189e+09 0 0.067946585
3200 5.1835395e+09 0 0.067951909
3300 5.2762112e+09 0 0.067963199
3400 5.3224133e+09 0 0.067944918
3500 5.2314242e+09 0 0.06795318
3600 5.2760337e+09 0 0.067958005
3700 5.2549349e+09 0 0.06795228
3800 5.3343065e+09 0 0.067944561
3900 5.2440993e+09 0 0.067947433
4000 5.2565026e+09 0 0.067962624
4100 5.1766738e+09 0 0.067949542
4200 5.2058437e+09 0 0.067959946
4300 5.2777775e+09 0 0.067945883
4400 5.2020331e+09 0 0.067953495
4500 5.1417619e+09 0 0.067944161
4600 5.2672994e+09 0 0.067936777
4700 5.222847e+09 0 0.067943025
4800 5.2467842e+09 0 0.06794191
4900 5.2784378e+09 0 0.067939495
5000 5.2563969e+09 0 0.067940246
Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms
Performance: 0.028 tau/day, 3208.260 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.15304 | 0.15677 | 0.16459 | 1.2 | 10.06
Output | 0.0012078 | 0.0021182 | 0.0047011 | 3.2 | 0.14
Modify | 1.1966 | 1.2236 | 1.2761 | 2.8 | 78.51
Other | | 0.176 | | | 11.29
Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 353.000 ave 353 max 353 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# MSD to demonstrate expected diffusive behaviour for ideal active
# brownian motion, which is
#
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
#
# with d being simulation dimension
compute msd all msd
thermo_style custom step ke pe c_msd[*] c_press
timestep 0.00001
thermo 1000
# main run
run 12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 5.2563969e+09 0 0 0 0 0 0.067940246
1000 52568.549 0 0.0067249858 0.0066478843 0.0066014231 0.019974293 0.066777589
2000 52836.937 0 0.013611101 0.013799663 0.013161144 0.040571907 0.066769693
3000 52129.467 0 0.020360834 0.02089829 0.01995025 0.061209374 0.060026879
4000 52075.177 0 0.027638751 0.028062314 0.026895904 0.082596969 0.078290387
5000 52203.996 0 0.034087112 0.034933104 0.033832559 0.10285278 0.083657551
6000 52986.764 0 0.041562413 0.042238976 0.040542538 0.12434393 0.11542014
7000 51941.229 0 0.049216989 0.049250201 0.047598008 0.1460652 0.13739893
8000 52618.713 0 0.057198947 0.057409217 0.05404895 0.16865711 0.13681938
9000 52501.332 0 0.066447829 0.065262287 0.062271789 0.19398191 0.14306596
10000 52545.628 0 0.073800792 0.072510553 0.070100713 0.21641206 0.14689578
11000 52416.561 0 0.081881868 0.080638809 0.078969817 0.24149049 0.15608324
12000 52271.578 0 0.090521937 0.088555992 0.08592156 0.26499949 0.1474981
Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms
Performance: 3307.113 tau/day, 3827.677 timesteps/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 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00060225 | 0.00060934 | 0.00061345 | 0.0 | 0.02
Comm | 0.029197 | 0.029376 | 0.029582 | 0.1 | 0.94
Output | 0.00060606 | 0.00087148 | 0.0016448 | 0.0 | 0.03
Modify | 2.84 | 2.8773 | 2.8942 | 1.3 | 91.78
Other | | 0.2269 | | | 7.24
Nlocal: 1024.00 ave 1037 max 999 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 73
Dangerous builds = 0
# if you want to check that rotational diffusion is behaving as expected,
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
# which should decay exponentially with timescale (d-1)*D_r (with d
# being simulation dimension)
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
#run 120000
Total wall time: 0:00:04

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@ -9,6 +9,9 @@ to the final states.
* `CH4hyd` -- free energy of hydration of methane (simple). FEP
and FDTI methods.
* `SPCEhyd` -- free energy of hydration of SPCE water (simple). FEP
in separate steps for the LJ sites and the atomic charges.
* `CH4-CF4` -- free energy difference of transforming methane into
perfluoromethane, in water (quite simple). FEP and BAR methods.

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Free Energy of Hydration of SPCE Water
======================================
Example calculation of the free energy of hydration of water with
LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/soft*.
The Lennard-Jones sites and the electrostatic charges are
created/annihilated in separate runs, which simplifies the use of
*fix adapt/fep* and *compute fep*. The Lennard-Jones sites are handled
using soft core potentials (*pair lj/cut/soft*). Trajectories are at
constant NpT, so corrections for the fluctuating volume are included.
The following directories contain input files and results for
calculations using free-energy perturbation (FEP):
* `mols` -- molecule description files and force field database used
to create the initial configuration used for the simulations
`data.lmp`
* `fep01` -- Calculation using FEP, multi-stage creation of one SPC/E
molecule, LJ and q. Results in `fep01-lj.fep` and `fep01-lj.fep`
* `fep10` -- Calculation using FEP, multi-stage deletion of one SPC/E
molecule, q and LJ. Results in `fep10-q.fep` and `fep10-lj.fep`
The Python script `fep.py` found in the
`tools` directory can be used to calculate the free-energy differences
corresponding to the transformations above:
fep.py 300 < fep01-lj.fep
fep.py 300 < fep01-q.fep
fep.py 300 < fep10-q.fep
fep.py 300 < fep10-lj.fep
The outputs are in kcal/mol and can be compared with the experimental
value of -6.3 kcal/mol, or with a simulation value from the literature
of -6.7 kcal/mol
[Gonçalves, Stassen, Pure Appl Chem 76 (2004) 231](https://doi.org/10.1351/pac200476010231).
These example calculations are for tutorial purposes only. The results
may not be of research quality (not enough sampling, size of the step
in lambda not optimized, etc.)

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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.00203701 17656.7 17717
200000 0.0148799 17235.9 17669.1
300000 0.0478517 16378 17736.4
400000 0.100195 15034.8 17725.7
500000 0.218866 12390.7 17698.7
600000 0.371395 9907.37 17731.1
700000 0.613593 7317.6 17750.5
800000 0.895639 5984.39 17714.3
900000 0.638838 8921.42 17726.2
1000000 0.372214 11782.7 17728.6
1100000 0.295555 12613 17730.3
1200000 0.152975 15013.7 17792.5
1300000 0.106403 15927.4 17737.2
1400000 0.0570002 16875.1 17725.9
1500000 0.0182185 17924.9 17790.8
1600000 -0.0319612 19263.7 17775.1
1700000 -0.0684472 20338.7 17786.9
1800000 -0.0941487 21136.1 17764.8
1900000 -0.132444 22374 17750.6
2000000 -0.153928 23156.8 17744.8

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LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526)
2 by 2 by 3 MPI processor grid
reading atoms ...
1800 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
1200 bonds
reading angles ...
600 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.018 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
600 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
find clusters CPU = 0.001 seconds
Setting atom values ...
3 settings made for charge
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25066829
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0030719151
estimated relative force accuracy = 9.250981e-06
using double precision FFTW3
3d grid and FFT values/proc = 3757 800
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 1344.7207 1251.046 93.67475 54.469999 30049.554 -30010.349 300 10284.691 24908.667 0.72058313
5000 28.694564 -5486.1043 1288.3881 -6774.4924 1379.4864 21688.643 -30296.277 308.95461 54.310852 17485.125 1.0265163
10000 60.154999 -5445.984 1289.4468 -6735.4308 1414.0583 21715.025 -30296.898 309.2085 479.66554 17890.87 1.003236
15000 93.146023 -5513.8313 1247.6759 -6761.5072 1299.4795 21790.371 -30301.687 299.19185 -508.0062 17325.35 1.0359828
20000 125.27418 -5449.2886 1284.4959 -6733.7844 1413.7763 21713.785 -30296.156 308.02126 590.93324 17813.863 1.0075729
25000 159.91521 -5488.9702 1263.558 -6752.5282 1419.1433 21691.575 -30298.164 303.00038 745.03072 17529.113 1.0239403
30000 192.99516 -5560.7692 1261.1821 -6821.9512 1417.204 21619.369 -30296.506 302.43062 247.03569 17579.175 1.0210243
35000 226.31455 -5475.9339 1217.5826 -6693.5164 1416.6051 21740.37 -30296.23 291.97549 585.78922 17897.211 1.0028805
40000 257.38113 -5547.1985 1242.3037 -6789.5022 1368.836 21696.099 -30299.114 297.90361 -308.25384 17644.122 1.017266
45000 290.1833 -5546.482 1247.5586 -6794.0405 1478.3456 21579.538 -30298.856 299.16372 1088.2882 17592.834 1.0202316
50000 323.27342 -5587.1305 1245.2866 -6832.4171 1494.5555 21518.708 -30301.175 298.6189 1294.6268 17477.389 1.0269707
55000 357.01676 -5579.512 1240.4584 -6819.9704 1395.6861 21642.898 -30295.857 297.46109 -99.93318 17770.807 1.0100141
60000 388.82447 -5489.9387 1234.3341 -6724.2728 1285.7293 21870.543 -30295.028 295.99251 -1147.8529 17885.706 1.0035257
65000 422.87575 -5552.7156 1212.0793 -6764.7949 1333.565 21754.173 -30298.11 290.65582 -712.18036 17669.638 1.015797
70000 457.6093 -5497.6045 1258.538 -6756.1425 1322.4574 21754.169 -30297.784 301.79659 -688.38797 17616.532 1.0188592
75000 491.97196 -5625.4891 1179.169 -6804.6581 1390.1744 21637.212 -30297.753 282.76395 42.978393 17500.681 1.0256038
80000 525.96216 -5522.0997 1232.6571 -6754.7568 1341.1534 21770.924 -30301.663 295.59035 -265.75148 17495.977 1.0258796
85000 559.772 -5429.8519 1249.9284 -6679.7803 1347.2093 21813.241 -30297.861 299.732 -111.81756 17957.604 0.9995078
90000 593.75975 -5560.9592 1265.0979 -6826.0571 1463.6326 21567.748 -30297.643 303.36965 599.30412 17830.144 1.0066528
95000 627.953 -5544.2442 1277.7084 -6821.9526 1407.1904 21633.729 -30299.133 306.39364 192.51289 17668.067 1.0158873
100000 662.08715 -5474.8467 1286.3434 -6761.1902 1377.3305 21690.898 -30299.316 308.46431 -161.00615 17888.012 1.0033963
Loop time of 662.087 on 12 procs for 100000 steps with 1800 atoms
Performance: 13.050 ns/day, 1.839 hours/ns, 151.038 timesteps/s
94.9% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 345.52 | 374.93 | 410.41 | 88.0 | 56.63
Bond | 1.2655 | 1.3414 | 1.443 | 5.2 | 0.20
Kspace | 99.52 | 135.77 | 165.42 | 148.0 | 20.51
Neigh | 28.904 | 28.95 | 28.997 | 0.6 | 4.37
Comm | 41.498 | 45.503 | 50.663 | 51.8 | 6.87
Output | 0.0013665 | 0.0014183 | 0.0018614 | 0.4 | 0.00
Modify | 49.685 | 64.033 | 72.601 | 117.1 | 9.67
Other | | 11.56 | | | 1.75
Nlocal: 150.000 ave 169 max 133 min
Histogram: 1 2 1 1 2 1 0 3 0 1
Nghost: 6036.17 ave 6092 max 5976 min
Histogram: 3 1 0 0 0 1 3 2 0 2
Neighs: 86433.7 ave 96904 max 78425 min
Histogram: 3 1 1 0 2 1 1 0 1 2
Total # of neighbors = 1037204
Ave neighs/atom = 576.22444
Ave special neighs/atom = 2.0000000
Neighbor list builds = 4498
Dangerous builds = 9
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25099061
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0035434233
estimated relative force accuracy = 1.0670914e-05
using double precision FFTW3
3d grid and FFT values/proc = 3328 648
FEP settings ...
temperature = 300.000000
tail no
lj/cut/soft lambda 1-2 3-4
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 9.473 | 9.524 | 9.885 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda
0 -5474.8313 1286.3434 -6761.1748 1377.3305 21729.814 -30338.216 308.46431 -145.89091 1.0033963 0
5000 -5501.3742 1227.5839 -6728.9581 1383.6091 21832.227 -30338.792 294.37381 197.29783 1.0066092 0.0025
10000 -5464.6748 1299.6003 -6764.2751 1422.869 21700.714 -30339.338 311.64329 911.1393 1.0308533 0.005
15000 -5570.8381 1254.6639 -6825.502 1432.6295 21661.321 -30337.889 300.86757 606.08029 1.0232505 0.0075
20000 -5517.9977 1279.1 -6797.0976 1408.873 21713.571 -30334.986 306.72733 71.014518 1.00536 0.01
25000 -5502.8662 1256.1509 -6759.0171 1354.4185 21819.904 -30335.966 301.22416 -280.3804 1.0121715 0.0125
30000 -5479.0987 1247.8675 -6726.9662 1413.5362 21734.153 -30338.534 299.23779 347.7292 1.0037264 0.015
35000 -5507.6469 1301.4131 -6809.06 1460.033 21614.564 -30336.109 312.07801 771.56011 1.0011707 0.0175
40000 -5487.2955 1295.7159 -6783.0113 1321.8494 21814.192 -30340.297 310.71181 -399.68468 1.0295009 0.02
45000 -5582.7908 1203.9957 -6786.7865 1428.232 21690.272 -30335.2 288.71737 516.0938 1.0238261 0.0225
50000 -5543.0112 1239.5077 -6782.5189 1442.8695 21660.077 -30336.998 297.23314 966.89878 1.0234172 0.025
55000 -5590.3604 1232.4497 -6822.8101 1322.5893 21772.961 -30338.359 295.54062 -790.54432 1.0210518 0.0275
60000 -5479.6266 1218.6941 -6698.3207 1363.233 21839.328 -30336.264 292.24204 102.67075 1.0069364 0.03
65000 -5492.8433 1277.3976 -6770.2409 1361.2794 21754.915 -30335.072 306.31909 -345.94035 1.0111736 0.0325
70000 -5564.9632 1256.2689 -6821.2322 1418.089 21663.812 -30334.208 301.25246 -235.62062 1.0000081 0.035
75000 -5431.4667 1233.6963 -6665.163 1385.2972 21867.508 -30337.413 295.83957 605.68584 1.015264 0.0375
80000 -5560.6719 1236.9415 -6797.6134 1374.1241 21748.636 -30335.156 296.61776 -202.53528 1.015924 0.04
85000 -5636.8905 1233.835 -6870.7255 1480.1666 21576.608 -30340.174 295.87281 827.4631 1.0212177 0.0425
90000 -5551.2917 1222.5755 -6773.8672 1452.5674 21638.206 -30335.595 293.1728 661.99097 1.0090475 0.045
95000 -5543.8224 1249.9355 -6793.758 1396.082 21724.933 -30339.764 299.73372 201.87719 1.0163116 0.0475
100000 -5558.5664 1227.1814 -6785.7479 1463.1907 21666.038 -30337.879 294.2773 955.6758 1.0158894 0.05
105000 -5507.0698 1233.0098 -6740.0796 1356.1635 21774.574 -30334.594 295.67493 -359.01022 1.0056685 0.0525
110000 -5561.0676 1221.0774 -6782.145 1403.5966 21692.913 -30337.463 292.81355 -87.113696 1.0133037 0.055
115000 -5526.6141 1243.9541 -6770.5682 1475.7194 21626.703 -30337.179 298.29937 855.85038 1.0118327 0.0575
120000 -5555.6741 1253.3796 -6809.0538 1346.5604 21755.315 -30340.743 300.55961 -1079.5856 0.98312027 0.06
125000 -5620.4084 1221.0146 -6841.423 1406.8142 21677.116 -30335.053 292.7985 -61.600379 1.0173627 0.0625
130000 -5586.4001 1204.2423 -6790.6425 1352.9098 21770.892 -30339.505 288.77651 -460.92375 1.0164837 0.065
135000 -5568.5186 1239.2748 -6807.7934 1401.8615 21748.687 -30340.555 297.17728 371.66677 1.0241473 0.0675
140000 -5526.4808 1249.0145 -6775.4953 1424.2185 21664.576 -30340.16 299.51285 520.63161 1.0238118 0.07
145000 -5532.8733 1254.9515 -6787.8248 1379.0629 21737.241 -30337.358 300.93654 -64.517937 1.0105756 0.0725
150000 -5549.4332 1228.3832 -6777.8163 1428.5036 21702.196 -30337.055 294.56547 363.42307 1.0052127 0.075
155000 -5547.9284 1256.6973 -6804.6257 1379.9059 21727.03 -30338.382 301.35519 35.503942 1.0222903 0.0775
160000 -5481.1383 1320.4344 -6801.5727 1390.3369 21729.299 -30337.062 316.63929 50.667563 1.0171266 0.08
165000 -5560.7321 1247.5004 -6808.2325 1422.2771 21662.917 -30341.024 299.14978 56.116137 1.0020068 0.0825
170000 -5541.3469 1257.9624 -6799.3094 1381.0133 21739.612 -30336.303 301.65856 -176.83515 1.0084433 0.085
175000 -5481.784 1239.9656 -6721.7496 1366.9952 21834.266 -30335.454 297.34293 377.28019 1.0297034 0.0875
180000 -5609.1447 1180.414 -6789.5587 1410.9273 21683.391 -30338.821 283.06249 203.46781 1.013427 0.09
185000 -5508.6637 1237.4229 -6746.0866 1401.5929 21736.318 -30334.806 296.7332 287.44715 1.0114427 0.0925
190000 -5524.666 1249.3421 -6774.008 1414.6887 21711.574 -30338.223 299.5914 108.63857 0.99681381 0.095
195000 -5613.4475 1179.1603 -6792.6078 1415.5702 21704.669 -30335.058 282.76187 -4.252137 1.0025742 0.0975
200000 -5577.1744 1219.3392 -6796.5136 1358.774 21688.932 -30339.219 292.39674 -339.31655 1.0272643 0.1
205000 -5473.5241 1291.8332 -6765.3573 1364.0148 21747.958 -30335.578 309.78075 -140.98482 1.0134706 0.1025
210000 -5412.6987 1304.0334 -6716.7321 1399.175 21790.687 -30338.388 312.70635 475.62089 1.0077929 0.105
215000 -5498.5445 1272.4319 -6770.9765 1305.2038 21853.899 -30334.099 305.12834 -964.41064 1.0117303 0.1075
220000 -5552.46 1236.8433 -6789.3033 1413.5383 21633.766 -30337.007 296.59421 126.59413 1.0135386 0.11
225000 -5463.5199 1281.9539 -6745.4738 1391.2426 21760.978 -30337.489 307.41171 372.98508 1.0154691 0.1125
230000 -5556.2415 1213.9742 -6770.2157 1373.9439 21746.355 -30331.29 291.11021 310.03784 1.0411894 0.115
235000 -5468.6139 1256.2727 -6724.8866 1419.9068 21755.903 -30337.057 301.25335 446.80106 1.008653 0.1175
240000 -5505.2272 1297.8543 -6803.0815 1389.9299 21721.555 -30336.374 311.22461 -216.33356 1.0007317 0.12
245000 -5556.4175 1231.9791 -6788.3966 1385.1734 21697.589 -30334.804 295.42778 -115.65689 1.0127289 0.1225
250000 -5570.5583 1261.1376 -6831.6959 1404.3069 21667.366 -30337.205 302.41997 -90.154201 1.0161797 0.125
255000 -5581.0101 1222.6213 -6803.6314 1393.6905 21687.538 -30336.542 293.18377 -58.781363 1.013542 0.1275
260000 -5552.6506 1225.5794 -6778.2299 1446.9969 21648.822 -30336.275 293.89312 749.70391 1.0136121 0.13
265000 -5527.9133 1245.5123 -6773.4255 1328.166 21792.912 -30336.854 298.67302 -825.99884 1.0063806 0.1325
270000 -5565.2798 1266.7326 -6832.0124 1488.6605 21582.46 -30339.347 303.76165 1592.7435 1.0374567 0.135
275000 -5567.4599 1211.9673 -6779.4272 1306.1895 21846.2 -30334.296 290.62895 -1062.6911 1.0107451 0.1375
280000 -5456.1965 1291.476 -6747.6725 1324.4174 21839.645 -30339.854 309.69509 -531.26163 1.0140474 0.14
285000 -5561.638 1229.3427 -6790.9808 1353.7161 21794.932 -30334.258 294.79557 -269.97414 1.0110394 0.1425
290000 -5486.1623 1276.1413 -6762.3036 1380.4775 21777.115 -30336.678 306.01784 -56.691362 1.0105051 0.145
295000 -5531.2556 1253.1859 -6784.4415 1354.9857 21750.76 -30338.549 300.51314 -555.4993 1.0159961 0.1475
300000 -5583.1864 1250.0209 -6833.2073 1431.4702 21654.547 -30337.557 299.75419 360.48799 1.0226237 0.15
305000 -5492.9399 1263.2527 -6756.1925 1385.9115 21749.132 -30337.333 302.92716 -94.633279 1.0008411 0.1525
310000 -5583.9951 1217.2631 -6801.2582 1439.2175 21660.614 -30332.833 291.89889 575.48041 1.0264848 0.155
315000 -5554.3025 1247.1517 -6801.4542 1305.5379 21807.382 -30337.478 299.06616 -1206.257 1.0085908 0.1575
320000 -5596.1914 1233.0393 -6829.2307 1431.9073 21667.612 -30337.859 295.682 745.35002 1.0291 0.16
325000 -5532.0063 1245.6006 -6777.6069 1479.6102 21640.94 -30338.346 298.69419 1390.0859 1.0311996 0.1625
330000 -5511.0183 1236.8356 -6747.854 1332.4766 21826.148 -30335.853 296.59237 -346.80349 1.020578 0.165
335000 -5512.3188 1238.1769 -6750.4957 1324.5201 21836.682 -30338.607 296.91401 -457.67242 1.0274241 0.1675
340000 -5504.0924 1242.6354 -6746.7278 1432.7958 21708.299 -30333.659 297.98314 674.26615 1.0055018 0.17
345000 -5522.5796 1265.0266 -6787.6062 1382.0078 21743.218 -30338.398 303.35254 -151.81029 1.0067371 0.1725
350000 -5545.7535 1267.9089 -6813.6624 1404.8847 21674.34 -30337.099 304.04372 128.71982 1.0135501 0.175
355000 -5499.0073 1275.2358 -6774.2431 1484.721 21658.719 -30337.688 305.80071 1468.7411 1.0346991 0.1775
360000 -5540.4144 1242.034 -6782.4484 1440.0683 21684.985 -30338.578 297.83892 662.99982 1.0085045 0.18
365000 -5472.9692 1267.5044 -6740.4736 1350.7945 21806.742 -30338.576 303.94672 -303.53857 1.0149794 0.1825
370000 -5563.7998 1257.4972 -6821.297 1363.9578 21745.681 -30339.039 301.54699 -616.39894 1.0015708 0.185
375000 -5494.3434 1204.4931 -6698.8365 1308.4989 21883.359 -30336.609 288.83665 -1009.8181 0.99179087 0.1875
380000 -5516.3392 1223.7518 -6740.0911 1355.9449 21816.149 -30337.588 293.45488 36.407556 1.02042 0.19
385000 -5534.8879 1226.8136 -6761.7015 1433.131 21698.233 -30336.201 294.18909 1224.3283 1.0416014 0.1925
390000 -5506.0676 1262.1264 -6768.194 1449.4667 21692.815 -30334.182 302.65707 932.23514 1.0216439 0.195
395000 -5601.9693 1234.2373 -6836.2066 1425.5787 21658.64 -30337.816 295.96929 254.00155 1.0148905 0.1975
400000 -5523.9324 1254.811 -6778.7434 1371.5302 21763.333 -30334.914 300.90286 -41.512594 1.0129399 0.2
405000 -5615.7822 1209.5514 -6825.3336 1431.7105 21604.804 -30336.544 290.04963 385.86176 1.02069 0.2025
410000 -5564.9317 1238.9308 -6803.8625 1334.6011 21725.649 -30342.03 297.09479 -668.14712 1.0114204 0.205
415000 -5565.723 1201.4165 -6767.1395 1407.6153 21731.714 -30339.794 288.09888 284.39352 1.0181526 0.2075
420000 -5514.1574 1259.6967 -6773.8542 1397.8555 21765.77 -30335.098 302.07445 -93.583513 1.003494 0.21
425000 -5566.4826 1233.6609 -6800.1435 1354.6757 21745.391 -30337.658 295.83106 -543.91774 1.0113019 0.2125
430000 -5544.9786 1227.5367 -6772.5153 1391.971 21756.332 -30337.075 294.36248 -52.853646 1.0029339 0.215
435000 -5457.9703 1243.8289 -6701.7992 1355.8144 21842.63 -30336.263 298.26936 96.07031 1.0162599 0.2175
440000 -5444.1352 1261.5679 -6705.7031 1327.5589 21849.174 -30337.667 302.52315 -159.33457 1.0201548 0.22
445000 -5569.3089 1253.1592 -6822.4681 1450.3256 21615.072 -30333.867 300.50675 497.07257 1.0162108 0.2225
450000 -5499.4632 1276.3744 -6775.8376 1436.3419 21681.852 -30337.613 306.07374 416.13585 1.0087874 0.225
455000 -5527.7917 1199.0123 -6726.804 1371.2866 21773.376 -30335.146 287.52235 -330.60298 0.99153512 0.2275
460000 -5634.9316 1214.1147 -6849.0463 1471.6124 21618.634 -30339.723 291.14391 831.79551 1.0154836 0.23
465000 -5492.5994 1247.2074 -6739.8067 1425.1188 21720.998 -30333.086 299.0795 782.63379 1.0210767 0.2325
470000 -5528.6598 1242.3825 -6771.0422 1413.2305 21674.806 -30339.41 297.9225 371.75935 1.018354 0.235
475000 -5570.6679 1274.1035 -6844.7714 1423.8596 21624.648 -30335.904 305.52919 243.67178 1.0157084 0.2375
480000 -5487.1119 1241.0548 -6728.1667 1421.7563 21732.588 -30338.933 297.60413 814.07568 1.0255732 0.24
485000 -5575.4172 1242.9613 -6818.3785 1402.7921 21677.417 -30338.336 298.0613 20.597793 1.0229831 0.2425
490000 -5578.303 1221.4158 -6799.7188 1430.5395 21694.761 -30336.572 292.89469 430.02647 1.0131845 0.245
495000 -5573.1773 1222.1238 -6795.3011 1502.7203 21609.264 -30338.892 293.06448 1494.9905 1.0226527 0.2475
500000 -5470.7153 1208.6593 -6679.3745 1401.9799 21819.612 -30335.747 289.83569 552.82762 1.003873 0.25
505000 -5626.3096 1246.8303 -6873.1399 1504.3826 21517.763 -30336.928 298.98909 1008.6542 1.0255205 0.2525
510000 -5562.1313 1242.0291 -6804.1604 1360.6445 21745.689 -30334.283 297.83775 -300.55499 1.021938 0.255
515000 -5558.6681 1241.9812 -6800.6493 1399.186 21683.627 -30339.266 297.82628 -293.22181 1.0035268 0.2575
520000 -5450.6773 1276.8169 -6727.4943 1246.5956 21918.914 -30335.226 306.17986 -1527.0713 1.0017384 0.26
525000 -5495.0769 1260.1524 -6755.2294 1413.8065 21708.663 -30338.153 302.18372 193.49778 1.0090792 0.2625
530000 -5519.0236 1258.9944 -6778.018 1423.1288 21726.251 -30338.72 301.90602 402.81349 1.0058563 0.265
535000 -5523.3166 1265.8203 -6789.1369 1403.2616 21669.617 -30333.964 303.54286 -212.90176 1.0022662 0.2675
540000 -5469.6354 1267.2634 -6736.8988 1354.6136 21815.059 -30334.909 303.88893 -143.78705 1.0102562 0.27
545000 -5475.0926 1332.0416 -6807.1342 1362.668 21728.374 -30335.495 319.42269 -408.94813 1.008036 0.2725
550000 -5604.8235 1220.5785 -6825.4021 1466.9259 21609.628 -30340.185 292.69392 562.0671 0.99832249 0.275
555000 -5546.9498 1194.3285 -6741.2783 1324.6404 21805.776 -30334.506 286.39919 -831.67066 1.0068815 0.2775
560000 -5505.8852 1231.4127 -6737.2978 1403.1199 21743.566 -30336.518 295.29195 134.18023 1.0068652 0.28
565000 -5620.5688 1225.712 -6846.2808 1418.5638 21624.884 -30336.305 293.92493 -45.194557 1.0148173 0.2825
570000 -5522.2261 1265.1646 -6787.3907 1431.1348 21666.003 -30337.479 303.38564 470.11582 1.0164271 0.285
575000 -5586.7521 1277.3002 -6864.0523 1411.585 21610.013 -30338.867 306.29575 3.3115648 1.0213675 0.2875
580000 -5612.9476 1236.9792 -6849.9268 1385.7307 21698.533 -30334.246 296.62679 -180.75952 1.0145947 0.29
585000 -5564.6816 1225.6381 -6790.3197 1333.2129 21796.701 -30335.104 293.90721 -690.26993 1.0116307 0.2925
590000 -5505.6734 1225.965 -6731.6383 1388.9635 21758.959 -30333.889 293.98559 227.32836 1.0145465 0.295
595000 -5547.8043 1248.8277 -6796.632 1360.0327 21712.026 -30336.566 299.46806 -375.66988 1.0129675 0.2975
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605000 -5491.3585 1261.835 -6753.1935 1362.4507 21774.232 -30332.849 302.58721 -165.60547 1.0153308 0.3025
610000 -5614.7624 1197.5896 -6812.352 1337.5281 21753.381 -30338.757 287.1812 -750.69767 1.0108767 0.305
615000 -5576.4304 1197.4926 -6773.9229 1360.9065 21756.815 -30335.31 287.15793 -693.56508 0.99901143 0.3075
620000 -5548.9351 1231.926 -6780.861 1367.5138 21765.942 -30335.526 295.41503 -447.87437 1.0071454 0.31
625000 -5478.0177 1304.9593 -6782.9771 1472.1656 21630.028 -30337.864 312.92838 902.38662 1.0047677 0.3125
630000 -5488.216 1246.0606 -6734.2767 1409.7407 21771.095 -30336.403 298.80451 480.81355 1.0089233 0.315
635000 -5539.378 1232.3758 -6771.7538 1370.1156 21731.482 -30335.377 295.52291 -713.31325 0.98843736 0.3175
640000 -5432.8862 1296.4151 -6729.3012 1343.8929 21825.715 -30336.397 310.87948 -397.39803 1.0014659 0.32
645000 -5588.6649 1238.8032 -6827.4681 1428.9906 21666.562 -30335.249 297.06419 599.51702 1.0293674 0.3225
650000 -5519.3466 1230.0381 -6749.3847 1453.0003 21705.846 -30339.941 294.96233 1124.8857 1.026394 0.325
655000 -5533.8266 1258.3233 -6792.1499 1371.5049 21733.113 -30338.134 301.74509 -435.07103 0.99919968 0.3275
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665000 -5545.4581 1249.7274 -6795.1854 1412.241 21718.149 -30338.751 299.6838 275.8861 1.0143558 0.3325
670000 -5565.5948 1226.9318 -6792.5266 1315.7564 21812.516 -30339.437 294.21745 -830.3758 1.0195327 0.335
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685000 -5498.7222 1275.9994 -6774.7216 1415.2483 21718.812 -30334.721 305.98383 159.13649 1.0044781 0.3425
690000 -5566.4304 1231.9604 -6798.3908 1457.3283 21668.417 -30337.919 295.42329 287.07228 0.98982439 0.345
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705000 -5503.7028 1288.0097 -6791.7124 1430.0691 21713.551 -30338.914 308.86387 480.01323 1.0067532 0.3525
710000 -5483.2647 1299.6448 -6782.9095 1336.3828 21780.796 -30336.31 311.65398 -744.40786 0.9955777 0.355
715000 -5552.0795 1213.1147 -6765.1942 1367.5913 21780.545 -30334.566 290.90411 -182.26292 1.0179523 0.3575
720000 -5560.2543 1223.8905 -6784.1448 1469.5204 21612.085 -30334.718 293.48814 686.798 1.0061298 0.36
725000 -5352.2877 1277.7298 -6630.0175 1247.1535 21984.591 -30332.503 306.39876 -1113.3988 1.0031932 0.3625
730000 -5460.2162 1294.0163 -6754.2324 1328.4251 21812.669 -30338.962 310.30425 -703.10487 1.0076915 0.365
735000 -5484.3003 1263.9561 -6748.2564 1391.8724 21763.598 -30333.325 303.09585 358.57571 1.0159982 0.3675
740000 -5561.5146 1232.365 -6793.8795 1417.041 21689.319 -30337.153 295.52031 292.49943 1.0148461 0.37
745000 -5630.3272 1239.8819 -6870.2091 1474.7847 21577.482 -30336.129 297.32287 691.90387 1.0121157 0.3725
750000 -5568.5982 1252.3637 -6820.9619 1394.8143 21677.258 -30335.92 300.31599 -119.75657 1.0137126 0.375
755000 -5612.0848 1219.7512 -6831.8361 1443.772 21640.182 -30334.138 292.49554 419.10212 1.0092041 0.3775
760000 -5558.6692 1246.8503 -6805.5195 1383.8773 21739.076 -30332.761 298.99389 -360.94924 1.0057415 0.38
765000 -5549.313 1264.7175 -6814.0305 1361.0876 21760.857 -30334.954 303.27841 -657.15125 0.99708711 0.3825
770000 -5529.7814 1271.3249 -6801.1063 1515.765 21530.178 -30335.782 304.86287 1252.2865 1.0144338 0.385
775000 -5590.0803 1229.8806 -6819.9609 1497.7379 21574.205 -30337.017 294.92455 875.72015 1.0034086 0.3875
780000 -5453.0919 1304.4967 -6757.5885 1382.0095 21780.373 -30336.825 312.81744 94.669052 1.0004685 0.39
785000 -5534.5816 1224.2253 -6758.8069 1434.4738 21697.922 -30337.941 293.56842 992.15486 1.0337883 0.3925
790000 -5502.6322 1265.271 -6767.9032 1398.8135 21757.098 -30337.587 303.41116 116.52301 1.0001157 0.395
795000 -5493.1146 1274.5478 -6767.6624 1388.2754 21742.779 -30337.47 305.63572 140.01039 1.0236842 0.3975
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810000 -5562.8317 1225.0571 -6787.8888 1387.1409 21714.016 -30338.516 293.76787 -132.30834 1.0033838 0.405
815000 -5450.6822 1281.7205 -6732.4027 1384.0948 21802.411 -30334.816 307.35573 457.40601 1.0295805 0.4075
820000 -5517.3791 1253.0874 -6770.4665 1342.5725 21767.666 -30338.348 300.48953 -677.2962 1.0045618 0.41
825000 -5521.6442 1253.7177 -6775.3619 1356.0902 21761.083 -30338.876 300.64068 -148.29882 1.0214802 0.4125
830000 -5480.2275 1296.3533 -6776.5808 1364.7623 21737.884 -30340.245 310.86468 -335.51468 1.0183724 0.415
835000 -5553.6513 1255.3646 -6809.0158 1422.3832 21678.078 -30336.06 301.03559 240.25343 1.0133683 0.4175
840000 -5487.5608 1239.6145 -6727.1753 1346.503 21835.502 -30338.024 297.25873 -317.28429 1.0034118 0.42
845000 -5515.8021 1255.1208 -6770.9229 1514.9877 21605.011 -30337.481 300.97715 1627.3413 1.0134437 0.4225
850000 -5540.0383 1285.5034 -6825.5417 1428.3295 21672.551 -30335.853 308.26287 466.86907 1.0199088 0.425
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1625000 -5456.168 1228.6159 -6684.7839 1372.1719 21806.244 -30336.186 294.62128 293.33707 1.0094967 0.8125
1630000 -5650.3002 1225.7447 -6876.0449 1465.0474 21543.498 -30336.757 293.93277 417.30626 1.0158098 0.815
1635000 -5450.49 1275.0111 -6725.5011 1481.2268 21684.726 -30337.105 305.74683 1426.6931 1.0094353 0.8175
1640000 -5617.7996 1227.1912 -6844.9908 1412.9007 21647.959 -30339.808 294.27965 -64.670241 1.0184979 0.82
1645000 -5479.4668 1286.8935 -6766.3603 1430.311 21716.402 -30338.791 308.59622 613.1652 1.002358 0.8225
1650000 -5500.2183 1280.3487 -6780.567 1385.4426 21748.104 -30337.348 307.02677 -65.179279 1.0098634 0.825
1655000 -5560.2962 1223.2516 -6783.5478 1311.1561 21783.296 -30335.262 293.33493 -1444.809 0.98862533 0.8275
1660000 -5560.1654 1221.3779 -6781.5433 1384.641 21766.196 -30337.4 292.88562 -30.809802 1.0055892 0.83
1665000 -5459.1135 1261.4358 -6720.5493 1334.6877 21855.177 -30336.221 302.49147 -691.93836 0.98631443 0.8325
1670000 -5426.4876 1277.2456 -6703.7331 1301.4361 21883.289 -30338.807 306.28264 -769.6473 1.0029395 0.835
1675000 -5560.3658 1228.1155 -6788.4813 1421.5285 21710.575 -30339.538 294.50128 134.14929 0.99950546 0.8375
1680000 -5533.0079 1239.2308 -6772.2386 1466.9684 21661.29 -30336.838 297.16672 1000.7926 1.0093582 0.84
1685000 -5532.7803 1282.6992 -6815.4795 1387.5896 21673.135 -30336.269 307.59043 -293.90054 1.0036548 0.8425
1690000 -5533.8573 1242.0398 -6775.8971 1295.4859 21813.204 -30335.918 297.84032 -1072.3783 1.0103958 0.845
1695000 -5569.1131 1236.3099 -6805.423 1391.4947 21734.459 -30337.665 296.46629 -42.852437 1.0020314 0.8475
1700000 -5514.6926 1236.9596 -6751.6522 1297.2083 21861.079 -30337.966 296.6221 -1035.3111 1.0148487 0.85
1705000 -5481.7854 1264.9348 -6746.7202 1394.4051 21765.618 -30334.989 303.33053 68.230386 0.99805471 0.8525
1710000 -5628.7652 1218.5732 -6847.3385 1424.8975 21629.726 -30339.018 292.21306 -18.822494 1.0061359 0.855
1715000 -5535.4768 1269.0696 -6804.5464 1310.4991 21778.662 -30338.107 304.32206 -1128.3429 1.0076215 0.8575
1720000 -5612.6083 1193.1968 -6805.8051 1383.4907 21742.438 -30339.657 286.12782 -186.2314 1.0077134 0.86
1725000 -5483.1527 1278.2192 -6761.3719 1414.7937 21718.362 -30332.789 306.51613 275.89425 0.99757317 0.8625
1730000 -5507.2292 1239.3969 -6746.626 1349.4125 21760.595 -30336.33 297.20655 -160.96278 1.0175868 0.865
1735000 -5471.6725 1274.6169 -6746.2893 1353.4867 21778.13 -30334.321 305.65228 -455.73375 0.99473861 0.8675
1740000 -5457.1173 1292.0777 -6749.195 1354.1425 21798.549 -30337.698 309.83938 105.28166 1.013856 0.87
1745000 -5526.7699 1217.2299 -6743.9998 1374.1349 21775.087 -30335.943 291.89093 21.249651 1.0097813 0.8725
1750000 -5558.9441 1238.0218 -6796.966 1398.6419 21742.403 -30337.165 296.87681 258.79723 1.0189989 0.875
1755000 -5510.581 1278.8181 -6789.3991 1388.2658 21710.876 -30337.981 306.65974 475.10366 1.0315721 0.8775
1760000 -5530.9869 1295.8685 -6826.8554 1479.5118 21573.341 -30338.944 310.74841 748.89788 1.0132734 0.88
1765000 -5533.3839 1317.0507 -6850.4347 1435.6808 21644.207 -30333.746 315.8279 594.0529 1.0192713 0.8825
1770000 -5465.8084 1240.5045 -6706.3129 1292.0385 21900.378 -30339.129 297.47215 -1025.2013 1.0024888 0.885
1775000 -5599.0359 1221.6792 -6820.7151 1462.1624 21619.581 -30339.425 292.95787 626.3862 1.0091902 0.8875
1780000 -5538.0385 1264.6729 -6802.7114 1372.7663 21730.471 -30338.894 303.26773 -192.55416 1.0065058 0.89
1785000 -5428.1822 1333.9892 -6762.1715 1389.1017 21728.7 -30336.27 319.88974 104.29655 1.0139352 0.8925
1790000 -5508.9545 1287.0739 -6796.0284 1445.185 21652.743 -30336.902 308.63947 391.87637 1.0000323 0.895
1795000 -5523.6516 1235.1646 -6758.8162 1418.1244 21721.296 -30337.575 296.19166 666.61502 1.0229146 0.8975
1800000 -5572.6377 1214.1205 -6786.7582 1392.4223 21722.483 -30335.66 291.14528 -97.658277 1.0013673 0.9
1805000 -5546.2419 1219.6808 -6765.9227 1366.9631 21762.107 -30337.944 292.47866 -57.351578 1.0188349 0.9025
1810000 -5570.7715 1247.1279 -6817.8994 1386.5773 21707.994 -30338.467 299.06045 128.40982 1.018309 0.905
1815000 -5527.1768 1236.8139 -6763.9907 1370.0226 21756.947 -30337.433 296.58716 -58.429002 1.0156077 0.9075
1820000 -5392.8702 1296.598 -6689.4682 1422.7107 21835.725 -30339.535 310.92334 1096.9698 1.0098001 0.91
1825000 -5403.1407 1273.2353 -6676.3761 1398.7473 21821.771 -30338.272 305.32099 575.09164 1.009625 0.9125
1830000 -5533.275 1223.962 -6757.237 1302.4782 21879.688 -30335.303 293.50528 -794.93635 1.0164392 0.915
1835000 -5537.9594 1230.3716 -6768.331 1359.2088 21780.105 -30337.746 295.04229 -301.96771 1.012533 0.9175
1840000 -5496.5607 1259.4196 -6755.9803 1392.4138 21810.816 -30335.129 302.00799 308.79809 1.0087261 0.92
1845000 -5516.8276 1233.6195 -6750.4471 1356.0628 21770.257 -30336.985 295.82114 -563.13925 0.99534053 0.9225
1850000 -5551.2862 1216.2779 -6767.5641 1315.4137 21779.186 -30338.525 291.66263 -1234.4928 0.9977088 0.925
1855000 -5514.4008 1278.8525 -6793.2533 1477.9866 21661.793 -30338.935 306.668 1192.9778 1.0126178 0.9275
1860000 -5445.2459 1262.0113 -6707.2573 1295.8277 21920.956 -30333.967 302.62948 -1093.2105 0.98876382 0.93
1865000 -5479.9894 1263.9698 -6743.9592 1342.5201 21812.688 -30335.4 303.09913 -141.70262 1.018338 0.9325
1870000 -5526.4829 1205.3702 -6731.8531 1376.0037 21811.821 -30332.663 289.04698 186.81383 1.0172778 0.935
1875000 -5566.9793 1221.657 -6788.6363 1352.419 21753.184 -30332.134 292.95254 -421.96475 1.0091425 0.9375
1880000 -5497.1676 1282.0374 -6779.205 1398.213 21722.715 -30339.838 307.43173 37.827778 1.0039977 0.94
1885000 -5557.4404 1233.9174 -6791.3578 1449.936 21642.09 -30339.056 295.89259 883.49759 1.0130214 0.9425
1890000 -5506.733 1295.1267 -6801.8597 1297.6178 21817.614 -30338.332 310.57052 -1073.8778 1.0180788 0.945
1895000 -5533.7516 1257.448 -6791.1996 1345.2106 21764.458 -30338.571 301.53521 -526.55649 1.0121615 0.9475
1900000 -5541.0051 1258.9341 -6799.9391 1381.6398 21733.321 -30338.593 301.89155 -252.04317 1.008764 0.95
1905000 -5609.2146 1182.6597 -6791.8743 1350.4308 21757.084 -30338.743 283.60101 -97.157492 1.0309631 0.9525
1910000 -5571.9982 1254.2855 -6826.2837 1389.361 21684.388 -30336.514 300.77683 -350.37238 1.0002085 0.955
1915000 -5504.046 1277.8838 -6781.9299 1392.3191 21732.799 -30339.549 306.43569 295.58866 1.0234965 0.9575
1920000 -5500.6241 1311.1129 -6811.737 1384.3734 21674.326 -30341.238 314.40401 84.788637 1.0209565 0.96
1925000 -5529.7992 1229.6795 -6759.4787 1408.9276 21763.324 -30339.966 294.87632 215.06361 1.0061547 0.9625
1930000 -5444.6302 1282.6892 -6727.3194 1334.5948 21864.664 -30333.059 307.58803 -76.344233 1.0195039 0.965
1935000 -5506.5314 1250.2755 -6756.8069 1346.0266 21804.791 -30335.384 299.81524 -400.10311 1.009444 0.9675
1940000 -5595.6735 1257.0187 -6852.6922 1445.275 21568.516 -30337.62 301.43225 543.8544 1.0288045 0.97
1945000 -5555.7495 1224.7877 -6780.5372 1333.6985 21795.754 -30338.445 293.70329 -560.62987 1.0145559 0.9725
1950000 -5481.8697 1239.3038 -6721.1735 1436.353 21745.545 -30335.269 297.18424 1090.0854 1.024844 0.975
1955000 -5586.7772 1263.8812 -6850.6584 1479.012 21594.084 -30335.219 303.07787 1031.8973 1.018222 0.9775
1960000 -5495.753 1254.4979 -6750.2508 1386.5525 21763.46 -30336.981 300.82776 72.271681 1.0073177 0.98
1965000 -5532.6074 1226.085 -6758.6924 1373.4537 21763.717 -30335.48 294.01437 49.27447 1.0207726 0.9825
1970000 -5592.2371 1226.5746 -6818.8117 1393.679 21701.959 -30338.233 294.13177 150.06013 1.0325882 0.985
1975000 -5564.1305 1237.5805 -6801.711 1398.2423 21736.76 -30338.459 296.77099 278.42773 1.0180523 0.9875
1980000 -5482.7493 1267.38 -6750.1292 1354.4265 21816.978 -30337.136 303.91688 -264.92549 1.0116111 0.99
1985000 -5486.0145 1244.3436 -6730.358 1338.1288 21844.074 -30336.86 298.39277 76.865939 1.0287137 0.9925
1990000 -5518.5592 1251.3748 -6769.9341 1251.2427 21885.87 -30337.966 300.07886 -1536.5189 1.0130877 0.995
1995000 -5487.626 1271.8163 -6759.4423 1356.5853 21769.656 -30337.831 304.9807 -374.70018 1.0071102 0.9975
2000000 -5510.6051 1219.5403 -6730.1454 1414.2091 21757.343 -30335.348 292.44495 576.54022 1.0102751 1
Loop time of 13908.6 on 12 procs for 2000000 steps with 1800 atoms
Performance: 12.424 ns/day, 1.932 hours/ns, 143.796 timesteps/s
95.4% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7652.9 | 8199.2 | 8886.6 | 354.2 | 58.95
Bond | 25.21 | 26.012 | 27.096 | 14.0 | 0.19
Kspace | 2159 | 2762 | 3232.9 | 533.0 | 19.86
Neigh | 571.65 | 572.66 | 573.54 | 2.5 | 4.12
Comm | 806.99 | 869.79 | 940.86 | 190.9 | 6.25
Output | 0.032536 | 0.034245 | 0.041095 | 1.2 | 0.00
Modify | 959.22 | 1140.3 | 1306.8 | 448.8 | 8.20
Other | | 338.6 | | | 2.43
Nlocal: 150.000 ave 159 max 140 min
Histogram: 1 0 2 2 0 2 2 1 0 2
Nghost: 6121.33 ave 6236 max 6003 min
Histogram: 2 0 0 3 0 2 2 2 0 1
Neighs: 87038.7 ave 96826 max 77686 min
Histogram: 2 0 1 3 0 1 2 1 1 1
Total # of neighbors = 1044464
Ave neighs/atom = 580.25778
Ave special neighs/atom = 2.0000000
Neighbor list builds = 89191
Dangerous builds = 0
Total wall time: 4:02:50

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# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 -0.00130466 18193.2 17742.3
200000 -0.027526 18951.4 17742.7
300000 -0.0459414 19629.2 17752.3
400000 -0.0857092 21019.8 17772.6
500000 -0.0982497 21457.5 17731.3
600000 -0.137334 23057.4 17808.5
700000 -0.170804 24395.7 17801
800000 -0.223064 26797.3 17738.8
900000 -0.261826 28800 17791.7
1000000 -0.286374 30143.5 17783.4
1100000 -0.349306 33728.2 17757.7
1200000 -0.408164 37435.9 17787.7
1300000 -0.496871 43896.5 17766.2
1400000 -0.602917 53115.7 17749.9
1500000 -0.72768 65474.3 17765
1600000 -0.793802 73873.7 17785.7
1700000 -0.912421 92487.7 17754.8
1800000 -1.02249 109518 17762.7
1900000 -1.12599 130115 17752.5
2000000 -1.2899 174891 17768.3

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LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526)
2 by 2 by 3 MPI processor grid
reading atoms ...
1800 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
1200 bonds
reading angles ...
600 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.019 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
600 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
find clusters CPU = 0.001 seconds
Setting atom values ...
3 settings made for charge
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25066829
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0030719151
estimated relative force accuracy = 9.250981e-06
using double precision FFTW3
3d grid and FFT values/proc = 3757 800
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313
5000 26.813 -5450.5713 1282.0681 -6732.6394 1325.6489 21834.91 -30297.994 307.43909 -699.90679 18234.717 0.98431826
10000 55.604067 -5588.263 1217.9162 -6806.1792 1414.4085 21633.044 -30301.477 292.05551 23.383255 17964.154 0.99914336
15000 85.625894 -5502.4932 1306.1963 -6808.6896 1448.9698 21589.863 -30300.506 313.22502 674.44388 17764.828 1.010354
20000 119.30994 -5551.8753 1255.7906 -6807.6659 1438.0508 21600.534 -30296.631 301.13775 626.57778 17521.241 1.0244003
25000 153.36332 -5513.3214 1262.2974 -6775.6188 1448.1692 21624.738 -30300.649 302.69809 1082.1686 17539.064 1.0233594
30000 185.73754 -5517.07 1232.0851 -6749.1552 1351.1278 21743.778 -30297.746 295.45321 -345.74832 17641.782 1.0174009
35000 219.88466 -5461.9885 1261.1109 -6723.0993 1320.5321 21811.17 -30298.154 302.41356 -633.99545 17793.771 1.0087106
40000 250.59178 -5478.4688 1259.9078 -6738.3767 1361.0965 21772.195 -30298.632 302.12507 251.40827 17555.015 1.0224295
45000 284.497 -5586.9018 1253.0148 -6839.9166 1368.2811 21661.619 -30296.221 300.47212 -485.67054 17692.537 1.0144823
50000 318.07759 -5566.6473 1284.4686 -6851.116 1421.3632 21574.213 -30298.299 308.01473 123.81461 17666.827 1.0159586
55000 342.2475 -5571.8668 1241.516 -6813.3827 1320.1575 21745.617 -30297.514 297.71471 -757.9971 17553.891 1.0224949
60000 369.92714 -5405.9904 1244.2976 -6650.288 1321.6833 21864.494 -30297.613 298.38174 -252.7118 17729.038 1.0123936
65000 400.90471 -5536.8199 1222.3639 -6759.1838 1335.2142 21756.337 -30299.402 293.12205 -425.71516 17495.348 1.0259165
70000 421.35603 -5552.3284 1260.2509 -6812.5793 1340.624 21697.664 -30296.839 302.20732 -845.04229 17882.237 1.0037204
75000 441.98615 -5494.066 1286.3299 -6780.3959 1404.289 21683.326 -30293.835 308.46107 382.75947 17905.291 1.002428
80000 462.4957 -5550.6324 1269.8456 -6820.4779 1356.8274 21698.112 -30298.489 304.50813 -534.46185 17874.446 1.0041579
85000 483.079 -5656.6158 1200.4648 -6857.0807 1457.2846 21562.254 -30300.6 287.87068 686.28181 17521.518 1.0243841
90000 510.58296 -5480.2188 1242.2417 -6722.4605 1325.1999 21772.005 -30296.2 297.88874 -353.59603 17662.908 1.016184
95000 531.29699 -5537.8929 1265.7042 -6803.5971 1376.1449 21683.369 -30297.657 303.51504 -263.8525 17673.753 1.0155605
100000 563.33023 -5538.2683 1254.8684 -6793.1367 1343.4731 21751.843 -30299.503 300.91662 -623.47098 17857.853 1.0050909
Loop time of 563.33 on 12 procs for 100000 steps with 1800 atoms
Performance: 15.337 ns/day, 1.565 hours/ns, 177.516 timesteps/s
94.5% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 284.09 | 305.4 | 330.52 | 90.7 | 54.21
Bond | 1.0744 | 1.1159 | 1.1633 | 3.1 | 0.20
Kspace | 101.59 | 125.93 | 147.73 | 141.3 | 22.35
Neigh | 22.44 | 22.466 | 22.486 | 0.3 | 3.99
Comm | 39.278 | 41.789 | 46.639 | 43.5 | 7.42
Output | 0.0012299 | 0.0012852 | 0.0017706 | 0.4 | 0.00
Modify | 42.543 | 55.366 | 62.194 | 102.3 | 9.83
Other | | 11.26 | | | 2.00
Nlocal: 150.000 ave 163 max 133 min
Histogram: 1 1 0 0 1 3 3 0 1 2
Nghost: 6108.25 ave 6187 max 6048 min
Histogram: 3 0 2 1 1 1 1 1 1 1
Neighs: 86944.1 ave 96258 max 75267 min
Histogram: 2 0 1 0 1 0 3 3 1 1
Total # of neighbors = 1043329
Ave neighs/atom = 579.62722
Ave special neighs/atom = 2.0000000
Neighbor list builds = 4470
Dangerous builds = 9
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25102555
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0035374557
estimated relative force accuracy = 1.0652943e-05
using double precision FFTW3
3d grid and FFT values/proc = 3328 648
FEP settings ...
temperature = 300.000000
tail no
1-1 charge
2-2 charge
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 8.592 | 8.613 | 8.629 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH
0 -5538.2733 1254.8684 -6793.1417 1343.4731 21794.974 -30342.64 300.91662 -475.71492 1.0050909 0 -0 0
5000 -5579.9374 1246.75 -6826.6874 1443.8973 21614.133 -30343.039 298.96983 785.16037 1.0322471 0.0025 -0.002119 0.0010595
10000 -5528.9995 1276.273 -6805.2725 1375.6345 21734.24 -30343.779 306.04943 -41.209531 1.0207823 0.005 -0.004238 0.002119
15000 -5506.4227 1270.5724 -6776.9951 1356.298 21760.893 -30339.74 304.68242 -483.58254 1.0055775 0.0075 -0.006357 0.0031785
20000 -5520.1985 1271.766 -6791.9645 1413.5454 21705.741 -30340.672 304.96864 -25.849632 0.9997261 0.01 -0.008476 0.004238
25000 -5538.0793 1260.547 -6798.6264 1362.2032 21772.012 -30341.973 302.27834 -32.008776 1.0238659 0.0125 -0.010595 0.0052975
30000 -5519.1594 1267.066 -6786.2254 1327.6996 21784.187 -30341.191 303.84159 -919.77668 0.99978921 0.015 -0.012714 0.006357
35000 -5565.8849 1244.6201 -6810.505 1384.6297 21700.099 -30337.317 298.45908 -41.645325 1.0154185 0.0175 -0.014833 0.0074165
40000 -5610.4882 1225.8647 -6836.3529 1416.9133 21661.893 -30343.456 293.96154 86.229199 1.0091158 0.02 -0.016952 0.008476
45000 -5609.3562 1208.1008 -6817.457 1387.4135 21711.193 -30343.791 289.70178 -101.30213 1.0155204 0.0225 -0.019071 0.0095355
50000 -5512.9435 1272.9818 -6785.9253 1379.4084 21746.829 -30342.184 305.2602 -12.658236 1.0143328 0.025 -0.02119 0.010595
55000 -5568.845 1249.4227 -6818.2677 1397.4685 21704.581 -30340.419 299.61074 -409.12372 0.99849506 0.0275 -0.023309 0.0116545
60000 -5519.3972 1216.5292 -6735.9264 1369.8115 21830.467 -30342.642 291.72291 117.70437 1.0138535 0.03 -0.025428 0.012714
65000 -5525.0539 1229.5034 -6754.5573 1354.6275 21755.174 -30340.101 294.8341 -462.0909 1.0102225 0.0325 -0.027547 0.0137735
70000 -5472.0836 1237.9936 -6710.0772 1352.7747 21872.795 -30340.246 296.87006 -5.9707079 1.010185 0.035 -0.029666 0.014833
75000 -5514.8966 1241.7822 -6756.6788 1369.2902 21788.901 -30344.123 297.77855 -36.505421 1.0055449 0.0375 -0.031785 0.0158925
80000 -5501.5809 1244.4839 -6746.0648 1406.1414 21762.858 -30338.116 298.42642 356.6391 1.0044866 0.04 -0.033904 0.016952
85000 -5522.8846 1243.4435 -6766.3281 1277.631 21834.13 -30341.071 298.17693 -1501.0557 1.0030405 0.0425 -0.036023 0.0180115
90000 -5521.2512 1226.9606 -6748.2118 1426.6301 21707.584 -30342.842 294.22434 431.61937 1.0037325 0.045 -0.038142 0.019071
95000 -5606.4261 1239.7565 -6846.1826 1458.2919 21603.577 -30341.265 297.2928 452.3491 1.0064454 0.0475 -0.040261 0.0201305
100000 -5526.6029 1244.4811 -6771.084 1442.7891 21665.95 -30338.28 298.42575 499.20413 1.0045851 0.05 -0.04238 0.02119
105000 -5589.4951 1234.4407 -6823.9358 1418.2214 21663.025 -30341.483 296.01807 101.88725 1.0139383 0.0525 -0.044499 0.0222495
110000 -5511.859 1262.1425 -6774.0015 1353.5279 21783.245 -30339.283 302.66093 -199.18931 1.0257755 0.055 -0.046618 0.023309
115000 -5647.3449 1229.413 -6876.758 1408.5179 21641.362 -30341.598 294.81243 -298.02921 1.0020969 0.0575 -0.048737 0.0243685
120000 -5449.7674 1281.3875 -6731.155 1304.5518 21888.494 -30341.641 307.27589 -694.089 1.0046108 0.06 -0.050856 0.025428
125000 -5430.3553 1247.5854 -6677.9407 1342.5284 21899.097 -30343.376 299.17016 125.17161 1.0091105 0.0625 -0.052975 0.0264875
130000 -5604.2229 1198.864 -6803.0869 1343.9437 21741.913 -30342.105 287.4868 -1029.1103 0.99252488 0.065 -0.055094 0.027547
135000 -5550.2149 1233.8869 -6784.1018 1298.4466 21844.496 -30341.697 295.88527 -1083.9932 1.0128891 0.0675 -0.057213 0.0286065
140000 -5526.9114 1246.4353 -6773.3466 1346.6874 21790.011 -30343.164 298.89435 -384.65885 1.0089922 0.07 -0.059332 0.029666
145000 -5594.7954 1213.2963 -6808.0917 1391.4251 21671.653 -30341.641 290.94766 -59.474002 1.0195886 0.0725 -0.061451 0.0307255
150000 -5580.5229 1259.8574 -6840.3803 1384.5548 21703.974 -30342.483 302.11297 -91.974674 1.0257584 0.075 -0.06357 0.031785
155000 -5566.2712 1230.138 -6796.4093 1366.5696 21707.576 -30336.313 294.98629 -482.01244 1.0070735 0.0775 -0.065689 0.0328445
160000 -5491.8647 1293.2326 -6785.0974 1386.5259 21718.735 -30343.487 310.11633 -89.376893 1.0093767 0.08 -0.067808 0.033904
165000 -5531.3681 1279.7729 -6811.1409 1354.4198 21753.203 -30342.651 306.88869 -392.95774 1.0134907 0.0825 -0.069927 0.0349635
170000 -5594.2308 1213.4715 -6807.7023 1482.6412 21600.249 -30341.895 290.98966 928.50126 1.0132201 0.085 -0.072046 0.036023
175000 -5519.3482 1257.2925 -6776.6407 1420.4909 21726.753 -30340.213 301.49792 254.94623 0.98901793 0.0875 -0.074165 0.0370825
180000 -5426.929 1250.4297 -6677.3587 1356.866 21886.349 -30343.3 299.85221 -245.8457 0.98302571 0.09 -0.076284 0.038142
185000 -5512.2746 1245.7072 -6757.9817 1380.9844 21794.2 -30342.884 298.71976 149.05128 1.0150091 0.0925 -0.078403 0.0392015
190000 -5449.1514 1266.5892 -6715.7406 1324.6562 21889.348 -30342.468 303.72725 -620.02591 1.0004189 0.095 -0.080522 0.040261
195000 -5479.3945 1315.5655 -6794.96 1485.0588 21649.278 -30344.957 315.47174 1314.4492 1.0231026 0.0975 -0.082641 0.0413205
200000 -5563.7047 1217.2005 -6780.9051 1358.0191 21745.737 -30342.731 291.88386 -588.88047 1.0064764 0.1 -0.08476 0.04238
205000 -5580.3808 1230.1745 -6810.5553 1411.4424 21686.461 -30344.166 294.99504 214.77057 1.0029345 0.1025 -0.086879 0.0434395
210000 -5498.3534 1242.7043 -6741.0576 1370.6141 21796.013 -30341.015 297.99966 -26.716679 1.0117516 0.105 -0.088998 0.044499
215000 -5458.5956 1250.9454 -6709.541 1395.6557 21783.461 -30338.225 299.97588 406.41699 1.0137518 0.1075 -0.091117 0.0455585
220000 -5626.602 1214.9754 -6841.5774 1473.3289 21571.914 -30341.748 291.3503 599.47976 1.0096167 0.11 -0.093236 0.046618
225000 -5600.5356 1224.9039 -6825.4395 1342.4891 21754.804 -30341.025 293.73115 -626.27228 1.0198862 0.1125 -0.095355 0.0476775
230000 -5454.9477 1275.1464 -6730.0941 1372.8993 21798.515 -30340.963 305.77926 154.34847 1.0029435 0.115 -0.097474 0.048737
235000 -5481.9555 1227.4931 -6709.4486 1352.587 21840.233 -30343.313 294.35203 -208.20676 1.0008406 0.1175 -0.099593 0.0497965
240000 -5558.573 1218.8864 -6777.4595 1385.8452 21752.45 -30343.537 292.28816 162.10969 1.0215047 0.12 -0.101712 0.050856
245000 -5520.9207 1225.4691 -6746.3898 1338.4141 21841.905 -30342.557 293.86667 -587.07136 0.99909027 0.1225 -0.103831 0.0519155
250000 -5469.8293 1274.8021 -6744.6315 1384.4128 21775.904 -30342.629 305.69671 64.465989 1.0105027 0.125 -0.10595 0.052975
255000 -5583.4632 1209.565 -6793.0282 1426.1758 21667.168 -30342.466 290.0529 515.82984 1.0156235 0.1275 -0.108069 0.0540345
260000 -5536.1405 1237.073 -6773.2135 1357.8241 21771.52 -30340.823 296.64929 -438.57147 1.0071049 0.13 -0.110188 0.055094
265000 -5611.0013 1237.3831 -6848.3844 1417.6236 21598.469 -30339.452 296.72365 -367.70672 0.99925355 0.1325 -0.112307 0.0561535
270000 -5551.1345 1227.3483 -6778.4827 1430.3281 21692.104 -30340.818 294.31731 287.00159 1.0010721 0.135 -0.114426 0.057213
275000 -5602.2651 1241.1358 -6843.4009 1391.9031 21673.697 -30343.58 297.62355 -264.79926 1.014186 0.1375 -0.116545 0.0582725
280000 -5505.2292 1277.7478 -6782.9769 1380.5349 21747.333 -30343.992 306.40307 39.871379 1.0224709 0.14 -0.118664 0.059332
285000 -5527.7736 1230.4336 -6758.2072 1397.1892 21732.299 -30342.417 295.05716 276.95418 1.0126839 0.1425 -0.120783 0.0603915
290000 -5450.4061 1265.2269 -6715.6329 1360.3141 21842.086 -30344 303.40057 207.59349 1.0147077 0.145 -0.122902 0.061451
295000 -5617.5993 1217.4105 -6835.0098 1487.1573 21606.767 -30340.365 291.93424 808.20982 1.0058589 0.1475 -0.125021 0.0625105
300000 -5543.8664 1236.4411 -6780.3075 1377.4792 21755.298 -30344.078 296.49776 -182.45633 1.0097782 0.15 -0.12714 0.06357
305000 -5609.1426 1227.6292 -6836.7719 1437.6073 21603.923 -30343.337 294.38468 575.20852 1.0196556 0.1525 -0.129259 0.0646295
310000 -5549.1828 1228.5889 -6777.7717 1394.6395 21691.45 -30340.369 294.61482 348.39727 1.0352996 0.155 -0.131378 0.065689
315000 -5535.243 1248.2444 -6783.4874 1342.2366 21792.192 -30343.483 299.32819 -625.73677 1.0050826 0.1575 -0.133497 0.0667485
320000 -5534.3687 1255.4471 -6789.8158 1391.0816 21739.717 -30344.081 301.05539 302.16436 1.0216155 0.16 -0.135616 0.067808
325000 -5471.3922 1279.3669 -6750.759 1350.9981 21795.148 -30342.392 306.79133 -197.30703 1.0143436 0.1625 -0.137735 0.0688675
330000 -5598.8232 1226.4651 -6825.2883 1398.7718 21677.079 -30344.7 294.10553 -213.61646 1.0148836 0.165 -0.139854 0.069927
335000 -5551.2529 1259.6937 -6810.9465 1387.3662 21685.187 -30344.308 302.07371 138.36812 1.0229544 0.1675 -0.141973 0.0709865
340000 -5614.9057 1204.9401 -6819.8458 1400.0625 21668.036 -30343.31 288.94385 -386.78257 0.99685483 0.17 -0.144092 0.072046
345000 -5520.3252 1245.9691 -6766.2942 1428.7502 21696.415 -30345.482 298.78256 768.45616 1.0192108 0.1725 -0.146211 0.0731055
350000 -5513.6753 1249.7279 -6763.4032 1284.3535 21864.411 -30343.729 299.68392 -1040.9933 1.0093189 0.175 -0.14833 0.074165
355000 -5547.2549 1244.5392 -6791.7941 1428.3735 21662.08 -30340.69 298.43968 593.10891 1.0193921 0.1775 -0.150449 0.0752245
360000 -5589.7133 1245.8181 -6835.5314 1358.8909 21676.184 -30346.212 298.74637 -615.61801 1.0169406 0.18 -0.152568 0.076284
365000 -5487.1246 1223.3024 -6710.427 1333.6832 21894.405 -30339.2 293.34711 -385.63992 0.99614598 0.1825 -0.154687 0.0773435
370000 -5557.3434 1261.7301 -6819.0735 1430.6594 21657.49 -30341.935 302.56204 256.97472 1.0130616 0.185 -0.156806 0.078403
375000 -5453.0587 1250.9921 -6704.0508 1417.9533 21782.943 -30342.475 299.98708 759.88581 1.005535 0.1875 -0.158925 0.0794625
380000 -5556.3547 1222.266 -6778.6207 1358.5536 21812.006 -30343.775 293.09858 -190.9931 1.0101874 0.19 -0.161044 0.080522
385000 -5501.4025 1265.3304 -6766.7328 1424.8468 21722.251 -30342.613 303.42538 676.19284 1.0082991 0.1925 -0.163163 0.0815815
390000 -5553.0922 1226.1248 -6779.217 1386.2701 21755.237 -30343.024 294.02392 -55.846714 1.0141611 0.195 -0.165282 0.082641
395000 -5464.7179 1292.5065 -6757.2245 1391.9142 21755.809 -30342.569 309.94221 143.63086 1.001399 0.1975 -0.167401 0.0837005
400000 -5552.2274 1226.6092 -6778.8365 1437.5354 21706.283 -30344.844 294.14007 383.64397 0.99717814 0.2 -0.16952 0.08476
405000 -5465.9964 1302.7208 -6768.7172 1272.3678 21868.849 -30344.642 312.39159 -1291.0003 1.0128426 0.2025 -0.171639 0.0858195
410000 -5502.6819 1234.6487 -6737.3307 1351.0308 21789.612 -30344.433 296.06795 -265.76646 1.0210657 0.205 -0.173758 0.086879
415000 -5633.7475 1231.4568 -6865.2043 1369.0122 21700.285 -30343.991 295.30253 -446.38607 1.0197817 0.2075 -0.175877 0.0879385
420000 -5501.9642 1301.7275 -6803.6917 1383.0254 21739.249 -30343.668 312.1534 167.94828 1.0154563 0.21 -0.177996 0.088998
425000 -5532.9109 1273.6513 -6806.5622 1353.034 21735.703 -30341.962 305.42074 -386.7674 1.0176249 0.2125 -0.180115 0.0900575
430000 -5610.4928 1229.6066 -6840.0994 1384.0534 21685.85 -30340.003 294.85885 -392.26296 1.0166946 0.215 -0.182234 0.091117
435000 -5485.4138 1292.946 -6778.3598 1331.4915 21809.953 -30343.379 310.04759 -684.00607 0.99728831 0.2175 -0.184353 0.0921765
440000 -5423.494 1275.8582 -6699.3523 1355.0802 21885.761 -30344.38 305.94996 -61.348045 1.0030785 0.22 -0.186472 0.093236
445000 -5543.7469 1262.7456 -6806.4925 1292.6629 21801.211 -30345.175 302.80557 -942.29675 1.019957 0.2225 -0.188591 0.0942955
450000 -5508.6756 1254.0646 -6762.7401 1336.3483 21793.153 -30345.515 300.72385 -424.30387 1.0135307 0.225 -0.19071 0.095355
455000 -5536.23 1241.0621 -6777.2921 1356.0154 21765.992 -30341.02 297.60588 -415.44019 1.013923 0.2275 -0.192829 0.0964145
460000 -5519.3214 1227.2661 -6746.5875 1350.5669 21793.876 -30345.691 294.2976 -838.27228 0.98835279 0.23 -0.194948 0.097474
465000 -5569.5398 1206.1409 -6775.6808 1341.3479 21779.493 -30347.065 289.2318 -1009.2997 0.98862235 0.2325 -0.197067 0.0985335
470000 -5477.9533 1252.9751 -6730.9284 1332.4765 21850.802 -30347.395 300.46261 -434.01812 1.0083102 0.235 -0.199186 0.099593
475000 -5454.9313 1285.8036 -6740.7349 1455.9404 21718.761 -30341.504 308.33485 1197.5128 1.018547 0.2375 -0.201305 0.1006525
480000 -5500.6228 1264.0646 -6764.6874 1416.1687 21720.5 -30344.339 303.12185 658.63999 1.0148714 0.24 -0.203424 0.101712
485000 -5487.2301 1267.1551 -6754.3852 1393.3235 21727.438 -30344.266 303.86296 203.85856 1.0140199 0.2425 -0.205543 0.1027715
490000 -5542.8719 1257.8965 -6800.7685 1425.7521 21626.135 -30342.879 301.64276 372.74667 1.0129528 0.245 -0.207662 0.103831
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500000 -5537.0419 1260.1365 -6797.1784 1368.6229 21717.765 -30341.664 302.17989 -282.78916 1.0246698 0.25 -0.2119 0.10595
505000 -5476.9332 1287.4238 -6764.357 1473.5981 21665.477 -30346.513 308.72338 1132.7688 1.0122147 0.2525 -0.214019 0.1070095
510000 -5467.851 1267.0655 -6734.9165 1378.6348 21778.869 -30344.441 303.84146 69.208146 1.0140451 0.255 -0.216138 0.108069
515000 -5551.9713 1245.7115 -6797.6828 1403.6528 21721.547 -30342.376 298.72079 364.60527 1.0219092 0.2575 -0.218257 0.1091285
520000 -5611.3897 1244.7924 -6856.1821 1408.031 21638.811 -30344.364 298.5004 190.73446 1.0278442 0.26 -0.220376 0.110188
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530000 -5490.5915 1254.3538 -6744.9453 1387.0893 21799.214 -30343.112 300.79321 143.30552 1.0061614 0.265 -0.224614 0.112307
535000 -5625.8769 1218.1946 -6844.0715 1520.0402 21545.685 -30344.513 292.12226 1447.1785 1.0166808 0.2675 -0.226733 0.1133665
540000 -5469.8413 1287.4258 -6757.2671 1334.5626 21829.046 -30343.092 308.72386 -673.21682 1.0017181 0.27 -0.228852 0.114426
545000 -5512.6863 1236.8449 -6749.5313 1318.7318 21858.112 -30344.481 296.5946 -863.71117 0.99129185 0.2725 -0.230971 0.1154855
550000 -5639.1715 1217.2608 -6856.4322 1434.9176 21593.482 -30346.132 291.89833 253.12123 1.0171626 0.275 -0.23309 0.116545
555000 -5519.0565 1267.6791 -6786.7356 1405.1048 21738.951 -30344.793 303.98862 48.101225 0.99694182 0.2775 -0.235209 0.1176045
560000 -5652.7174 1173.1335 -6825.851 1439.7187 21641.222 -30344.805 281.31664 253.14906 1.0090928 0.28 -0.237328 0.118664
565000 -5669.4656 1195.4457 -6864.9113 1456.9433 21573.732 -30345.136 286.66708 192.38017 1.0032964 0.2825 -0.239447 0.1197235
570000 -5497.9803 1237.3935 -6735.3738 1357.9081 21789.301 -30345.378 296.72614 -251.982 1.0069437 0.285 -0.241566 0.120783
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580000 -5490.5569 1271.9789 -6762.5359 1373.9183 21766.793 -30344.227 305.01971 17.578848 1.0172064 0.29 -0.245804 0.122902
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590000 -5488.4278 1288.5886 -6777.0164 1468.0208 21640.734 -30343.206 309.00269 759.61005 1.0084625 0.295 -0.250042 0.125021
595000 -5588.7416 1194.6582 -6783.3998 1372.9575 21791.426 -30342.728 286.47825 -143.90808 1.0132126 0.2975 -0.252161 0.1260805
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610000 -5549.338 1238.8653 -6788.2032 1429.9285 21684.29 -30344.283 297.07907 123.93393 0.98486733 0.305 -0.258518 0.129259
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620000 -5557.3108 1229.2075 -6786.5184 1428.7497 21675.082 -30342.962 294.76316 221.88021 0.99717009 0.31 -0.262756 0.131378
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630000 -5596.2646 1223.2613 -6819.5259 1310.3452 21748.215 -30349.483 293.33726 -956.30387 1.0193588 0.315 -0.266994 0.133497
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655000 -5512.6624 1274.7595 -6787.4218 1407.8255 21738.349 -30345.234 305.68648 315.34392 1.0159005 0.3275 -0.277589 0.1387945
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685000 -5488.859 1304.9527 -6793.8117 1364.554 21763.427 -30348.59 312.92679 -211.30923 1.0149918 0.3425 -0.290303 0.1451515
690000 -5504.5878 1248.5637 -6753.1515 1384.0982 21716.14 -30343.281 299.40474 -82.795916 1.0093095 0.345 -0.292422 0.146211
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1970000 -5460.8469 1294.812 -6755.6589 1403.377 21789.971 -30387.038 310.49507 67.767671 0.99695881 0.985 -0.834886 0.417443
1975000 -5562.7016 1276.5904 -6839.292 1381.4683 21781.499 -30385.8 306.12554 -104.19545 1.0255706 0.9875 -0.837005 0.4185025
1980000 -5519.6646 1253.4527 -6773.1173 1464.4023 21698.419 -30387.375 300.57712 1035.4507 1.0129337 0.99 -0.839124 0.419562
1985000 -5465.34 1288.7347 -6754.0747 1312.8409 21917.192 -30385.618 309.03772 -632.51392 1.0142034 0.9925 -0.841243 0.4206215
1990000 -5579.8472 1232.0079 -6811.8551 1325.3706 21848.546 -30387.507 295.43468 -736.79929 1.0087938 0.995 -0.843362 0.421681
1995000 -5474.4313 1277.8474 -6752.2787 1377.0964 21856.577 -30388.53 306.42697 -223.13166 0.99592342 0.9975 -0.845481 0.4227405
2000000 -5530.4657 1243.1127 -6773.5784 1448.1254 21758.477 -30388.792 298.09761 750.74861 1.0102049 1 -0.8476 0.4238
Loop time of 13807.9 on 12 procs for 2000000 steps with 1800 atoms
Performance: 12.515 ns/day, 1.918 hours/ns, 144.845 timesteps/s
95.3% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7308.6 | 8043.1 | 8855.3 | 457.7 | 58.25
Bond | 24.229 | 25.717 | 27.246 | 21.9 | 0.19
Kspace | 2227.1 | 3047.3 | 3772.6 | 744.0 | 22.07
Neigh | 525.14 | 526.08 | 527.05 | 2.6 | 3.81
Comm | 809.43 | 867.32 | 940.11 | 181.0 | 6.28
Output | 0.033333 | 0.034507 | 0.043203 | 1.4 | 0.00
Modify | 880.49 | 1047.6 | 1183.6 | 402.0 | 7.59
Other | | 250.7 | | | 1.82
Nlocal: 150.000 ave 167 max 140 min
Histogram: 2 3 2 0 2 0 0 1 1 1
Nghost: 6112.58 ave 6193 max 6037 min
Histogram: 3 0 2 0 0 3 1 1 0 2
Neighs: 87266.4 ave 94192 max 79682 min
Histogram: 2 0 1 0 1 4 2 0 0 2
Total # of neighbors = 1047197
Ave neighs/atom = 581.77611
Ave special neighs/atom = 2.0000000
Neighbor list builds = 89139
Dangerous builds = 0
Total wall time: 3:59:31

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# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
# remove hybrid if not necessary
pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0
pair_modify tail no
kspace_style pppm 1.0e-5
read_data data.lmp
pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hwh
pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Owh
pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Hw
pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 0.0 # Hwh Ow
pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 0.0 # Owh Owh
pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 0.0 # Owh Hw
pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 0.0 # Owh Ow
pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow
pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow
# minimize 1.0e-4 1.0e-6 100 1000
# reset_timestep 0
fix SHAKE all shake 0.0001 20 0 b 1
neighbor 2.0 bin
# neigh_modify delay 0 every 1 check yes
timestep 1.0
variable TK equal 300.0
variable PBAR equal 1.0
velocity all create ${TK} 12345
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 5000
set type 1*2 charge 0.0
run 100000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
fix ADAPT all adapt/fep 100000 &
pair lj/cut/soft lambda 1*2 3*4 v_lambda &
after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda
variable dlambda equal 0.05
compute FEP all fep ${TK} &
pair lj/cut/soft lambda 1*2 3*4 v_dlambda &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-lj.fep
run 2000000

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# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
# remove hybrid if not necessary
pair_style lj/cut/coul/long 12.0 12.0
pair_modify tail no
kspace_style pppm 1.0e-5
read_data data.lmp
pair_coeff 1 1 0.000000 1.000000 # Hwh Hwh
pair_coeff 1 2 0.000000 1.000000 # Hwh Owh
pair_coeff 1 3 0.000000 1.000000 # Hwh Hw
pair_coeff 1 4 0.000000 1.000000 # Hwh Ow
pair_coeff 2 2 0.155425 3.165500 # Owh Owh
pair_coeff 2 3 0.000000 1.000000 # Owh Hw
pair_coeff 2 4 0.155425 3.165500 # Owh Ow
pair_coeff 3 3 0.000000 1.000000 # Hw Hw
pair_coeff 3 4 0.000000 1.000000 # Hw Ow
pair_coeff 4 4 0.155425 3.165500 # Ow Ow
# minimize 1.0e-4 1.0e-6 100 1000
# reset_timestep 0
fix SHAKE all shake 0.0001 20 0 b 1
neighbor 2.0 bin
# neigh_modify delay 0 every 1 check yes
timestep 1.0
variable TK equal 300.0
variable PBAR equal 1.0
velocity all create ${TK} 12345
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 5000
set type 1*2 charge 0.0
run 100000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable qH equal 0.4238*v_lambda
variable qO equal -0.8476*v_lambda
fix ADAPT all adapt/fep 100000 &
atom charge 1 v_qH &
atom charge 2 v_qO &
after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_qO v_qH
variable dlambda equal 0.05
variable dqH equal 0.4238*v_dlambda
variable dqO equal -0.8476*v_dlambda
compute FEP all fep ${TK} &
atom charge 1 v_dqH &
atom charge 2 v_dqO &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01-q.fep
run 2000000

22
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# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.164332 13580.8 17770.4
200000 0.129134 14470.4 17769.5
300000 0.113694 14856.5 17741.9
400000 0.0945078 15445.3 17780.8
500000 0.0562545 16508.6 17735.1
600000 0.0490523 16733.2 17757.8
700000 -0.0236465 19372.6 17801.7
800000 -0.0387399 19901 17785.3
900000 -0.0718098 21703.2 17802.6
1000000 -0.118193 24005.7 17774.1
1100000 -0.170254 26527.3 17789.9
1200000 -0.297445 41864.5 17773.6
1300000 -0.431516 50576.8 17744
1400000 -0.467669 44025.5 17719.1
1500000 -0.317884 31440.4 17731.3
1600000 -0.218939 25792.6 17718.6
1700000 -0.107798 21322.2 17753.1
1800000 -0.0458874 19135.5 17706.5
1900000 -0.015392 18211.1 17744.9
2000000 -0.00224303 17811.3 17744.3

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LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526)
2 by 2 by 3 MPI processor grid
reading atoms ...
1800 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
1200 bonds
reading angles ...
600 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.033 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
600 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
find clusters CPU = 0.001 seconds
Setting atom values ...
3 settings made for charge
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25066829
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0030719151
estimated relative force accuracy = 9.250981e-06
using double precision FFTW3
3d grid and FFT values/proc = 3757 800
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 9.477 | 9.489 | 9.507 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 1344.0739 1251.046 93.027896 53.823145 30049.554 -30010.349 300 10284.878 24908.667 0.72058313
5000 26.829054 -5531.3966 1246.7673 -6778.164 1430.5662 21645.326 -30297.767 298.97398 343.00879 17939.671 1.0005069
10000 60.375331 -5491.2737 1280.0525 -6771.3262 1384.6297 21688.032 -30298.393 306.95574 -300.16806 18083.581 0.99254483
15000 94.076576 -5632.0108 1185.0761 -6817.0868 1373.1572 21657.834 -30299.165 284.18046 -509.30462 17853.507 1.0053356
20000 126.53271 -5557.9837 1273.3985 -6831.3822 1276.3348 21807.204 -30296.619 305.36012 -1423.8804 17810.87 1.0077422
25000 159.26926 -5561.3614 1271.5975 -6832.9588 1454.6816 21523.277 -30299.954 304.92823 245.53675 17839.133 1.0061456
30000 191.17362 -5569.1628 1224.4664 -6793.6292 1459.7735 21613.44 -30298.475 293.62623 1166.8411 17466.628 1.0276033
35000 225.54672 -5505.5765 1289.9333 -6795.5098 1374.8138 21675.444 -30297.568 309.32515 -277.00241 17845.641 1.0057787
40000 259.24748 -5529.8329 1222.5071 -6752.34 1368.482 21714.343 -30299.714 293.15639 -48.777351 17595.097 1.0201004
45000 292.69855 -5541.3772 1261.5499 -6802.9272 1371.5857 21681.912 -30295.814 302.51884 -335.65528 17817.714 1.0073551
50000 326.91392 -5573.7012 1222.2121 -6795.9133 1327.6979 21746.391 -30299.712 293.08565 -955.31142 17840.793 1.006052
55000 361.16613 -5449.164 1267.4384 -6716.6024 1412.1093 21720 -30299.63 303.9309 428.04385 18036.511 0.99513513
60000 393.91884 -5546.8912 1190.623 -6737.5143 1330.3252 21806.541 -30300.582 285.51061 -430.37809 17636.451 1.0177085
65000 428.22428 -5622.5584 1259.3301 -6881.8885 1509.1614 21478.163 -30299.496 301.98652 975.06072 17605.779 1.0194815
70000 462.45487 -5570.183 1218.0018 -6788.1847 1354.4694 21727.024 -30300.976 292.07602 -258.76822 17759.422 1.0106616
75000 496.90314 -5627.876 1230.7285 -6858.6045 1476.5693 21530.846 -30297.953 295.12788 553.50896 17749.215 1.0112428
80000 531.33879 -5494.2101 1259.607 -6753.8171 1380.283 21711.161 -30298.881 302.05292 211.62464 17627.074 1.0182499
85000 564.97941 -5519.5052 1245.7068 -6765.212 1413.8079 21662.496 -30297.084 298.71966 464.57065 17574.97 1.0212686
90000 597.70815 -5541.7394 1221.3799 -6763.1193 1438.245 21673.718 -30296.608 292.8861 594.92053 17785.328 1.0091894
95000 630.00979 -5506.2477 1292.8624 -6799.1101 1435.7457 21640.887 -30297.759 310.02754 746.74628 17535.628 1.0235599
100000 664.4401 -5517.294 1249.4101 -6766.7041 1435.9513 21681.832 -30299.249 299.60772 863.4493 17594.707 1.020123
Loop time of 664.44 on 12 procs for 100000 steps with 1800 atoms
Performance: 13.003 ns/day, 1.846 hours/ns, 150.503 timesteps/s
95.1% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 354.67 | 370.51 | 389.45 | 60.8 | 55.76
Bond | 1.2832 | 1.3258 | 1.3684 | 2.3 | 0.20
Kspace | 122.53 | 141.54 | 156.98 | 99.1 | 21.30
Neigh | 28.973 | 29.038 | 29.092 | 0.6 | 4.37
Comm | 42.452 | 45.845 | 51.532 | 54.0 | 6.90
Output | 0.0013313 | 0.0013703 | 0.0017405 | 0.3 | 0.00
Modify | 48.441 | 63.192 | 71.445 | 115.5 | 9.51
Other | | 12.99 | | | 1.95
Nlocal: 150.000 ave 163 max 141 min
Histogram: 2 3 2 0 1 0 1 0 2 1
Nghost: 6146.42 ave 6218 max 6094 min
Histogram: 3 3 0 0 0 0 4 0 1 1
Neighs: 87791.7 ave 98973 max 80440 min
Histogram: 2 0 3 3 0 2 0 1 0 1
Total # of neighbors = 1053500
Ave neighs/atom = 585.27778
Ave special neighs/atom = 2.0000000
Neighbor list builds = 4499
Dangerous builds = 9
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.2513327
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0034853969
estimated relative force accuracy = 1.0496169e-05
using double precision FFTW3
3d grid and FFT values/proc = 3328 648
FEP settings ...
temperature = 300.000000
tail no
lj/cut/soft lambda 1-2 3-4
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 9.472 | 9.556 | 10.27 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda
0 -5517.3031 1249.4101 -6766.7132 1435.9513 21762.036 -30379.462 299.60772 824.0149 1.020123 1
5000 -5558.3835 1278.7173 -6837.1007 1334.2641 21745.448 -30378.941 306.63556 -767.88312 1.0259151 0.9975
10000 -5536.0094 1281.998 -6818.0074 1400.7848 21722.638 -30382.662 307.42228 286.89597 1.0190965 0.995
15000 -5481.3474 1257.9731 -6739.3206 1399.5036 21761.099 -30377.92 301.66113 181.6173 1.0045157 0.9925
20000 -5576.3444 1286.5841 -6862.9285 1415.5303 21648.92 -30380.138 308.52201 -153.48635 1.0085717 0.99
25000 -5514.2625 1300.4887 -6814.7513 1407.9812 21728.21 -30379.084 311.85634 425.39113 1.018525 0.9875
30000 -5547.7134 1261.8317 -6809.5451 1380.2714 21733.843 -30375.593 302.58642 -17.777892 1.0150161 0.985
35000 -5477.5978 1281.4333 -6759.0311 1368.0059 21793.139 -30378.187 307.28686 -71.109919 1.0111779 0.9825
40000 -5508.6633 1240.2261 -6748.8893 1315.5039 21866.643 -30379.36 297.40539 -903.80351 1.0010855 0.98
45000 -5549.0382 1255.1907 -6804.2289 1427.4722 21710.804 -30378.942 300.9939 585.69847 1.0195923 0.9775
50000 -5475.0264 1312.3734 -6787.3998 1297.1559 21838.086 -30379.004 314.70627 -1273.035 1.0008054 0.975
55000 -5491.7123 1248.8257 -6740.538 1363.4371 21862.536 -30380.311 299.46758 99.128465 1.0180508 0.9725
60000 -5609.488 1190.986 -6800.474 1436.0545 21719.642 -30378.046 285.59765 701.33839 1.0113551 0.97
65000 -5518.7824 1259.5561 -6778.3385 1358.5984 21791.343 -30380.334 302.04072 -321.61092 1.023541 0.9675
70000 -5494.8931 1242.4517 -6737.3448 1305.9749 21912.178 -30379.338 297.9391 -630.02692 1.0139124 0.965
75000 -5546.698 1230.9889 -6777.6869 1335.3375 21837.661 -30375.416 295.19033 -852.37291 0.9905341 0.9625
80000 -5539.855 1242.8348 -6782.6898 1419.4903 21739.313 -30377.932 298.03096 412.87427 1.01156 0.96
85000 -5539.3458 1252.4243 -6791.7701 1324.7893 21793.186 -30381.357 300.33052 -863.18781 1.008687 0.9575
90000 -5481.581 1307.2598 -6788.8408 1346.6475 21844.712 -30381.327 313.48005 -408.54122 1.0084955 0.955
95000 -5529.9471 1250.3938 -6780.3409 1375.6186 21766.839 -30380.379 299.84361 -208.47283 1.0041284 0.9525
100000 -5611.8507 1205.3447 -6817.1954 1432.4671 21667.619 -30379.262 289.04087 575.38545 1.0196531 0.95
105000 -5516.1732 1249.0519 -6765.2251 1510.0799 21652.904 -30376.319 299.52182 1595.0527 1.0142387 0.9475
110000 -5465.4173 1258.6931 -6724.1103 1349.0925 21850.539 -30376.601 301.83377 -603.2308 0.98281583 0.945
115000 -5551.5788 1260.591 -6812.1698 1512.1661 21629.589 -30379.324 302.28889 1408.8013 1.0119216 0.9425
120000 -5507.219 1271.1602 -6778.3792 1287.9978 21860.629 -30381.307 304.82338 -1063.0529 1.0271704 0.94
125000 -5537.13 1258.8105 -6795.9405 1382.8613 21762.733 -30377.383 301.86193 -158.02523 1.0108426 0.9375
130000 -5549.0946 1266.6866 -6815.7812 1372.5433 21748.74 -30377.189 303.75061 -643.27667 0.99432531 0.935
135000 -5573.4448 1286.5394 -6859.9842 1446.9417 21606.202 -30379.095 308.51131 579.59371 1.0183103 0.9325
140000 -5486.2607 1218.2948 -6704.5555 1391.8317 21866.056 -30379.705 292.14629 239.66325 1.0017938 0.93
145000 -5528.1392 1237.3437 -6765.4829 1343.2831 21851.228 -30378.61 296.71421 -443.27605 1.0094072 0.9275
150000 -5524.9227 1258.9283 -6783.851 1371.8204 21782.513 -30377.396 301.89018 -100.72793 1.0162581 0.925
155000 -5559.5874 1249.0683 -6808.6557 1298.8221 21822.678 -30380.108 299.52576 -1283.9404 1.0098295 0.9225
160000 -5574.1599 1259.0423 -6833.2022 1386.5012 21768.271 -30378.898 301.91751 -274.81981 1.0036715 0.92
165000 -5558.2274 1268.7313 -6826.9587 1366.6284 21720.826 -30379.54 304.24093 -723.57468 1.0031713 0.9175
170000 -5558.0458 1243.1304 -6801.1762 1359.415 21794.026 -30377.538 298.10185 -284.08503 1.0125849 0.915
175000 -5557.9939 1250.5207 -6808.5146 1344.1211 21819.765 -30375.934 299.87403 -742.04372 1.008519 0.9125
180000 -5562.2438 1245.4126 -6807.6564 1442.5917 21688.098 -30381.444 298.64912 834.40431 1.0283372 0.91
185000 -5494.5329 1238.0904 -6732.6233 1374.4489 21815.526 -30379.394 296.89325 -127.96552 1.0129962 0.9075
190000 -5512.3632 1282.3603 -6794.7235 1331.0347 21826.906 -30381.177 307.50916 -975.48387 0.99030439 0.905
195000 -5555.5139 1268.6099 -6824.1238 1579.0357 21509.544 -30380.501 304.21181 2298.8088 1.0238224 0.9025
200000 -5561.6068 1235.0747 -6796.6815 1341.7814 21791.238 -30377.819 296.1701 -569.19717 1.0181737 0.9
205000 -5408.9255 1277.421 -6686.3465 1384.0288 21847.016 -30376.919 306.3247 306.84932 1.0058379 0.8975
210000 -5574.4209 1249.0534 -6823.4743 1390.0917 21708.289 -30375.252 299.52217 -137.92578 1.020659 0.895
215000 -5533.5343 1256.0469 -6789.5812 1397.7965 21759.307 -30379.639 301.19922 -167.33553 0.99448086 0.8925
220000 -5525.1497 1272.4337 -6797.5834 1349.1947 21798.064 -30375.86 305.12875 -636.29714 1.0040906 0.89
225000 -5504.1279 1280.7318 -6784.8598 1373.0777 21811.329 -30381.594 307.11864 -109.03674 1.0126578 0.8875
230000 -5556.0721 1227.0604 -6783.1325 1460.4513 21700.918 -30378.062 294.24828 1031.1913 1.0144785 0.885
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255000 -5527.2234 1305.1549 -6832.3783 1450.6004 21675.372 -30380.236 312.97529 568.31787 1.0194011 0.8725
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365000 -5589.4166 1229.8012 -6819.2178 1445.1399 21656.389 -30379.255 294.90552 421.5138 1.0090829 0.8175
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375000 -5552.4603 1258.4199 -6810.8802 1378.5865 21748.986 -30378.675 301.76827 -383.52078 0.99353397 0.8125
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385000 -5555.4347 1224.5956 -6780.0303 1375.7528 21743.978 -30382.275 293.65722 150.61285 1.033997 0.8075
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1760000 -5403.3906 1295.0506 -6698.4412 1376.6218 21890.749 -30379.696 310.55227 307.40852 1.0147058 0.12
1765000 -5516.242 1249.2409 -6765.4828 1382.647 21758.198 -30377.246 299.56714 167.93234 1.0231885 0.1175
1770000 -5582.0367 1264.8589 -6846.8955 1451.9857 21613.33 -30377.524 303.31232 595.73197 1.0185845 0.115
1775000 -5537.7575 1229.4186 -6767.1761 1369.0153 21805.496 -30381.159 294.81376 13.517698 1.0260482 0.1125
1780000 -5494.5434 1303.1737 -6797.7171 1436.2813 21746.59 -30380.854 312.50019 737.63948 1.019697 0.11
1785000 -5506.8968 1245.4135 -6752.3103 1381.9664 21814.635 -30377.185 298.64934 53.072035 1.0092991 0.1075
1790000 -5570.6629 1257.0357 -6827.6986 1389.5682 21752.819 -30378.813 301.43633 -254.1322 1.0049075 0.105
1795000 -5403.0983 1313.5161 -6716.6144 1299.9894 21921.198 -30378.568 314.98029 -534.90063 1.0142742 0.1025
1800000 -5571.5716 1221.6883 -6793.2599 1459.5581 21671.077 -30379.985 292.96006 1199.0646 1.0291174 0.1
1805000 -5576.3609 1224.1212 -6800.4821 1353.5425 21807.985 -30380.553 293.54345 -387.59054 1.0179841 0.0975
1810000 -5606.1276 1268.2463 -6874.3738 1461.2712 21629.806 -30377.587 304.12462 705.686 1.032963 0.095
1815000 -5528.0175 1213.0379 -6741.0554 1404.3111 21772.221 -30376.182 290.88569 360.59394 1.0146256 0.0925
1820000 -5519.9749 1246.5714 -6766.5463 1333.2785 21832.117 -30376.792 298.927 -490.34561 1.0222947 0.09
1825000 -5445.4758 1293.818 -6739.2938 1310.9077 21908.662 -30376.428 310.25669 -505.90791 1.0175154 0.0875
1830000 -5541.7133 1258.3353 -6800.0486 1342.3151 21835.187 -30378.672 301.74797 -431.49631 1.0112617 0.085
1835000 -5455.3051 1261.9795 -6717.2846 1352.0659 21888.34 -30378.24 302.62186 -278.9793 1.0005135 0.0825
1840000 -5550.1255 1264.0761 -6814.2015 1457.0559 21643.406 -30381.124 303.12461 732.70062 1.0158677 0.08
1845000 -5534.0588 1215.4174 -6749.4762 1393.3056 21800.212 -30376.843 291.45629 318.75691 1.0144019 0.0775
1850000 -5470.5935 1240.7072 -6711.3007 1398.1611 21825.075 -30377.387 297.52076 246.47011 0.99682722 0.075
1855000 -5562.2126 1269.9488 -6832.1614 1405.7155 21717.318 -30382.767 304.5329 158.21904 1.0206821 0.0725
1860000 -5593.1478 1212.5719 -6805.7197 1431.8435 21688.522 -30377.259 290.77394 490.69887 1.0155469 0.07
1865000 -5547.7314 1230.6551 -6778.3865 1415.4128 21748.348 -30378.118 295.11029 184.13907 0.99833163 0.0675
1870000 -5530.8677 1219.9933 -6750.861 1379.1571 21831.652 -30375.929 292.55359 34.766398 1.0094217 0.065
1875000 -5568.1541 1254.3638 -6822.5179 1355.1579 21740.634 -30379.983 300.7956 -705.50446 1.0143892 0.0625
1880000 -5653.4584 1235.3915 -6888.8499 1430.7173 21633.442 -30379.735 296.24606 102.70794 1.0154835 0.06
1885000 -5465.2275 1218.1694 -6683.3969 1239.8122 21974.299 -30378.879 292.11621 -1526.9501 1.00297 0.0575
1890000 -5596.8191 1179.0514 -6775.8705 1375.6822 21763.894 -30376.484 282.73574 -135.80694 1.0180663 0.055
1895000 -5465.5228 1216.5423 -6682.0651 1399.7408 21824.803 -30381.567 291.72604 189.86203 0.9918745 0.0525
1900000 -5525.4584 1268.983 -6794.4415 1386.5598 21763.346 -30379.48 304.30129 -147.74084 1.0101088 0.05
1905000 -5629.8529 1254.2275 -6884.0804 1455.3465 21571.828 -30380.574 300.76293 536.16177 1.0309795 0.0475
1910000 -5498.7043 1240.937 -6739.6413 1343.971 21867.501 -30378.531 297.57587 -307.05181 1.00532 0.045
1915000 -5489.6666 1266.2052 -6755.8718 1356.677 21815.921 -30373.873 303.63517 41.753289 1.0289101 0.0425
1920000 -5534.4011 1264.7423 -6799.1433 1414.4972 21675.646 -30381.358 303.28436 307.25885 1.030805 0.04
1925000 -5504.0398 1249.1105 -6753.1503 1407.4242 21780.765 -30377.439 299.53588 416.81022 1.0112989 0.0375
1930000 -5486.5931 1291.1596 -6777.7527 1380.6453 21793.976 -30378.396 309.61922 -167.68264 1.0083434 0.035
1935000 -5482.2055 1242.0698 -6724.2753 1296.2668 21881.772 -30378.102 297.84751 -1240.512 1.0083689 0.0325
1940000 -5413.7616 1287.0265 -6700.788 1300.618 21943.573 -30379.549 308.6281 -822.10018 0.9947525 0.03
1945000 -5618.7196 1214.3524 -6833.072 1410.8621 21689.242 -30381.323 291.2009 177.78285 1.0261522 0.0275
1950000 -5559.1869 1277.5888 -6836.7757 1384.1924 21715.907 -30380.281 306.36495 -269.07872 1.01053 0.025
1955000 -5556.8805 1290.1761 -6847.0566 1420.3306 21702.458 -30379.354 309.38338 63.181765 1.0037638 0.0225
1960000 -5536.3473 1288.352 -6824.6993 1333.2341 21766.427 -30380.118 308.94596 -956.94729 1.0098248 0.02
1965000 -5560.7629 1271.8239 -6832.5868 1394.6008 21745.026 -30375.628 304.98253 27.022116 1.014722 0.0175
1970000 -5571.8348 1246.9662 -6818.801 1368.7901 21728.521 -30376.246 299.02167 -642.85981 1.0038267 0.015
1975000 -5448.1873 1277.5391 -6725.7263 1376.1799 21855.417 -30379.445 306.35302 158.55616 1.010898 0.0125
1980000 -5569.4362 1227.1456 -6796.5818 1384.1163 21747.316 -30379.52 294.26871 -224.4952 1.0128917 0.01
1985000 -5490.1779 1256.3196 -6746.4975 1376.0987 21800.479 -30378.853 301.26461 -23.927186 1.0117616 0.0075
1990000 -5568.4743 1216.0821 -6784.5564 1365.6444 21804.572 -30380.078 291.61568 -40.531986 1.024747 0.005
1995000 -5623.9072 1244.7555 -6868.6627 1444.7105 21613.58 -30377.599 298.49155 401.54781 1.0221617 0.0025
2000000 -5564.5636 1253.8102 -6818.3738 1394.5734 21742.16 -30376.703 300.66286 -89.748646 1.0114229 0
Loop time of 13852.8 on 12 procs for 2000000 steps with 1800 atoms
Performance: 12.474 ns/day, 1.924 hours/ns, 144.375 timesteps/s
95.5% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7431.1 | 8143.6 | 8773.3 | 379.5 | 58.79
Bond | 24.35 | 26.055 | 27.801 | 23.2 | 0.19
Kspace | 2212.7 | 2764.8 | 3391.2 | 573.6 | 19.96
Neigh | 568.42 | 569.87 | 570.75 | 2.7 | 4.11
Comm | 806.14 | 866.5 | 930.63 | 180.1 | 6.26
Output | 0.032719 | 0.034078 | 0.041882 | 1.3 | 0.00
Modify | 964.98 | 1144.9 | 1300.5 | 428.3 | 8.26
Other | | 337 | | | 2.43
Nlocal: 150.000 ave 166 max 139 min
Histogram: 3 0 2 0 2 3 0 0 1 1
Nghost: 6125.92 ave 6158 max 6091 min
Histogram: 1 1 0 2 1 2 2 1 1 1
Neighs: 87012.7 ave 102741 max 79216 min
Histogram: 2 1 2 3 3 0 0 0 0 1
Total # of neighbors = 1044152
Ave neighs/atom = 580.08444
Ave special neighs/atom = 2.0000000
Neighbor list builds = 89145
Dangerous builds = 0
Total wall time: 4:01:57

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# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 1.45025 1741.09 17759.6
200000 1.34275 2079.09 17751.2
300000 1.11463 3077.67 17744.5
400000 1.05072 3418.61 17752.1
500000 0.861524 4545.87 17736.9
600000 0.752417 5411.55 17755.8
700000 0.677848 6201.52 17715.7
800000 0.594413 7014.15 17718.2
900000 0.482601 8441.94 17738.8
1000000 0.44748 8942.75 17761.6
1100000 0.374076 9984.65 17731.4
1200000 0.310756 11050 17774.3
1300000 0.246639 12186.7 17783.6
1400000 0.201753 13117.8 17825.2
1500000 0.166052 13843.8 17784.7
1600000 0.136584 14486.5 17742.2
1700000 0.102778 15331.6 17778.7
1800000 0.0716746 16103 17743.1
1900000 0.0513218 16698.6 17801.1
2000000 0.0250996 17424.1 17780.5

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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (29.204526 29.204526 29.204526)
2 by 2 by 3 MPI processor grid
reading atoms ...
1800 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
1200 bonds
reading angles ...
600 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.020 seconds
Finding SHAKE clusters ...
0 = # of size 2 clusters
600 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
find clusters CPU = 0.001 seconds
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.2506685
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0030770287
estimated relative force accuracy = 9.2663804e-06
using double precision FFTW3
3d grid and FFT values/proc = 3757 800
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 8.214 | 8.226 | 8.244 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 1343.8082 1251.046 92.762256 53.823145 30098.377 -30059.438 300 10285.006 24908.667 0.72058313
5000 27.484029 -5481.5313 1291.2507 -6772.7821 1417.9265 21710.404 -30351.578 309.64107 573.94807 17792.658 1.0087737
10000 51.222479 -5557.9174 1247.8414 -6805.7588 1463.5652 21652.169 -30349.483 299.23155 1155.9001 17391.932 1.0320167
15000 81.534825 -5547.6429 1255.8047 -6803.4476 1434.9211 21679.801 -30351.564 301.14114 414.89266 17774.479 1.0098054
20000 108.19472 -5520.4365 1226.2567 -6746.6933 1363.6958 21763.102 -30350.115 294.05555 -159.5117 17640.377 1.017482
25000 139.47439 -5523.2547 1214.4617 -6737.7163 1403.2241 21727.256 -30347.421 291.2271 682.49951 17446.971 1.0287611
30000 173.52324 -5633.4887 1209.4695 -6842.9582 1384.9611 21696.903 -30350.921 290.02999 -439.40705 17870.41 1.0043846
35000 207.46148 -5609.1629 1202.7623 -6811.9252 1459.4041 21642.871 -30348.683 288.4216 870.04629 17620.845 1.0186098
40000 240.785 -5613.2727 1218.043 -6831.3157 1458.2338 21629.898 -30351.078 292.08591 578.74278 17728.011 1.0124523
45000 274.86574 -5567.9001 1234.3625 -6802.2626 1499.8464 21612.157 -30349.505 295.9993 1143.6708 17911.841 1.0020614
50000 308.33717 -5534.5804 1253.1529 -6787.7333 1383.4124 21740.111 -30349.237 300.50525 -236.43099 17808.85 1.0078565
55000 340.35767 -5558.5567 1237.2613 -6795.818 1472.1262 21640.69 -30349.9 296.69444 1169.6084 17518.859 1.0245396
60000 371.42788 -5620.3085 1217.3007 -6837.6091 1335.6617 21764.982 -30350.897 291.9079 -730.47206 17652.428 1.0167873
65000 400.4258 -5523.4332 1219.0927 -6742.5258 1377.9207 21790.846 -30351.438 292.33762 -67.377992 18008.535 0.99668103
70000 433.12056 -5549.9652 1278.9899 -6828.9551 1405.3901 21680.053 -30344.054 306.70094 -24.208971 17740.923 1.0117154
75000 465.43309 -5468.4134 1328.8758 -6797.2892 1404.3997 21721.55 -30346.155 318.66353 422.45424 17600.531 1.0197854
80000 498.33654 -5561.5506 1262.2191 -6823.7698 1375.8895 21728.477 -30350.941 302.67932 -480.08789 17936.63 1.0006765
85000 531.18843 -5561.7498 1243.7135 -6805.4633 1411.6336 21707.72 -30349.917 298.24169 31.756571 17844.951 1.0058176
90000 565.37172 -5548.2883 1305.5336 -6853.8219 1376.838 21698.95 -30345.634 313.06609 -580.39211 18032.442 0.99535964
95000 599.1335 -5491.6607 1249.0766 -6740.7373 1327.508 21805.341 -30346.173 299.52775 -747.34141 17928.72 1.001118
100000 632.97763 -5504.9781 1270.9776 -6775.9557 1348.4638 21759.337 -30349.51 304.7796 -112.23793 17469.352 1.0274431
Loop time of 632.978 on 12 procs for 100000 steps with 1800 atoms
Performance: 13.650 ns/day, 1.758 hours/ns, 157.983 timesteps/s
95.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 307.42 | 344.2 | 378.91 | 110.2 | 54.38
Bond | 1.1476 | 1.2339 | 1.3345 | 6.3 | 0.19
Kspace | 109.33 | 144.47 | 180.71 | 170.1 | 22.82
Neigh | 25.619 | 25.671 | 25.708 | 0.6 | 4.06
Comm | 41.234 | 45.135 | 50.464 | 52.8 | 7.13
Output | 0.0012664 | 0.001324 | 0.0018066 | 0.4 | 0.00
Modify | 46.059 | 59.064 | 69.016 | 114.7 | 9.33
Other | | 13.2 | | | 2.09
Nlocal: 150.000 ave 160 max 138 min
Histogram: 2 0 0 2 1 1 3 0 0 3
Nghost: 6169.08 ave 6215 max 6126 min
Histogram: 1 1 2 2 0 1 3 0 1 1
Neighs: 88745.0 ave 98807 max 82382 min
Histogram: 3 0 1 3 0 3 1 0 0 1
Total # of neighbors = 1064940
Ave neighs/atom = 591.63333
Ave special neighs/atom = 2.0000000
Neighbor list builds = 4480
Dangerous builds = 8
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.25148052
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0034663752
estimated relative force accuracy = 1.0438886e-05
using double precision FFTW3
3d grid and FFT values/proc = 3328 648
FEP settings ...
temperature = 300.000000
tail no
1-1 charge
2-2 charge
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 8.210 | 8.549 | 8.629 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_qO v_qH
0 -5504.9889 1270.9776 -6775.9665 1348.4638 21857.535 -30447.719 304.7796 -83.574867 1.0274431 1 -0.8476 0.4238
5000 -5524.9498 1270.0815 -6795.0313 1351.1305 21827.149 -30444.933 304.5647 -593.70775 1.005159 0.9975 -0.845481 0.4227405
10000 -5540.3394 1230.4582 -6770.7976 1419.9827 21833.217 -30447.512 295.06306 390.92433 1.0060179 0.995 -0.843362 0.421681
15000 -5552.7887 1238.4753 -6791.264 1335.4158 21841.316 -30448.525 296.98555 -977.57176 1.0018216 0.9925 -0.841243 0.4206215
20000 -5571.4362 1242.7492 -6814.1854 1430.7811 21758.542 -30446.37 298.01044 389.91739 1.0176182 0.99 -0.839124 0.419562
25000 -5460.6807 1271.7643 -6732.445 1445.8579 21824.91 -30444.435 304.96824 662.28347 0.99362968 0.9875 -0.837005 0.4185025
30000 -5454.6572 1289.2653 -6743.9226 1383.6837 21875.483 -30446.254 309.16498 76.696731 1.0117008 0.985 -0.834886 0.417443
35000 -5460.3689 1262.5044 -6722.8733 1424.7799 21854.486 -30444.887 302.74772 469.28759 0.99223648 0.9825 -0.832767 0.4163835
40000 -5617.7692 1259.5855 -6877.3547 1466.8238 21653.475 -30448.558 302.04777 518.56945 1.0149626 0.98 -0.830648 0.415324
45000 -5498.7892 1260.7599 -6759.5491 1354.8241 21911.823 -30445.433 302.32939 36.724958 1.0199193 0.9775 -0.828529 0.4142645
50000 -5556.2521 1276.3605 -6832.6126 1408.5453 21757.203 -30447.43 306.0704 38.976819 1.012915 0.975 -0.82641 0.413205
55000 -5513.8511 1239.4864 -6753.3375 1378.8961 21910.688 -30446.837 297.22802 -155.09229 0.99684598 0.9725 -0.824291 0.4121455
60000 -5482.86 1287.2484 -6770.1084 1383.4644 21876.85 -30446.035 308.68131 -23.984269 1.002056 0.97 -0.822172 0.411086
65000 -5556.4674 1243.4649 -6799.9323 1374.1364 21841.845 -30449.652 298.18207 13.80546 1.0185986 0.9675 -0.820053 0.4100265
70000 -5509.3689 1255.8787 -6765.2476 1342.6439 21905.378 -30448.437 301.15889 -636.57169 1.0013923 0.965 -0.817934 0.408967
75000 -5599.5463 1235.6343 -6835.1807 1391.5344 21779.525 -30444.409 296.3043 -272.25195 1.0096277 0.9625 -0.815815 0.4079075
80000 -5505.7102 1228.1399 -6733.8502 1402.1931 21862.826 -30444.663 294.50714 287.56695 1.007265 0.96 -0.813696 0.406848
85000 -5615.9836 1228.8806 -6844.8643 1412.2136 21728.301 -30447.357 294.68477 88.808898 1.0201101 0.9575 -0.811577 0.4057885
90000 -5445.8525 1286.0493 -6731.9017 1365.0964 21944.508 -30446.123 308.39376 -159.5813 0.99818678 0.955 -0.809458 0.404729
95000 -5555.6599 1255.1923 -6810.8522 1487.4112 21697.426 -30446.382 300.99428 1056.7026 1.0047794 0.9525 -0.807339 0.4036695
100000 -5423.2205 1299.4514 -6722.6719 1340.3931 21969.252 -30445.58 311.60759 -104.22862 1.0205672 0.95 -0.80522 0.40261
105000 -5510.0668 1219.7044 -6729.7712 1422.1714 21857.811 -30444.935 292.48431 965.21304 1.0267571 0.9475 -0.803101 0.4015505
110000 -5487.6062 1264.3775 -6751.9838 1383.7805 21872.105 -30438.176 303.19689 5.0812841 1.0038721 0.945 -0.800982 0.400491
115000 -5584.4825 1223.5314 -6808.0139 1305.413 21904.363 -30442.927 293.40202 -578.05444 1.0328242 0.9425 -0.798863 0.3994315
120000 -5523.0074 1287.4784 -6810.4858 1458.6493 21678.215 -30441.67 308.73646 671.54744 1.0055922 0.94 -0.796744 0.398372
125000 -5523.9631 1261.6061 -6785.5692 1451.4065 21774.541 -30440.463 302.5323 943.71106 1.023251 0.9375 -0.794625 0.3973125
130000 -5480.6587 1228.3138 -6708.9725 1318.5357 22013.43 -30444.357 294.54883 -484.16808 1.0024483 0.935 -0.792506 0.396253
135000 -5515.4922 1236.63 -6752.1222 1405.2286 21838.239 -30444.636 296.54306 -33.044871 0.99099073 0.9325 -0.790387 0.3951935
140000 -5636.9585 1190.5857 -6827.5442 1401.0211 21837.041 -30443.664 285.50167 -131.26918 1.0073498 0.93 -0.788268 0.394134
145000 -5520.4299 1242.8162 -6763.246 1425.5354 21801.806 -30441.82 298.02649 375.70839 1.0055963 0.9275 -0.786149 0.3930745
150000 -5466.2108 1221.5587 -6687.7695 1315.243 22002.492 -30445.561 292.92898 -458.87734 1.0111682 0.925 -0.78403 0.392015
155000 -5461.822 1239.1272 -6700.9492 1371.2953 21931.804 -30440.608 297.14189 404.63471 1.02125 0.9225 -0.781911 0.3909555
160000 -5581.5531 1235.5332 -6817.0862 1387.24 21799.458 -30439.508 296.28004 -313.78406 1.005984 0.92 -0.779792 0.389896
165000 -5518.8078 1273.6502 -6792.4581 1375.9673 21862.55 -30442.152 305.42049 -35.844433 1.0122448 0.9175 -0.777673 0.3888365
170000 -5515.2831 1285.6763 -6800.9594 1404.6207 21813.634 -30442.455 308.30433 -58.986086 1.010512 0.915 -0.775554 0.387777
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1450000 -5552.4255 1249.1142 -6801.5397 1361.7819 21785.875 -30399.912 299.53676 -769.48208 0.99105462 0.275 -0.23309 0.116545
1455000 -5517.8609 1220.2712 -6738.1321 1363.8136 21853.35 -30402.958 292.62024 -230.03249 1.0050729 0.2725 -0.230971 0.1154855
1460000 -5529.0421 1199.5637 -6728.6058 1281.1525 21947.817 -30402.254 287.65458 -1101.4619 1.0011538 0.27 -0.228852 0.114426
1465000 -5504.8124 1269.3051 -6774.1175 1397.0924 21778.739 -30400.882 304.37853 276.58705 1.0179163 0.2675 -0.226733 0.1133665
1470000 -5598.0732 1218.3941 -6816.4674 1418.8017 21718.631 -30401.044 292.17011 46.361297 1.0063797 0.265 -0.224614 0.112307
1475000 -5548.615 1254.4586 -6803.0737 1382.5152 21759.225 -30400 300.81835 -127.39812 1.0138223 0.2625 -0.222495 0.1112475
1480000 -5533.8343 1238.3003 -6772.1346 1436.9725 21759.67 -30400.105 296.94359 764.27767 1.0125907 0.26 -0.220376 0.110188
1485000 -5511.3105 1267.9695 -6779.28 1392.4351 21768.579 -30400.786 304.05824 -33.083281 1.008625 0.2575 -0.218257 0.1091285
1490000 -5492.7081 1249.7278 -6742.4359 1386.2265 21831.194 -30404.729 299.68391 167.62116 1.0065458 0.255 -0.216138 0.108069
1495000 -5565.5529 1257.6075 -6823.1605 1407.2006 21760.612 -30400.372 301.57346 -193.96975 0.99445457 0.2525 -0.214019 0.1070095
1500000 -5553.7271 1254.476 -6808.203 1411.4789 21739.068 -30400.776 300.82251 284.45877 1.0111814 0.25 -0.2119 0.10595
1505000 -5528.2919 1246.7404 -6775.0322 1494.6724 21668.724 -30400.534 298.96752 1503.5259 1.0199262 0.2475 -0.209781 0.1048905
1510000 -5529.2222 1256.6597 -6785.8818 1372.3032 21783.884 -30400.704 301.34616 -356.21245 1.0030809 0.245 -0.207662 0.103831
1515000 -5474.306 1292.5933 -6766.8993 1423.7446 21792.826 -30400.201 309.96302 458.75001 0.99603453 0.2425 -0.205543 0.1027715
1520000 -5533.15 1215.0608 -6748.2108 1345.4887 21859.918 -30402.082 291.37078 -574.91731 1.0075838 0.24 -0.203424 0.101712
1525000 -5534.3424 1275.3714 -6809.7138 1424.5986 21730.717 -30399.28 305.83323 403.09345 1.0170271 0.2375 -0.201305 0.1006525
1530000 -5594.0315 1228.3372 -6822.3687 1400.2671 21729.871 -30399.71 294.55445 -117.3201 1.0085693 0.235 -0.199186 0.099593
1535000 -5478.4978 1224.412 -6702.9097 1367.3472 21857.313 -30397.796 293.61318 -207.09591 1.0035875 0.2325 -0.197067 0.0985335
1540000 -5412.0571 1263.2997 -6675.3568 1365.2658 21913.322 -30400.612 302.93843 217.05159 1.0080531 0.23 -0.194948 0.097474
1545000 -5467.8087 1273.7408 -6741.5495 1392.9907 21826.459 -30393.776 305.44219 216.50192 1.0091255 0.2275 -0.192829 0.0964145
1550000 -5566.797 1224.1437 -6790.9407 1482.8048 21668.571 -30397.373 293.54885 729.69096 1.0040464 0.225 -0.19071 0.095355
1555000 -5497.5888 1259.6664 -6757.2552 1337.6561 21869.942 -30398.222 302.06718 -474.89321 1.0102649 0.2225 -0.188591 0.0942955
1560000 -5571.1541 1227.5401 -6798.6942 1443.2923 21702.982 -30401.053 294.36331 600.44478 1.0119193 0.22 -0.186472 0.093236
1565000 -5532.4484 1257.767 -6790.2154 1497.098 21657.763 -30398.914 301.61169 1582.7596 1.0279581 0.2175 -0.184353 0.0921765
1570000 -5491.3602 1250.8628 -6742.2231 1381.5334 21840.747 -30399 299.95608 319.87288 1.0172885 0.215 -0.182234 0.091117
1575000 -5448.4462 1268.2421 -6716.6883 1377.0235 21863.493 -30397.202 304.12362 -262.01917 0.98610142 0.2125 -0.180115 0.0900575
1580000 -5580.594 1226.2656 -6806.8595 1422.4858 21713.685 -30396.22 294.05768 357.25756 1.0113499 0.21 -0.177996 0.088998
1585000 -5541.0825 1278.2507 -6819.3331 1366.9139 21790.142 -30396.888 306.52367 -743.11524 0.98669546 0.2075 -0.175877 0.0879385
1590000 -5531.6035 1232.4292 -6764.0326 1395.465 21795.559 -30398.665 295.5357 42.444177 1.0126547 0.205 -0.173758 0.086879
1595000 -5461.4159 1287.0769 -6748.4928 1385.5573 21847.874 -30400.803 308.64018 618.18057 1.023846 0.2025 -0.171639 0.0858195
1600000 -5579.7572 1252.3883 -6832.1456 1403.3853 21764.717 -30403.163 300.3219 2.4209385 1.0090886 0.2 -0.16952 0.08476
1605000 -5491.6523 1248.6296 -6740.282 1420.4767 21788.29 -30399.543 299.42056 239.38793 0.99225234 0.1975 -0.167401 0.0837005
1610000 -5568.2821 1246.7876 -6815.0697 1370.1076 21752.385 -30399.233 298.97885 -468.73385 1.0081855 0.195 -0.165282 0.082641
1615000 -5530.1214 1224.1728 -6754.2942 1323.3884 21897.077 -30396.775 293.55582 -898.2112 0.99067847 0.1925 -0.163163 0.0815815
1620000 -5462.953 1253.936 -6716.889 1363.9087 21844.806 -30397.011 300.69303 49.460617 1.0189897 0.19 -0.161044 0.080522
1625000 -5568.5656 1231.6103 -6800.1759 1439.4406 21713.002 -30399.751 295.33933 590.45469 1.0150474 0.1875 -0.158925 0.0794625
1630000 -5513.0103 1230.3044 -6743.3148 1335.981 21895.338 -30397.086 295.02619 -710.37919 0.99994929 0.185 -0.156806 0.078403
1635000 -5580.5477 1231.076 -6811.6238 1376.4886 21798.044 -30400.814 295.21122 -206.8981 1.0081086 0.1825 -0.154687 0.0773435
1640000 -5540.3331 1256.5851 -6796.9181 1426.8142 21744.777 -30399.595 301.32827 745.57089 1.025877 0.18 -0.152568 0.076284
1645000 -5501.1298 1220.0238 -6721.1536 1389.073 21803.781 -30396.275 292.56091 131.20821 1.0089626 0.1775 -0.150449 0.0752245
1650000 -5628.1664 1220.696 -6848.8624 1362.9547 21731.445 -30400.636 292.7221 -616.61903 1.0201592 0.175 -0.14833 0.074165
1655000 -5592.5867 1211.2372 -6803.8239 1395.9179 21759.947 -30397.15 290.45388 18.913469 1.0103871 0.1725 -0.146211 0.0731055
1660000 -5428.2327 1278.6419 -6706.8747 1330.8879 21912.263 -30395.724 306.61749 -481.32774 0.99495838 0.17 -0.144092 0.072046
1665000 -5594.5998 1205.962 -6800.5618 1375.2659 21806.513 -30400.577 289.18889 -235.35107 1.0075357 0.1675 -0.141973 0.0709865
1670000 -5524.7971 1260.2713 -6785.0684 1344.6328 21851.941 -30396.671 302.21221 -544.14669 1.0114915 0.165 -0.139854 0.069927
1675000 -5468.1251 1274.7582 -6742.8834 1380.0088 21825.405 -30396.487 305.68618 38.686488 1.0120959 0.1625 -0.137735 0.0688675
1680000 -5473.7314 1242.9607 -6716.6921 1415.1549 21844.285 -30395.776 298.06116 641.25473 1.0114522 0.16 -0.135616 0.067808
1685000 -5636.5209 1211.507 -6848.0278 1459.7789 21659.328 -30400.565 290.51857 617.46049 1.0173888 0.1575 -0.133497 0.0667485
1690000 -5519.679 1240.1554 -6759.8344 1372.6554 21847.523 -30401.094 297.38845 -401.52343 0.99153655 0.155 -0.131378 0.065689
1695000 -5560.9528 1229.8902 -6790.843 1408.2004 21760.223 -30400.762 294.92687 100.67238 1.0033753 0.1525 -0.129259 0.0646295
1700000 -5554.1929 1255.6687 -6809.8616 1428.6747 21710.122 -30400.905 301.10854 159.06223 0.99158358 0.15 -0.12714 0.06357
1705000 -5542.8539 1230.6745 -6773.5285 1366.5362 21810.674 -30399.629 295.11494 -316.17067 0.99672752 0.1475 -0.125021 0.0625105
1710000 -5592.0441 1235.1898 -6827.2339 1407.2236 21724.16 -30397.816 296.19769 -171.98585 1.0010712 0.145 -0.122902 0.061451
1715000 -5456.289 1285.0566 -6741.3456 1366.6379 21844.445 -30394.859 308.15573 -103.28366 1.0059297 0.1425 -0.120783 0.0603915
1720000 -5492.3095 1254.7872 -6747.0967 1374.291 21873.54 -30397.737 300.89714 -10.335506 1.0122212 0.14 -0.118664 0.059332
1725000 -5518.9901 1240.2306 -6759.2207 1293.1765 21919.538 -30398.262 297.40649 -1112.3904 1.0060258 0.1375 -0.116545 0.0582725
1730000 -5461.6627 1250.9471 -6712.6098 1312.9461 21924.032 -30396.911 299.97629 -905.20686 0.99780548 0.135 -0.114426 0.057213
1735000 -5520.9229 1260.6697 -6781.5926 1351.3162 21851.369 -30398.186 302.30776 -380.34032 1.00967 0.1325 -0.112307 0.0561535
1740000 -5587.9319 1198.4018 -6786.3336 1377.0754 21811.513 -30398.588 287.37595 21.848644 1.019459 0.13 -0.110188 0.055094
1745000 -5548.2449 1238.1127 -6786.3576 1403.8402 21747.153 -30395.629 296.8986 135.03046 1.01201 0.1275 -0.108069 0.0540345
1750000 -5526.8784 1242.7978 -6769.6761 1309.8228 21913.235 -30398.337 298.02209 -850.35833 1.0059241 0.125 -0.10595 0.052975
1755000 -5508.0743 1308.7599 -6816.8341 1353.359 21760.125 -30400.191 313.83975 -749.9998 0.99685375 0.1225 -0.103831 0.0519155
1760000 -5542.8446 1265.3408 -6808.1854 1391.2186 21776.776 -30396.482 303.42789 117.90427 1.0236881 0.12 -0.101712 0.050856
1765000 -5526.6876 1268.5243 -6795.2119 1302.7664 21799.054 -30396.406 304.1913 -1161.5113 1.0216099 0.1175 -0.099593 0.0497965
1770000 -5579.5803 1246.8977 -6826.478 1486.5854 21651.454 -30399.954 299.00526 880.22447 1.0109541 0.115 -0.097474 0.048737
1775000 -5551.5053 1292.1271 -6843.6324 1405.0247 21688.07 -30398.863 309.85123 -251.03455 0.99873347 0.1125 -0.095355 0.0476775
1780000 -5515.8126 1282.9801 -6798.7927 1395.0164 21747.704 -30395.937 307.65779 333.80114 1.0239628 0.11 -0.093236 0.046618
1785000 -5510.7284 1208.8107 -6719.5391 1346.5399 21876.38 -30394.751 289.87201 -249.43776 1.0110945 0.1075 -0.091117 0.0455585
1790000 -5518.3081 1260.6355 -6778.9436 1399.7684 21796.94 -30397.3 302.29957 82.30008 1.0094344 0.105 -0.088998 0.044499
1795000 -5513.5389 1303.7533 -6817.2921 1421.97 21751.65 -30398.865 312.63917 500.03335 1.0096349 0.1025 -0.086879 0.0434395
1800000 -5572.7653 1214.8677 -6787.6331 1383.7533 21813.337 -30398.789 291.32448 -172.24736 1.0106323 0.1 -0.08476 0.04238
1805000 -5533.6069 1246.7853 -6780.3922 1412.9435 21800.334 -30394.707 298.97828 594.59696 1.0209456 0.0975 -0.082641 0.0413205
1810000 -5567.1324 1275.7954 -6842.9277 1442.9318 21676.766 -30398.215 305.93489 453.89649 1.0132054 0.095 -0.080522 0.040261
1815000 -5465.3294 1255.0662 -6720.3956 1341.0775 21912.58 -30394.54 300.96405 -302.59143 1.0016089 0.0925 -0.078403 0.0392015
1820000 -5588.4657 1233.5824 -6822.0481 1393.0967 21740.859 -30396.671 295.81224 -147.72631 1.0070758 0.09 -0.076284 0.038142
1825000 -5599.7235 1244.5645 -6844.288 1527.9294 21571.627 -30396.257 298.44576 1698.1117 1.0275341 0.0875 -0.074165 0.0370825
1830000 -5472.5833 1264.0019 -6736.5852 1327.0089 21908.977 -30394.568 303.10682 -394.05428 1.0135733 0.085 -0.072046 0.036023
1835000 -5559.5998 1243.4443 -6803.0442 1292.0778 21846.42 -30398.288 298.17713 -1254.4294 1.0141937 0.0825 -0.069927 0.0349635
1840000 -5498.5276 1283.2205 -6781.7481 1416.3308 21752.285 -30399.697 307.71542 317.53074 1.003693 0.08 -0.067808 0.033904
1845000 -5551.7395 1252.4882 -6804.2277 1374.7399 21772.215 -30396.489 300.34585 -263.50361 1.0114613 0.0775 -0.065689 0.0328445
1850000 -5525.5278 1240.7565 -6766.2843 1361.6208 21839.689 -30397.722 297.53259 -186.31575 1.0187838 0.075 -0.06357 0.031785
1855000 -5521.2867 1243.7856 -6765.0724 1347.4178 21874.625 -30396.108 298.25898 -284.75269 1.0228705 0.0725 -0.061451 0.0307255
1860000 -5640.4121 1146.9485 -6787.3606 1396.2408 21749.618 -30394.203 275.03749 -187.09544 1.006743 0.07 -0.059332 0.029666
1865000 -5525.2602 1260.9215 -6786.1817 1402.4348 21758.857 -30397.319 302.36813 -161.29785 0.99503244 0.0675 -0.057213 0.0286065
1870000 -5623.139 1216.967 -6840.1059 1413.5807 21703.495 -30397.576 291.82788 76.112007 1.0246491 0.065 -0.055094 0.027547
1875000 -5450.2615 1268.385 -6718.6465 1405.9759 21866.321 -30398.11 304.15789 307.93878 0.99773745 0.0625 -0.052975 0.0264875
1880000 -5539.8922 1245.1416 -6785.0337 1409.1823 21774.294 -30395.574 298.58413 82.127006 1.0058947 0.06 -0.050856 0.025428
1885000 -5514.3045 1240.5608 -6754.8653 1443.7995 21752.107 -30397.218 297.48566 611.17045 1.0085937 0.0575 -0.048737 0.0243685
1890000 -5438.3073 1258.3645 -6696.6718 1361.8049 21892.331 -30397.348 301.75497 -267.35927 0.9953092 0.055 -0.046618 0.023309
1895000 -5596.2731 1226.9718 -6823.2449 1402.9241 21732.185 -30395.165 294.22702 44.339776 1.0153331 0.0525 -0.044499 0.0222495
1900000 -5497.1413 1266.3676 -6763.5089 1373.9826 21832.991 -30399.356 303.67411 -27.290874 1.0132323 0.05 -0.04238 0.02119
1905000 -5517.4875 1236.6892 -6754.1767 1367.726 21857.698 -30393.874 296.55726 -499.76394 0.99284077 0.0475 -0.040261 0.0201305
1910000 -5552.0873 1269.7208 -6821.8081 1378.8021 21718.781 -30396.478 304.4782 -369.12045 1.0171861 0.045 -0.038142 0.019071
1915000 -5499.6451 1278.5051 -6778.1502 1430.6032 21725.761 -30396.795 306.58468 577.53122 1.01326 0.0425 -0.036023 0.0180115
1920000 -5487.2658 1251.9078 -6739.1736 1381.7635 21779.483 -30396.642 300.20666 -47.157489 1.0090288 0.04 -0.033904 0.016952
1925000 -5538.2174 1250.4348 -6788.6522 1378.1601 21776.002 -30397.01 299.85343 -635.20274 0.98963246 0.0375 -0.031785 0.0158925
1930000 -5539.4427 1260.8629 -6800.3057 1358.8021 21770.968 -30400.271 302.3541 -702.50699 0.99578271 0.035 -0.029666 0.014833
1935000 -5559.5408 1246.2889 -6805.8297 1426.6663 21737.226 -30396.429 298.85926 214.01347 1.0055051 0.0325 -0.027547 0.0137735
1940000 -5527.5821 1225.3364 -6752.9184 1378.8724 21850.255 -30395.169 293.83485 14.506752 1.0028753 0.03 -0.025428 0.012714
1945000 -5473.5551 1280.9318 -6754.4869 1425.106 21803.831 -30396.584 307.16659 506.19708 1.0032233 0.0275 -0.023309 0.0116545
1950000 -5567.2517 1222.2431 -6789.4948 1305.8232 21889.919 -30396.867 293.09308 -1294.1142 0.99788741 0.025 -0.02119 0.010595
1955000 -5484.5853 1260.6694 -6745.2547 1384.597 21831.404 -30392.929 302.30769 156.43697 1.0117059 0.0225 -0.019071 0.0095355
1960000 -5620.4544 1193.7438 -6814.1983 1383.8209 21783.257 -30401.598 286.25899 -66.845911 1.0220849 0.02 -0.016952 0.008476
1965000 -5545.5269 1233.4885 -6779.0154 1344.2005 21855.912 -30398.255 295.78973 -628.47314 1.0059777 0.0175 -0.014833 0.0074165
1970000 -5513.9042 1266.1527 -6780.057 1392.318 21762.753 -30395.542 303.62259 75.831811 1.0061881 0.015 -0.012714 0.006357
1975000 -5544.7648 1274.4083 -6819.1731 1391.4464 21746.624 -30396.103 305.60227 -75.461691 1.0034389 0.0125 -0.010595 0.0052975
1980000 -5538.5817 1248.0952 -6786.6769 1364.256 21830.009 -30395.903 299.2924 -83.978588 1.0205031 0.01 -0.008476 0.004238
1985000 -5595.8323 1230.885 -6826.7174 1357.6211 21780.506 -30393.427 295.16542 -709.11924 1.0035546 0.0075 -0.006357 0.0031785
1990000 -5482.4794 1286.6658 -6769.1452 1336.3899 21858.921 -30393.729 308.54161 -827.89365 1.0005728 0.005 -0.004238 0.002119
1995000 -5501.4886 1239.738 -6741.2266 1409.7478 21799.031 -30400.217 297.28836 653.89683 1.0202266 0.0025 -0.002119 0.0010595
2000000 -5611.4713 1229.0661 -6840.5373 1478.3644 21615.338 -30394.928 294.72923 480.97836 1.00402 0 -0 0
Loop time of 13776.2 on 12 procs for 2000000 steps with 1800 atoms
Performance: 12.543 ns/day, 1.913 hours/ns, 145.178 timesteps/s
95.3% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7579.8 | 8070.7 | 8564.2 | 287.6 | 58.58
Bond | 24.942 | 25.514 | 26.056 | 6.9 | 0.19
Kspace | 2484.3 | 2979.3 | 3459.7 | 467.2 | 21.63
Neigh | 523.25 | 524.15 | 525.06 | 2.5 | 3.80
Comm | 806.39 | 872.63 | 948.24 | 194.3 | 6.33
Output | 0.033634 | 0.034536 | 0.042227 | 1.2 | 0.00
Modify | 864.36 | 1044.2 | 1191.5 | 438.5 | 7.58
Other | | 259.6 | | | 1.88
Nlocal: 150.000 ave 158 max 141 min
Histogram: 1 0 0 2 2 3 2 1 0 1
Nghost: 6106.00 ave 6170 max 6046 min
Histogram: 2 1 1 1 0 1 2 2 1 1
Neighs: 86710.6 ave 92374 max 78975 min
Histogram: 1 0 0 3 0 3 1 0 2 2
Total # of neighbors = 1040527
Ave neighs/atom = 578.07056
Ave special neighs/atom = 2.0000000
Neighbor list builds = 89189
Dangerous builds = 0
Total wall time: 4:00:09

72
examples/USER/fep/SPCEhyd/fep10/in-fep10-lj.lmp Normal file
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@ -0,0 +1,72 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
# remove hybrid if not necessary
pair_style hybrid lj/cut/coul/long 12.0 12.0 lj/cut/soft 2 0.5 12.0
pair_modify tail no
kspace_style pppm 1.0e-5
read_data data.lmp
pair_coeff 1 1 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hwh
pair_coeff 1 2 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Owh
pair_coeff 1 3 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Hw
pair_coeff 1 4 lj/cut/soft 0.000000 1.000000 1.0 # Hwh Ow
pair_coeff 2 2 lj/cut/soft 0.155425 3.165500 1.0 # Owh Owh
pair_coeff 2 3 lj/cut/soft 0.000000 1.000000 1.0 # Owh Hw
pair_coeff 2 4 lj/cut/soft 0.155425 3.165500 1.0 # Owh Ow
pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000 # Hw Hw
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # Hw Ow
pair_coeff 4 4 lj/cut/coul/long 0.155425 3.165500 # Ow Ow
# minimize 1.0e-4 1.0e-6 100 1000
# reset_timestep 0
fix SHAKE all shake 0.0001 20 0 b 1
neighbor 2.0 bin
# neigh_modify delay 0 every 1 check yes
timestep 1.0
variable TK equal 300.0
variable PBAR equal 1.0
velocity all create ${TK} 12345
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 5000
set type 1*2 charge 0.0
run 100000
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
fix ADAPT all adapt/fep 100000 &
pair lj/cut/soft lambda 1*2 3*4 v_lambda &
after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda
variable dlambda equal -0.05
compute FEP all fep ${TK} &
pair lj/cut/soft lambda 1*2 3*4 v_dlambda &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10-lj.fep
run 2000000

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