ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'develop' of github.com:lammps/lammps into replicate_labelmap

Browse Source
This commit is contained in:
Germain Clavier
2023-11-28 12:09:57 +01:00
parent dcb4127631 bbef545675
commit d57979eede
839 changed files with 74835 additions and 24403 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
.github/CODEOWNERS vendored
View File

@ -61,6 +61,7 @@ src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
@ -135,6 +136,7 @@ src/timer.* @akohlmey
src/utils.* @akohlmey @rbberger
src/verlet.* @sjplimp @stanmoore1
src/math_eigen_impl.h @jewettaij
src/fix_press_langevin.* @Bibobu
# tools
tools/coding_standard/* @akohlmey @rbberger
@ -151,12 +153,12 @@ tools/vim/* @hammondkd
unittest/* @akohlmey
# cmake
cmake/* @rbberger
cmake/* @akohlmey
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
cmake/Modules/Packages/KIM.cmake @ellio167
cmake/presets/*.cmake @akohlmey
# python

22
.github/CONTRIBUTING.md vendored
View File

@ -5,9 +5,9 @@ Thank you for considering to contribute to the LAMMPS software project.
The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
Thus please also have a look at:
* [The guide for submitting new features in the LAMMPS manual](https://www.lammps.org/doc/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
## Table of Contents
@ -27,17 +27,17 @@ __
## 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 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 posted to a more general category.
> **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 Material Science Discourse forum](https://matsci.org/lammps). Before posting to the forum, please read the general [guidelines](https://www.lammps.org/guidelines.html) and the forum specific [suggestions](https://matsci.org/t/please-read-this-first-guidelines-and-suggestions-for-posting-lammps-questions/49913). Following those guidelines and suggestions will help greatly to get a helpful response. *Always* mention which LAMMPS version you are using. The MatSci website may be also used for discussions that would be off-topic for the LAMMPS categories. Those will just have to be posted to a different 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 or the forum, 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.
to one of the [LAMMPS core developers](https://www.lammps.org/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
The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://www.lammps.org/guidelines.html) to maximize your chances to receive a helpful response.
Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
@ -47,7 +47,7 @@ The LAMMPS Materials Science Discourse forum was created recently to facilitate
### 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.
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://www.lammps.org/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.
When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
@ -65,9 +65,9 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
and recommendations are in the following sections of the LAMMPS manual:
* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
## GitHub Workflows
@ -85,7 +85,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
### Pull Requests
Pull requests are the **only** way that changes get made to the LAMMPS distribution. So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub. Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request. That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub. If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
Immediately after the submission, the LAMMPS continuing integration server at https://ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub. If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you submitted a draft pull request, this will not happen unless you mark it "ready for review". If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository. As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.

6
.github/workflows/coverity.yml vendored
View File

@ -59,16 +59,13 @@ jobs:
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=SMALLBIG \
-D LAMMPS_EXCEPTIONS=off \
-D PKG_MESSAGE=on \
-D PKG_MPIIO=on \
-D PKG_ATC=on \
-D PKG_AWPMD=on \
-D PKG_BOCS=on \
-D PKG_EFF=on \
-D PKG_H5MD=on \
-D PKG_INTEL=on \
-D PKG_LATBOLTZ=on \
-D PKG_MANIFOLD=on \
-D PKG_MDI=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
@ -77,7 +74,6 @@ jobs:
-D PKG_PTM=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-D PKG_TALLY=on \
../cmake
- name: Run Coverity Scan

39
cmake/CMakeLists.txt
View File

@ -2,7 +2,6 @@
########################################
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.16)
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
@ -106,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
endif()
endif()
endif()
@ -159,17 +158,20 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version when
# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
if (PYTHON_EXECUTABLE)
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
endif()
# set path to python interpreter and thus enforcing python version when
# in a virtual environment and Python_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
" Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
" Setting Python interpreter to: ${Python_EXECUTABLE}")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@ -425,6 +427,18 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
PROPERTIES COMPILE_OPTIONS "-std=c++14")
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
@ -794,9 +808,6 @@ install(
###############################################################################
if(BUILD_SHARED_LIBS)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
if(BUILD_IS_MULTI_CONFIG)
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)

4
cmake/Modules/LAMMPSUtils.cmake
View File

@ -83,12 +83,12 @@ function(check_for_autogen_files source_dir)
file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${source_dir}/${FILENAME})
message(FATAL_ERROR "\n########################################################################\n"
"Found header file(s) generated by the make-based build system\n"
"Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"

6
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -50,8 +50,8 @@ 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/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -76,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.1.00 REQUIRED CONFIG)
find_package(Kokkos 4.2.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

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

@ -1,6 +1,6 @@
if(NOT Python_INTERPRETER)
# backward compatibility
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()

2
cmake/presets/kokkos-cuda.cmake
View File

@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

4
doc/Makefile
View File

@ -63,6 +63,7 @@ help:
@echo " anchor_check scan for duplicate anchor labels"
@echo " style_check check for complete and consistent style lists"
@echo " package_check check for complete and consistent package lists"
@echo " role_check check for misformatted role keywords"
@echo " spelling spell-check the manual"
# ------------------------------------------
@ -98,6 +99,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -179,6 +181,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -227,6 +230,7 @@ char_check :
role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 August 2023" "2023-08-2"
.TH LAMMPS "1" "21 November 2023" "2023-11-21"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 August 2023
\- Molecular Dynamics Simulator. Version 21 November 2023
.SH SYNOPSIS
.B lmp

26
doc/src/Build_extras.rst
View File

@ -626,22 +626,22 @@ They must be specified in uppercase.
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
* - VEGA900
* - AMD_GFX906
- GPU
- AMD GPU MI25 GFX900
* - VEGA906
- AMD GPU MI50/MI60
* - AMD_GFX908
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI100 GFX908
* - VEGA90A
- AMD GPU MI200
* - AMD_GFX942
- GPU
- AMD GPU MI200 GFX90A
* - NAVI1030
- AMD GPU MI300
* - AMD_GFX1030
- GPU
- AMD GPU V620/W6800
* - NAVI1100
* - AMD_GFX1100
- GPU
- AMD GPU RX7900XTX
* - INTEL_GEN
@ -666,7 +666,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.0.1 of the Kokkos library.
This list was last updated for version 4.2 of the Kokkos library.
.. tabs::
@ -1056,12 +1056,12 @@ additional details.
.. code-block:: bash
-D PYTHON_EXECUTABLE=path # path to Python executable to use
-D Python_EXECUTABLE=path # path to Python executable to use
Without this setting, CMake will guess the default Python version
on your system. To use a different Python version, you can either
create a virtualenv, activate it and then run cmake. Or you can
set the PYTHON_EXECUTABLE variable to specify which Python
set the Python_EXECUTABLE variable to specify which Python
interpreter should be used. Note note that you will also need to
have the development headers installed for this version,
e.g. python2-devel.

3
doc/src/Commands_pair.rst
View File

@ -220,7 +220,8 @@ OPT.
* :doc:`morse/soft <pair_fep_soft>`
* :doc:`multi/lucy <pair_multi_lucy>`
* :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
* :doc:`nb3b/harmonic <pair_nb3b>`
* :doc:`nb3b/screened <pair_nb3b>`
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`

4
doc/src/Commands_removed.rst
View File

@ -88,7 +88,7 @@ The same functionality is available through
MPIIO package
-------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
@ -107,7 +107,7 @@ see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
MSCG package
------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software

18
doc/src/Developer_unittest.rst
View File

@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called
"death tests". Here the LAMMPS code will operate differently depending
on whether it was configured to throw C++ exceptions on errors or call
either ``exit()`` or ``MPI_Abort()``. In the latter case, the test code
also needs to detect whether LAMMPS was compiled with the OpenMPI
library, as OpenMPI is **only** compatible the death test options of the
GoogleTest library when C++ exceptions are enabled; otherwise those
"death tests" must be skipped to avoid reporting bogus failures. The
specifics of this step are implemented in the ``TEST_FAILURE()``
macro. These tests operate by capturing the screen output when executing
the failing command and then comparing that with a provided regular
expression string pattern. Example:
The specifics of so-called "death tests", i.e. conditions where LAMMPS
should fail and throw an exception, are implemented in the
``TEST_FAILURE()`` macro. These tests operate by capturing the screen
output when executing the failing command and then comparing that with a
provided regular expression string pattern. Example:
.. code-block:: c++

15
doc/src/Fortran.rst
View File

@ -3038,14 +3038,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
This function can be used to query if an error inside of LAMMPS
has thrown a :ref:`C++ exception <exceptions>`.
.. note::
This function will always report "no error" when the LAMMPS library
has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
errors aborting LAMMPS into C++ exceptions. You can use the library
function :cpp:func:`lammps_config_has_exceptions` to check if this is
the case.
:to: :cpp:func:`lammps_has_error`
:r has_error: ``.TRUE.`` if there is an error.
:rtype has_error: logical
@ -3068,13 +3060,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
would happen only in a single MPI rank and thus may not be recoverable, as
other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
.. note::
This function will do nothing when the LAMMPS library has been
compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
LAMMPS into C++ exceptions. You can use the function
:f:func:`config_has_exceptions` to check whether this is the case.
:p character(len=\*) buffer: string buffer to copy the error message into
:o integer(c_int) status [optional]: 1 when all ranks had the error,
2 on a single-rank error.

6
doc/src/Howto_body.rst
View File

@ -170,9 +170,9 @@ with this body style to compute body/body and body/non-body interactions.
The *rounded/polygon* body style represents body particles as a 2d
polygon with a variable number of N vertices. This style can only be
used for 2d models; see the :doc:`boundary <boundary>` command. See the
"pair_style body/rounded/polygon" page for a diagram of two
squares with rounded circles at the vertices. Special cases for N = 1
(circle) and N = 2 (rod with rounded ends) can also be specified.
:doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>` page for
a diagram of two squares with rounded circles at the vertices. Special cases
for N = 1 (circle) and N = 2 (rod with rounded ends) can also be specified.
One use of this body style is for 2d discrete element models, as
described in :ref:`Fraige <body-Fraige>`.

2
doc/src/Howto_pylammps.rst
View File

@ -133,7 +133,7 @@ to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPYTHON_EXECUTABLE=$(which python)
cmake . -DPython_EXECUTABLE=$(which python)
# install LAMMPS package in virtualenv
(testing) make install-python

39
doc/src/Howto_structured_data.rst
View File

@ -119,6 +119,45 @@ for example :doc:`dump yaml <dump>` or :doc:`fix ave/time <fix_ave_time>`
Depending on the kind of data being written, organization of the data
or the specific syntax used may change, but the principles are very
similar and all files should be readable with a suitable YAML parser.
A simple example for this is given below:
.. code-block:: python
import yaml
try:
from yaml import CSafeLoader as YamlLoader
except ImportError:
from yaml import SafeLoader as YamlLoader
timesteps = []
with open("dump.yaml", "r") as f:
data = yaml.load_all(f, Loader=YamlLoader)
for d in data:
print('Processing timestep %d' % d['timestep'])
timesteps.append(d)
print('Read %d timesteps from yaml dump' % len(timesteps))
print('Second timestep: ', timesteps[1]['timestep'])
print('Box info: x: ' , timesteps[1]['box'][0], ' y:', timesteps[1]['box'][1], ' z:',timesteps[1]['box'][2])
print('First 5 per-atom columns: ', timesteps[1]['keywords'][0:5])
print('Corresponding 10th atom data: ', timesteps[1]['data'][9][0:5])
The corresponding output for a YAML dump command added to the "melt" example is:
.. parsed-literal::
Processing timestep 0
Processing timestep 50
Processing timestep 100
Processing timestep 150
Processing timestep 200
Processing timestep 250
Read 6 timesteps from yaml dump
Second timestep: 50
Box info: x: [0, 16.795961913825074] y: [0, 16.795961913825074] z: [0, 16.795961913825074]
First 5 per-atom columns: ['id', 'type', 'x', 'y', 'z']
Corresponding 10th atom data: [10, 1, 4.43828, 0.968481, 0.108555]
Processing scalar data with Python
----------------------------------

16
doc/src/Library.rst
View File

@ -80,13 +80,15 @@ run LAMMPS in serial mode.
:class: note
If the LAMMPS executable encounters an error condition, it will abort
after printing an error message. For a library interface this is
usually not desirable. Thus LAMMPS can be compiled to to :ref:`throw
a C++ exception <exceptions>` instead. If enabled, the library
functions will catch those exceptions and return. The error status
:cpp:func:`can be queried <lammps_has_error>` and an :cpp:func:`error
message retrieved <lammps_get_last_error_message>`. We thus
recommend enabling C++ exceptions when using the library interface,
after printing an error message. It does so by catching the
exceptions that LAMMPS could throw. For a C library interface this
is usually not desirable since the calling code might lack the
ability to catch such exceptions. Thus, the library functions will
catch those exceptions and return from the affected functions. The
error status :cpp:func:`can be queried <lammps_has_error>` and an
:cpp:func:`error message retrieved <lammps_get_last_error_message>`.
This is, for example used by the :doc:`LAMMPS python module
<Python_module>` and then a suitable Python exception is thrown.
.. admonition:: Using the C library interface as a plugin
:class: note

4
doc/src/Python_error.rst
View File

@ -15,9 +15,7 @@ Python exception handling mechanism.
try:
# LAMMPS will normally terminate itself and the running process if an error
# occurs. This would kill the Python interpreter. To avoid this, make sure to
# compile with LAMMPS_EXCEPTIONS enabled. This ensures the library API calls
# will not terminate the parent process. Instead, the library wrapper will
# occurs. This would kill the Python interpreter. The library wrapper will
# detect that an error has occured and throw a Python exception
lmp.command('unknown')

3
doc/src/Python_install.rst
View File

@ -5,8 +5,7 @@ The LAMMPS Python module enables calling the :ref:`LAMMPS C library API
<lammps_c_api>` from Python by dynamically loading functions in the
LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`. It is also recommended to
compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
compiled in :ref:`"shared" mode <exe>`.
Two components are necessary for Python to be able to invoke LAMMPS code:

2
doc/src/compute.rst
View File

@ -74,7 +74,7 @@ Global, per-atom, local, and per-grid quantities can also be of three
for each atom, each local entity, or each grid cell.
Note that a single compute can produce any combination of global,
per-atom, local, or per-grid values. Likewise it can prouduce any
per-atom, local, or per-grid values. Likewise it can produce any
combination of scalar, vector, or array output for each style. The
exception is that for per-atom, local, and per-grid output, either a
vector or array can be produced, but not both. The doc page for each

2
doc/src/compute_composition_atom.rst
View File

@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 21Nov2023
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,

6
doc/src/compute_property_atom.rst
View File

@ -128,9 +128,9 @@ Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these attributes. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
which are the "name" portion of these attributes. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.

2
doc/src/compute_property_grid.rst
View File

@ -61,7 +61,7 @@ varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *proc* attribute is the ID of the processor which owns the grid
cell. Processor IDs range from 0 to Nprocs - 1, where Nprocs is the

2
doc/src/compute_reduce.rst
View File

@ -201,7 +201,7 @@ information in this context, the *replace* keywords will extract the
atom IDs for the two atoms in the bond of maximum stretch. These atom
IDs and the bond stretch will be printed with thermodynamic output.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *inputs* keyword allows selection of whether all the inputs are
per-atom or local quantities. As noted above, all the inputs must be

4
doc/src/compute_voronoi_atom.rst
View File

@ -190,7 +190,7 @@ Voro++ software in the src/VORONOI/README file.
Output info
"""""""""""
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The *peratom* keyword was removed as it is no longer required.
@ -232,4 +232,4 @@ Related commands
Default
"""""""
The default for the neighobrs keyword is no.
The default for the neighbors keyword is no.

22
doc/src/dump.rst
View File

@ -613,7 +613,7 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package and the the corresponding "/mpiio" dump styles, except
for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
@ -805,16 +805,16 @@ computes, fixes, or variables when they are evaluated, so this is a very
general means of creating quantities to output to a dump file.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
in the range from 1 to :math:`M`, where :math:`M` is the number of
columns in the custom array). See the discussion above for how :math:`i`
can be specified with a wildcard asterisk to effectively specify
multiple values.
custom per-atom integer and floating-point vectors or arrays that have
been added via the :doc:`fix property/atom <fix_property_atom>`
command. When that command is used specific names are given to each
attribute which are the "name" portion of these keywords. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
:math:`i` is in the range from 1 to :math:`M`, where :math:`M` is the
number of columns in the custom array). See the discussion above for
how :math:`i` can be specified with a wildcard asterisk to effectively
specify multiple values.
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

2
doc/src/dump_image.rst
View File

@ -599,7 +599,7 @@ image will appear. The *sfactor* value must be a value 0.0 <=
*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
and *sfactor* = 0 is a rough non-shiny surface.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *fsaa* keyword can be used with the dump image command to improve
the image quality by enabling full scene anti-aliasing. Internally the

2
doc/src/fix.rst
View File

@ -106,7 +106,7 @@ Global, per-atom, local, and per-grid quantities can also be of three
for each atom, each local entity, or each grid cell.
Note that a single fix can produce any combination of global,
per-atom, local, or per-grid values. Likewise it can prouduce any
per-atom, local, or per-grid values. Likewise it can produce any
combination of scalar, vector, or array output for each style. The
exception is that for per-atom, local, and per-grid output, either a
vector or array can be produced, but not both. The doc page for each

4
doc/src/fix_adapt_fep.rst
View File

@ -307,7 +307,9 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
none
The keyword "scale yes" is not supported for scaling per-atom parameters
diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
Related commands
""""""""""""""""

6
doc/src/fix_atom_swap.rst
View File

@ -181,6 +181,12 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
This fix cannot be used with systems that do not have per-type masses
(e.g. atom style sphere) since the implemented algorithm pre-computes
velocity rescaling factors from per-type masses and ignores any per-atom
masses, if present. In case both, per-type and per-atom masses are
present, a warning is printed.
Related commands
""""""""""""""""

8
doc/src/fix_ave_chunk.rst
View File

@ -541,10 +541,10 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, `fix
:doc:ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate
:doc:<fix_ave_correlate>`, `fix ave/atogrid <fix_ave_grid>`
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
:doc:`fix ave/grid <fix_ave_grid>`
Default

4
doc/src/fix_ave_histo.rst
View File

@ -106,7 +106,7 @@ attributes are per-atom vector values. See the page for individual
generate.
Note that a compute or fix can produce multiple kinds of data (global,
per-atom, local). If LAMMPS cannot unambiguosly determine which kind
per-atom, local). If LAMMPS cannot unambiguously determine which kind
of data to use, the optional *kind* keyword discussed below can force
the desired disambiguation.
@ -263,7 +263,7 @@ keyword is set to *vector*, then all input values must be global or
per-atom or local vectors, or columns of global or per-atom or local
arrays.
The *kind* keyword only needs to be used if any of the specfied input
The *kind* keyword only needs to be used if any of the specified input
computes or fixes produce more than one kind of output (global,
per-atom, local). If not, LAMMPS will determine the kind of data all
the inputs produce and verify it is all the same kind. If not, an

59
doc/src/fix_deposit.rst
View File

@ -17,12 +17,16 @@ Syntax
* M = insert a single atom or molecule every M steps
* seed = random # seed (positive integer)
* one or more keyword/value pairs may be appended to args
* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units*
* keyword = *region* or *var* or *set* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units*
.. parsed-literal::
*region* value = region-ID
region-ID = ID of region to use as insertion volume
*var* value = name = variable name to evaluate for test of atom creation
*set* values = dim name
dim = *x* or *y* or *z*
name = name of variable to set with x, y, or z atom position
*id* value = *max* or *next*
max = atom ID for new atom(s) is max ID of all current atoms plus one
next = atom ID for new atom(s) increments by one for every deposition
@ -193,17 +197,19 @@ simulation that is "nearby" the chosen x,y position. In this context,
particles is less than the *delta* setting.
Once a trial x,y,z position has been selected, the insertion is only
performed if no current atom in the simulation is within a distance R
of any atom in the new particle, including the effect of periodic
boundary conditions if applicable. R is defined by the *near*
keyword. Note that the default value for R is 0.0, which will allow
atoms to strongly overlap if you are inserting where other atoms are
present. This distance test is performed independently for each atom
in an inserted molecule, based on the randomly rotated configuration
of the molecule. If this test fails, a new random position within the
insertion volume is chosen and another trial is made. Up to Q
attempts are made. If the particle is not successfully inserted,
LAMMPS prints a warning message.
performed if both the *near* and *var* keywords are satisfied (see below).
If either the *near* or the *var* keyword is not satisfied, a new random
position within the insertion volume is chosen and another trial is made.
Up to Q attempts are made. If one or more particle insertions are not
successful, LAMMPS prints a warning message.
The *near* keyword ensures that no current atom in the simulation is within
a distance R of any atom in the new particle, including the effect of
periodic boundary conditions if applicable. Note that the default value
for R is 0.0, which will allow atoms to strongly overlap if you are
inserting where other atoms are present. This distance test is performed
independently for each atom in an inserted molecule, based on the randomly
rotated configuration of the molecule.
.. note::
@ -214,6 +220,26 @@ LAMMPS prints a warning message.
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
.. versionadded:: 21Nov2023
The *var* and *set* keywords can be used together to provide a criterion
for accepting or rejecting the addition of an individual atom, based on its
coordinates. The *name* specified for the *var* keyword is the name of an
:doc:`equal-style variable <variable>` that should evaluate to a zero or
non-zero value based on one or two or three variables that will store the
*x*, *y*, or *z* coordinates of an atom (one variable per coordinate). If
used, these other variables must be :doc:`internal-style variables
<variable>` defined in the input script; their initial numeric value can be
anything. They must be internal-style variables, because this command
resets their values directly. The *set* keyword is used to identify the
names of these other variables, one variable for the *x*-coordinate of a
created atom, one for *y*, and one for *z*. When an atom is created, its
:math:`(x,y,z)` coordinates become the values for any *set* variable that
is defined. The *var* variable is then evaluated. If the returned value
is 0.0, the atom is not created. If it is non-zero, the atom is created.
For an example of how to use these keywords, see the
:doc:`create_atoms <create_atoms>` command.
The *rate* option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a
successively higher height over time. Note that this parameter is
@ -289,10 +315,11 @@ operation of the fix continues in an uninterrupted fashion.
The fix will try to detect it and stop with an error.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
fix. This fix computes a global scalar, which can be accessed by various
output commands. The scalar is the cumulative number of insertions. The
scalar value calculated by this fix is "intensive". 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
""""""""""""

16
doc/src/fix_pimd.rst
View File

@ -31,7 +31,7 @@ Syntax
.. parsed-literal::
*keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
*method* value = *nmpimd*
*method* value = *nmpimd* (default) or *pimd*
*integrator* value = *obabo* or *baoab*
*fmmode* value = *physical* or *normal*
*fmass* value = scaling factor on mass
@ -137,8 +137,6 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
the real particle.
.. note::
Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
for most PIMD applications for quantum thermodynamics purpose.
Motion of the centroid can be effectively uncoupled from the other
normal modes by scaling the fictitious masses to achieve a partial
@ -151,6 +149,16 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
only the k > 0 modes are thermostatted, not the centroid degrees of
freedom.
.. versionadded:: 21Nov2023
Mode *pimd* added to fix pimd/langevin.
Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*.
If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion.
The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian.
If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion.
The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian.
The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
either of the two should work fine.
@ -207,6 +215,7 @@ The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *p
be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
.. note::
The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
@ -269,6 +278,7 @@ related tasks for each of the partitions, e.g.
read_restart system_${ibead}.restart2
.. note::
Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
forces in the normal mode representation. If the Cartesian velocities and forces are
needed, it is easy to perform the transformation when doing post-processing.

5
doc/src/fix_pour.rst
View File

@ -245,8 +245,9 @@ produce the same behavior if you adjust the fix pour parameters
appropriately.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
fix. This fix computes a global scalar, which can be accessed by various
output commands. The scalar is the cumulative number of insertions. The
scalar value calculated by this fix is "intensive". 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>`.

51
doc/src/fix_srd.rst
View File

@ -61,25 +61,30 @@ Description
Treat a group of particles as stochastic rotation dynamics (SRD)
particles that serve as a background solvent when interacting with big
(colloidal) particles in groupbig-ID. The SRD formalism is described
in :ref:`(Hecht) <Hecht>`. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
bodies containing multiple spheroids or ellipsoids or line segments
or triangles. The collision and rotation properties of the model
imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
be run more quickly, to measure solute properties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as :doc:`fix deform <fix_deform>`,
:doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
can be used in conjunction with the SRD model.
in :ref:`(Hecht) <Hecht>`. The same methodology is also called
multi-particle collision dynamics (MPCD) in the literature.
For more details on how the SRD model is implemented in LAMMPS,
:ref:`(Petersen) <Petersen1>` describes the implementation and usage of
pure SRD fluids. See the ``examples/srd`` directory for sample input
scripts using SRD particles for that and for mixture systems (solute
particles in an SRD fluid).
The key idea behind using SRD particles as a cheap coarse-grained
solvent is that SRD particles do not interact with each other, but
only with the solute particles, which in LAMMPS can be spheroids,
ellipsoids, or line segments, or triangles, or rigid bodies containing
multiple spheroids or ellipsoids or line segments or triangles. The
collision and rotation properties of the model imbue the SRD particles
with fluid-like properties, including an effective viscosity. Thus
simulations with large solute particles can be run more quickly, to
measure solute properties like diffusivity and viscosity in a
background fluid. The usual LAMMPS fixes for such simulations, such
as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity
<fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`, can be
used in conjunction with the SRD model.
These 3 papers give more details on how the SRD model is implemented
in LAMMPS. :ref:`(Petersen) <Petersen1>` describes pure SRD fluid
systems. :ref:`(Bolintineanu1) <Bolintineanu1>` describes models
where pure SRD fluids interact with boundary walls.
:ref:`(Bolintineanu2) <Bolintineanu2>` describes mixture models where
large colloidal particles are solvated by an SRD fluid. See the
``examples/srd`` directory for sample input scripts.
This fix does two things:
@ -404,3 +409,13 @@ no, and rescale = yes.
**(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
Chem Phys, 132, 174106 (2010).
.. _Bolintineanu1:
**(Bolintineanu1)**
Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
.. _Bolintineanu2:
**(Bolintineanu2)** Bolintineanu, Grest, Lechman, Pierce, Plimpton,
Schunk, Comp Particle Mechanics, 1, 321-356 (2014).

4
doc/src/improper_amoeba.rst
View File

@ -68,8 +68,8 @@ for more info.
Related commands
""""""""""""""""
:doc:`improper_coeff <improper_coeff>`, `improper_harmonic
:doc:<improper_harmonic>`
:doc:`improper_coeff <improper_coeff>`,
:doc:`improper_harmonic <improper_harmonic>`
Default
"""""""

2
doc/src/pair_body_rounded_polyhedron.rst
View File

@ -40,7 +40,7 @@ rounded/polyhedron particles.
This pairwise interaction between the rounded polyhedra is described
in :ref:`Wang <pair-Wang>`, where a polyhedron does not have sharp corners
and edges, but is rounded at its vertices and edges by spheres
centered on each vertex with a specified diameter. The edges if the
centered on each vertex with a specified diameter. The edges of the
polyhedron are defined between pairs of adjacent vertices. Its faces
are defined by a loop of edges. The sphere diameter for each polygon
is specified in the data file read by the :doc:`read data <read_data>`

30
doc/src/pair_nb3b_harmonic.rst → doc/src/pair_nb3b.rst
View File

@ -1,14 +1,20 @@
.. index:: pair_style nb3b/harmonic
.. index:: pair_style nb3b/screened
pair_style nb3b/harmonic command
================================
pair_style nb3b/screened command
================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style nb3b/harmonic
pair_style style
* style = *nb3b/harmonic* or *nb3b/screened*
Examples
""""""""
@ -18,10 +24,14 @@ Examples
pair_style nb3b/harmonic
pair_coeff * * MgOH.nb3bharmonic Mg O H
pair_style nb3b/screened
pair_coeff * * PO.nb3b.screened P NULL O
pair_coeff * * SiOH.nb3b.screened Si O H
Description
"""""""""""
This pair style computes a non-bonded 3-body harmonic potential for the
The pair style *nb3b/harmonic* computes a non-bonded 3-body harmonic potential for the
energy E of a system of atoms as
.. math::
@ -33,7 +43,17 @@ prefactor. Note that the usual 1/2 factor is included in *K*\ . The form
of the potential is identical to that used in angle_style *harmonic*,
but in this case, the atoms do not need to be explicitly bonded.
Only a single pair_coeff command is used with this style which
Style *nb3b/screened* adds an additional exponentially decaying factor to
the harmonic term, given by
.. math::
E = K (\theta - \theta_0)^2 \exp \left(- \frac{r_{ij}}{\rho_{ij}} - \frac{r_{ik}}{\rho_{ik}} \right)
where :math:`\rho_ij` and :math:`\rho_ik` are the screening factors along
the two bonds. Note that the usual 1/2 factor is included in *K*.
Only a single pair_coeff command is used with these styles which
specifies a potential file with parameters for specified elements.
These are mapped to LAMMPS atom types by specifying N additional
arguments after the filename in the pair_coeff command, where N is the
@ -61,8 +81,8 @@ type 4 to the C element in the potential file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when the potential is used as part of the *hybrid* pair style. The
NULL values are placeholders for atom types that will be used with
other potentials. An example of a pair_coeff command for use with the
*hybrid* pair style is:
other potentials. Two examples of pair_coeff command for use with the
*hybrid* pair style are:
.. code-block:: LAMMPS

15
doc/src/pair_reaxff.rst
View File

@ -72,8 +72,7 @@ from LAMMPS after the 12 December 2018 version.
LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N.
documented in potentials/README.reax.
The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of *pair_style reaxff* potential
@ -110,12 +109,14 @@ control variable. The format of the control file is described below.
not agree.
Examples using *pair_style reaxff* are provided in the examples/reax
subdirectory.
directory and its subdirectories.
Use of this pair style requires that a charge be defined for every
atom. See the :doc:`atom_style <atom_style>` and
:doc:`read_data <read_data>` commands for details on how to specify
charges.
Use of this pair style requires using an :doc:`atom_style <atom_style>`
that includes a per-atom charge property *or* using
:doc:`fix property/atom q <fix_property_atom>`. Charges can be set
via :doc:`read_data <read_data>` or :doc:`set <set>`. Using an initial
charge that is close to the result of charge equilibration will speed
up that process.
The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.

3
doc/src/pair_style.rst
View File

@ -297,7 +297,8 @@ accelerated styles exist.
* :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential
* :doc:`nb3b/harmonic <pair_nb3b>` - non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened harmonic potential
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb

4
doc/src/region.rst
View File

@ -24,6 +24,7 @@ Syntax
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
c1,c2,radlo,radhi,lo,hi can be a variable (see below)
*cylinder* args = dim c1 c2 radius lo hi
dim = *x* or *y* or *z* = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
@ -206,7 +207,8 @@ equal-style :doc:`variable <variable>`. Likewise, for style *sphere*
and *ellipsoid* the x-, y-, and z- coordinates of the center of the
sphere/ellipsoid can be specified as an equal-style variable. And for
style *cylinder* the two center positions c1 and c2 for the location
of the cylinder axes can be specified as a equal-style variable.
of the cylinder axes can be specified as a equal-style variable. For style *cone*
all properties can be defined via equal-style variables.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be

2
doc/src/thermo_style.rst
View File

@ -442,7 +442,7 @@ equal-style and vector-style variables can be referenced; the latter
requires a bracketed term to specify the Ith element of the vector
calculated by the variable. However, an equal-style variable can use
an atom-style variable in its formula indexed by the ID of an
individual atom. This is a way to output a speciic atom's per-atom
individual atom. This is a way to output a specific atom's per-atom
coordinates or other per-atom properties in thermo output. See the
:doc:`variable <variable>` command for details. Note that variables
of style *equal* and *vector* and *atom* define a formula which can

102
doc/src/variable.rst
View File

@ -53,7 +53,7 @@ Syntax
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
@ -71,6 +71,7 @@ Syntax
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
variable references = v_name, v_name[i]
@ -514,38 +515,40 @@ is a valid (though strange) variable formula:
Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
functions, special functions, feature functions, atom values, atom
vectors, compute references, fix references, and references to other
vectors, custom atom properties, compute references, fix references, and references to other
variables.
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Most of the formula elements produce a scalar value. Some produce a
global or per-atom vector of values. Global vectors can be produced
@ -703,6 +706,13 @@ library. Ceil() is the smallest integer not less than its argument.
Floor() if the largest integer not greater than its argument. Round()
is the nearest integer to its argument.
.. versionadded:: TBD
The ternary(x,y,z) function is the equivalent of the ternary operator
(? and :) in C or C++. It takes 3 arguments. The first argument is a
conditional. The result of the function is y if x evaluates to true
(non-zero). The result is z if x evaluates to false (zero).
The ramp(x,y) function uses the current timestep to generate a value
linearly interpolated between the specified x,y values over the course
of a run, according to this formula:
@ -1034,10 +1044,9 @@ to built-in commands. For all of these styles except *command*,
appending of active suffixes is also tried before reporting failure.
The *feature* category checks the availability of the following
compile-time enabled features: GZIP support, PNG support, JPEG
support, FFMPEG support, and C++ exceptions for error
handling. Corresponding names are *gzip*, *png*, *jpeg*, *ffmpeg* and
*exceptions*\ .
compile-time enabled features: GZIP support, PNG support, JPEG support,
FFMPEG support, and C++ exceptions for error handling. Corresponding
names are *gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ .
Example: Only dump in a given format if the compiled binary supports it.
@ -1139,8 +1148,45 @@ defines molecule IDs.
Note that many other atom attributes can be used as inputs to a
variable by using the :doc:`compute property/atom
<compute_property_atom>` command and then specifying a quantity from
that compute.
<compute_property_atom>` command and then referencing that compute.
----------
Custom atom properties
----------------------
.. versionadded:: TBD
Custom atom properties refer to per-atom integer and floating point
vectors or arrays that have been added via the :doc:`fix property/atom
<fix_property_atom>` command. When that command is used specific
names are given to each attribute which are the "name" portion of
these references. References beginning with *i* and *d* refer to
integer and floating point properties respectively. Per-atom vectors
are referenced by *i_name* and *d_name*; per-atom arrays are
referenced by *i2_name* and *d2_name*.
The various allowed references to integer custom atom properties in
the variable formulas for equal-, vector-, and atom-style variables
are listed in the following table. References to floating point
custom atom properties are the same; just replace the leading "i" with
"d".
+--------+---------------+------------------------------------------+
| equal | i_name[I] | element of per-atom vector (I = atom ID) |
| equal | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| vector | i_name[I] | element of per-atom vector (I = atom ID) |
| vector | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| atom | i_name | per-atom vector |
| atom | i2_name[I] | column of per-atom array |
+--------+---------------+------------------------------------------+
The I and J indices in these custom atom property references can be
integers or can be a variable name, specified as v_name, where name is
the name of the variable. The rules for this syntax are the same as
for indices in the "Atom Values and Vectors" discussion above.
----------
@ -1167,7 +1213,7 @@ variables), or global vectors of values. The latter can also be a
column of a global array.
Atom-style variables can use scalar values (same as for equal-style
varaibles), or per-atom vectors of values. The latter can also be a
variables), or per-atom vectors of values. The latter can also be a
column of a per-atom array.
The various allowed compute references in the variable formulas for
@ -1183,7 +1229,7 @@ table:
+--------+------------+------------------------------------------+
| vector | c_ID | global vector |
| vector | c_ID[I] | column of global array |
---------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | c_ID | per-atom vector |
| atom | c_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+
@ -1232,7 +1278,7 @@ variables), or global vectors of values. The latter can also be a
column of a global array.
Atom-style variables can use scalar values (same as for equal-style
varaibles), or per-atom vectors of values. The latter can also be a
variables), or per-atom vectors of values. The latter can also be a
column of a per-atom array.
The allowed fix references in variable formulas for equal-, vector-,
@ -1247,7 +1293,7 @@ and atom-style variables are listed in the following table:
+--------+------------+------------------------------------------+
| vector | f_ID | global vector |
| vector | f_ID[I] | column of global array |
---------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | f_ID | per-atom vector |
| atom | f_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+

26
doc/utils/sphinx-config/LAMMPSLexer.py
View File

@ -76,12 +76,12 @@ class LAMMPSLexer(RegexLexer):
include('conditionals'),
include('keywords'),
(r'#.*?\n', Comment),
('"', String, 'string'),
('\'', String, 'single_quote_string'),
(r'"', String, 'string'),
(r'\'', String, 'single_quote_string'),
(r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
(r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
('\$?\(', Name.Variable, 'expression'),
('\$\{', Name.Variable, 'variable'),
(r'\$?\(', Name.Variable, 'expression'),
(r'\$\{', Name.Variable, 'variable'),
(r'[\w_\.\[\]]+', Name),
(r'\$[\w_]+', Name.Variable),
(r'\s+', Whitespace),
@ -97,21 +97,21 @@ class LAMMPSLexer(RegexLexer):
]
,
'variable' : [
('[^\}]+', Name.Variable),
('\}', Name.Variable, '#pop'),
(r'[^\}]+', Name.Variable),
(r'\}', Name.Variable, '#pop'),
],
'string' : [
('[^"]+', String),
('"', String, '#pop'),
(r'[^"]+', String),
(r'"', String, '#pop'),
],
'single_quote_string' : [
('[^\']+', String),
('\'', String, '#pop'),
(r'[^\']+', String),
(r'\'', String, '#pop'),
],
'expression' : [
('[^\(\)]+', Name.Variable),
('\(', Name.Variable, 'expression'),
('\)', Name.Variable, '#pop'),
(r'[^\(\)]+', Name.Variable),
(r'\(', Name.Variable, 'expression'),
(r'\)', Name.Variable, '#pop'),
],
'modify_cmd' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),

28
examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal Normal file
View File

@ -0,0 +1,28 @@
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

2
examples/PACKAGES/pimd/langevin_metal_units/in.lmp → examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal
View File

@ -16,7 +16,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100

2
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++
View File

@ -1,2 +1,2 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Running on 4 partitions of processors

52
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 0
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -29,10 +30,10 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 01
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
The barostat mass is W = 2.3401256650800001e+01
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,14 +44,13 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
@ -66,31 +66,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 0 -7.3046601 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
100 149.95804 3.8573359 0 -7.7921375 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
200 245.00113 6.3021074 0 -8.2639651 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
300 300.57486 7.7316177 0 -8.2986331 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
400 368.08438 9.4681493 0 -8.4800193 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
500 419.32066 10.786088 0 -8.640773 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
600 385.4127 9.9138817 0 -8.4356035 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
700 360.14242 9.2638601 0 -8.2900275 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
800 346.92167 8.923786 0 -8.0694169 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
900 364.39442 9.3732334 0 -8.0415668 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
1000 390.77042 10.051697 0 -8.1948009 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
0 0 0 0 -7.3046601 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
100 149.95804 3.8573359 0 -7.7921375 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
200 245.00113 6.3021074 0 -8.2639651 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
300 300.57486 7.7316177 0 -8.2986331 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
400 368.08438 9.4681493 0 -8.4800193 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
500 419.32066 10.786088 0 -8.640773 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
600 385.4127 9.9138817 0 -8.4356035 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
700 360.14242 9.2638601 0 -8.2900275 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
800 346.92167 8.923786 0 -8.0694169 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
900 364.39442 9.3732334 0 -8.0415668 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
1000 390.77042 10.051697 0 -8.1948009 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14541 | 0.14541 | 0.14541 | 0.0 | 58.59
Neigh | 0.00099082 | 0.00099082 | 0.00099082 | 0.0 | 0.40
Comm | 0.0039966 | 0.0039966 | 0.0039966 | 0.0 | 1.61
Output | 0.00016346 | 0.00016346 | 0.00016346 | 0.0 | 0.07
Modify | 0.096205 | 0.096205 | 0.096205 | 0.0 | 38.76
Other | | 0.001425 | | | 0.57
Pair | 0.11918 | 0.11918 | 0.11918 | 0.0 | 54.56
Neigh | 0.0010314 | 0.0010314 | 0.0010314 | 0.0 | 0.47
Comm | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 2.11
Output | 0.0001329 | 0.0001329 | 0.0001329 | 0.0 | 0.06
Modify | 0.092616 | 0.092616 | 0.092616 | 0.0 | 42.40
Other | | 0.0008616 | | | 0.39
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

59
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 1
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -17,7 +18,7 @@ Reading data file ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
read_data CPU = 0.002 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 02
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 11.920908 -7.3063682 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
700 470.04548 12.090871 10.348757 -8.278182 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
0 0 0 11.920908 -7.3063682 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
700 470.04548 12.090871 10.348757 -8.278182 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.541 ns/day, 0.061 hours/ns, 4578.021 timesteps/s, 915.604 katom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14654 | 0.14654 | 0.14654 | 0.0 | 59.04
Neigh | 0.00099986 | 0.00099986 | 0.00099986 | 0.0 | 0.40
Comm | 0.0041628 | 0.0041628 | 0.0041628 | 0.0 | 1.68
Output | 0.00018019 | 0.00018019 | 0.00018019 | 0.0 | 0.07
Modify | 0.094878 | 0.094878 | 0.094878 | 0.0 | 38.23
Other | | 0.001424 | | | 0.57
Pair | 0.11791 | 0.11791 | 0.11791 | 0.0 | 53.98
Neigh | 0.0010247 | 0.0010247 | 0.0010247 | 0.0 | 0.47
Comm | 0.0035577 | 0.0035577 | 0.0035577 | 0.0 | 1.63
Output | 0.00011003 | 0.00011003 | 0.00011003 | 0.0 | 0.05
Modify | 0.09496 | 0.09496 | 0.09496 | 0.0 | 43.47
Other | | 0.0008711 | | | 0.40
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

59
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 2
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -17,7 +18,7 @@ Reading data file ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
read_data CPU = 0.002 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 03
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 10.862314 -7.320388 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503
100 455.18121 11.708521 11.48472 -7.8033686 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632
200 460.81997 11.853566 10.817157 -8.2276485 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924
300 481.48652 12.385166 10.035423 -8.3866916 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917
400 487.3584 12.536208 11.766522 -8.3643382 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427
500 446.36019 11.48162 12.144202 -8.680266 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395
600 500.3783 12.871115 11.075008 -8.47833 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361
700 435.40634 11.199857 10.923558 -8.3090105 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857
800 446.82793 11.493652 11.599712 -8.0900498 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243
900 448.28506 11.531133 12.130739 -8.0810557 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073
1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128
Loop time of 0.248185 on 1 procs for 1000 steps with 200 atoms
0 0 0 10.862314 -7.320388 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503
100 455.18121 11.708521 11.48472 -7.8033686 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632
200 460.81997 11.853566 10.817157 -8.2276485 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924
300 481.48652 12.385166 10.035423 -8.3866916 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917
400 487.3584 12.536208 11.766522 -8.3643382 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427
500 446.36019 11.48162 12.144202 -8.680266 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395
600 500.3783 12.871115 11.075008 -8.47833 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361
700 435.40634 11.199857 10.923558 -8.3090105 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857
800 446.82793 11.493652 11.599712 -8.0900498 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243
900 448.28506 11.531133 12.130739 -8.0810557 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073
1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128
Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
Performance: 348.128 ns/day, 0.069 hours/ns, 4029.259 timesteps/s, 805.852 katom-step/s
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.541 ns/day, 0.061 hours/ns, 4578.019 timesteps/s, 915.604 katom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14702 | 0.14702 | 0.14702 | 0.0 | 59.24
Neigh | 0.0010003 | 0.0010003 | 0.0010003 | 0.0 | 0.40
Comm | 0.0039821 | 0.0039821 | 0.0039821 | 0.0 | 1.60
Output | 0.00023527 | 0.00023527 | 0.00023527 | 0.0 | 0.09
Modify | 0.094519 | 0.094519 | 0.094519 | 0.0 | 38.08
Other | | 0.001427 | | | 0.58
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 55.30
Neigh | 0.0010224 | 0.0010224 | 0.0010224 | 0.0 | 0.47
Comm | 0.0035478 | 0.0035478 | 0.0035478 | 0.0 | 1.62
Output | 0.00010889 | 0.00010889 | 0.00010889 | 0.0 | 0.05
Modify | 0.092098 | 0.092098 | 0.092098 | 0.0 | 42.16
Other | | 0.0008684 | | | 0.40
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

57
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 → examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3
View File

@ -1,5 +1,6 @@
LAMMPS (28 Mar 2023)
LAMMPS (3 Aug 2023)
Processor partition = 3
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
@ -29,10 +30,7 @@ timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 04
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
Initializing PIMD BZP barostat...
The barostat mass is W = 2.3401256650800001e+01
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
@ -43,15 +41,6 @@ thermo_modify norm no
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -66,31 +55,31 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
0 0 0 10.794425 -7.3457072 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389
100 426.01705 10.958338 12.206372 -7.8040582 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271
200 414.52703 10.662783 11.934129 -8.2331312 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052
300 424.85622 10.928478 11.681713 -8.357621 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162
400 485.80103 12.496148 12.255827 -8.3658975 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486
500 462.99006 11.909386 11.187609 -8.6934698 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134
600 465.24407 11.967366 11.168375 -8.4422887 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413
700 426.16111 10.962044 11.000011 -8.2855512 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939
800 454.53159 11.691811 10.834606 -8.0654281 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907
900 441.72064 11.362278 10.4492 -8.0786302 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525
1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278
Loop time of 0.248175 on 1 procs for 1000 steps with 200 atoms
0 0 0 10.794425 -7.3457072 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389
100 426.01705 10.958338 12.206372 -7.8040582 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271
200 414.52703 10.662783 11.934129 -8.2331312 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052
300 424.85622 10.928478 11.681713 -8.357621 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162
400 485.80103 12.496148 12.255827 -8.3658975 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486
500 462.99006 11.909386 11.187609 -8.6934698 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134
600 465.24407 11.967366 11.168375 -8.4422887 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413
700 426.16111 10.962044 11.000011 -8.2855512 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939
800 454.53159 11.691811 10.834606 -8.0654281 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907
900 441.72064 11.362278 10.4492 -8.0786302 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525
1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278
Loop time of 0.218441 on 1 procs for 1000 steps with 200 atoms
Performance: 348.141 ns/day, 0.069 hours/ns, 4029.409 timesteps/s, 805.882 katom-step/s
98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 395.530 ns/day, 0.061 hours/ns, 4577.899 timesteps/s, 915.580 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14919 | 0.14919 | 0.14919 | 0.0 | 60.12
Neigh | 0.00099112 | 0.00099112 | 0.00099112 | 0.0 | 0.40
Comm | 0.0040992 | 0.0040992 | 0.0040992 | 0.0 | 1.65
Output | 0.0001723 | 0.0001723 | 0.0001723 | 0.0 | 0.07
Modify | 0.092299 | 0.092299 | 0.092299 | 0.0 | 37.19
Other | | 0.00142 | | | 0.57
Pair | 0.11655 | 0.11655 | 0.11655 | 0.0 | 53.35
Neigh | 0.0010236 | 0.0010236 | 0.0010236 | 0.0 | 0.47
Comm | 0.0035622 | 0.0035622 | 0.0035622 | 0.0 | 1.63
Output | 0.0001071 | 0.0001071 | 0.0001071 | 0.0 | 0.05
Modify | 0.096348 | 0.096348 | 0.096348 | 0.0 | 44.11
Other | | 0.0008537 | | | 0.39
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

2
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++ Normal file
View File

@ -0,0 +1,2 @@
LAMMPS (3 Aug 2023)
Running on 4 partitions of processors

103
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0 Normal file
View File

@ -0,0 +1,103 @@
LAMMPS (3 Aug 2023)
Processor partition = 0
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt01
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 01
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
1 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
2 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
3 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02
PILE_L thermostat successfully initialized!
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.8893303 -7.3046601 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -164.47373
100 248.24141 6.3854564 4.1458616 -7.7546467 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 26.894568
200 346.2569 8.9066861 2.6427185 -7.8943744 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 91.225638
300 217.65314 5.5986414 7.0223362 -7.788449 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -125.00786
400 266.83825 6.8638187 6.2507813 -7.7241546 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 21.104834
500 342.40379 8.8075736 5.1959052 -7.7020799 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 208.60351
600 280.37754 7.2120867 8.0025846 -7.5954127 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 162.09838
700 377.11625 9.700474 6.0049074 -7.5861377 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 389.35575
800 378.36221 9.7325237 6.1704761 -7.6170017 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 387.71781
900 271.99864 6.9965581 9.037081 -7.4781664 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.3664
1000 362.4753 9.3238683 8.0266514 -7.4835536 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 433.67079
Loop time of 0.166656 on 1 procs for 1000 steps with 200 atoms
Performance: 518.435 ns/day, 0.046 hours/ns, 6000.401 timesteps/s, 1.200 Matom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10478 | 0.10478 | 0.10478 | 0.0 | 62.87
Neigh | 0.00096007 | 0.00096007 | 0.00096007 | 0.0 | 0.58
Comm | 0.0035065 | 0.0035065 | 0.0035065 | 0.0 | 2.10
Output | 0.0001037 | 0.0001037 | 0.0001037 | 0.0 | 0.06
Modify | 0.056454 | 0.056454 | 0.056454 | 0.0 | 33.87
Other | | 0.0008515 | | | 0.51
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9544 ave 9544 max 9544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9544
Ave neighs/atom = 47.72
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1 Normal file
View File

@ -0,0 +1,95 @@
LAMMPS (3 Aug 2023)
Processor partition = 1
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt02
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 02
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.4854554 -7.3063682 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -167.65544
100 231.55472 5.9562285 3.9188988 -7.7552569 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -9.7693407
200 366.33366 9.423116 2.3606144 -7.8893287 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 131.05061
300 213.74457 5.4981021 6.4391043 -7.7947526 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -136.92734
400 273.60832 7.0379636 5.6777233 -7.7709858 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 -0.14681392
500 338.99655 8.7199299 5.4335645 -7.7194465 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 190.1705
600 298.58126 7.6803369 7.2512164 -7.5741948 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 226.78095
700 352.53291 9.0681226 5.4845895 -7.5875298 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 335.39327
800 389.70585 10.024313 5.143907 -7.6218106 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 409.36108
900 285.3019 7.3387547 7.6228894 -7.5140003 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.93105
1000 345.35667 8.8835299 6.9652602 -7.5180013 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 368.83819
Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
Performance: 518.420 ns/day, 0.046 hours/ns, 6000.230 timesteps/s, 1.200 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10798 | 0.10798 | 0.10798 | 0.0 | 64.79
Neigh | 0.00097784 | 0.00097784 | 0.00097784 | 0.0 | 0.59
Comm | 0.0035304 | 0.0035304 | 0.0035304 | 0.0 | 2.12
Output | 8.5625e-05 | 8.5625e-05 | 8.5625e-05 | 0.0 | 0.05
Modify | 0.05322 | 0.05322 | 0.05322 | 0.0 | 31.93
Other | | 0.0008694 | | | 0.52
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9552 ave 9552 max 9552 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9552
Ave neighs/atom = 47.76
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2 Normal file
View File

@ -0,0 +1,95 @@
LAMMPS (3 Aug 2023)
Processor partition = 2
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt03
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 03
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 8.4016332 -7.320388 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -175.34503
100 235.06814 6.0466034 4.1185166 -7.7660023 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -7.6578222
200 341.9927 8.7969992 2.7767151 -7.9109058 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 69.587081
300 206.29873 5.3065745 7.3388955 -7.7440046 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -118.3143
400 305.56268 7.8599181 5.7681208 -7.7110516 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 107.63706
500 313.47536 8.0634543 5.5086382 -7.7030371 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 145.14899
600 258.53638 6.6502715 8.1299001 -7.6530176 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 92.36234
700 357.63679 9.1994085 6.539048 -7.6186515 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 329.17147
800 391.32883 10.066061 5.7809035 -7.6148923 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 415.13205
900 308.61185 7.9383512 8.9544585 -7.4803275 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 341.46691
1000 317.70376 8.1722204 7.3013798 -7.4667312 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 352.92253
Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms
Performance: 518.420 ns/day, 0.046 hours/ns, 6000.235 timesteps/s, 1.200 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10509 | 0.10509 | 0.10509 | 0.0 | 63.06
Neigh | 0.00096379 | 0.00096379 | 0.00096379 | 0.0 | 0.58
Comm | 0.0035557 | 0.0035557 | 0.0035557 | 0.0 | 2.13
Output | 7.8072e-05 | 7.8072e-05 | 7.8072e-05 | 0.0 | 0.05
Modify | 0.05611 | 0.05611 | 0.05611 | 0.0 | 33.67
Other | | 0.0008601 | | | 0.52
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1364 ave 1364 max 1364 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9545 ave 9545 max 9545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9545
Ave neighs/atom = 47.725
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

95
examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3 Normal file
View File

@ -0,0 +1,95 @@
LAMMPS (3 Aug 2023)
Processor partition = 3
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
read_data data.metalnpt04
Reading data file ...
orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
reading velocities ...
200 velocities
read_data CPU = 0.001 seconds
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
velocity all create 0.0 04
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.5251
ghost atom cutoff = 11.5251
binsize = 5.76255, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
0 0 0 7.8012276 -7.3457072 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -191.02389
100 241.19035 6.2040835 3.9473764 -7.7641902 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 3.5720518
200 325.21166 8.3653443 2.3529831 -7.9137212 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 33.184125
300 209.19735 5.381135 6.7063061 -7.801056 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -154.10632
400 280.84513 7.2241142 5.8838331 -7.7320495 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 45.624285
500 367.15726 9.4443014 5.2842629 -7.6643085 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 283.59979
600 294.68254 7.5800508 6.5104311 -7.6234652 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 183.09906
700 356.64514 9.1739005 5.2769462 -7.6204507 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 334.31754
800 360.77353 9.2800941 5.7976264 -7.6946985 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 299.62001
900 291.14241 7.4889889 7.5124196 -7.5102882 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 277.94834
1000 362.48694 9.3241677 6.8711151 -7.4856221 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 428.98682
Loop time of 0.166662 on 1 procs for 1000 steps with 200 atoms
Performance: 518.414 ns/day, 0.046 hours/ns, 6000.167 timesteps/s, 1.200 Matom-step/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10817 | 0.10817 | 0.10817 | 0.0 | 64.90
Neigh | 0.00096402 | 0.00096402 | 0.00096402 | 0.0 | 0.58
Comm | 0.0044991 | 0.0044991 | 0.0044991 | 0.0 | 2.70
Output | 8.5449e-05 | 8.5449e-05 | 8.5449e-05 | 0.0 | 0.05
Modify | 0.052066 | 0.052066 | 0.052066 | 0.0 | 31.24
Other | | 0.00088 | | | 0.53
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1368 ave 1368 max 1368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9541 ave 9541 max 9541 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9541
Ave neighs/atom = 47.705
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

4
examples/PACKAGES/pimd/langevin_metal_units/run.sh
View File

@ -1 +1,3 @@
mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen
mpirun -np 4 $LMP -in in.langevin.metal -p 4x1 -log log.langevin.metal -screen screen
mpirun -np 4 $LMP -in in.pimd-langevin.metal -p 4x1 -log log.pimd-langevin.metal -screen screen

1
examples/balance/in.balance
View File

@ -50,5 +50,6 @@ fix 10 all balance 50 0.9 rcb
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000

1
examples/balance/in.balance.bond.fast
View File

@ -59,5 +59,6 @@ fix 10 all balance 50 0.9 rcb
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000

1
examples/balance/in.balance.bond.slow
View File

@ -58,5 +58,6 @@ fix 10 all balance 50 0.9 rcb
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 40000

242
examples/balance/log.27Nov18.balance.bond.fast.g++.2
View File

@ -1,242 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.000778913 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds many all all 1 1.0 1.5
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 10.0 # because bonds stretch a long ways
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 10
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.156 | 5.167 | 5.177 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -2.2032569 3.1039469 2 1.0193906
100 27.623422 -6.228166 2.6542136 1.0803324 1.0027701
200 33.35302 -15.746749 3.2018248 1.1246537 1.0027701
300 39.17734 -24.1557 4.9116986 1.1468144 1.0027701
400 41.660701 -27.615203 8.6214678 1.2077562 1.0027701
500 37.154935 -24.096954 3.2656298 1.2243767 1.0083102
600 35.062196 -21.527799 2.3688444 1.1800554 1.0027701
700 36.962955 -22.265373 3.0233424 1.1800554 1.0083102
800 38.514356 -24.625735 5.2876402 1.2077562 1.0027701
900 37.840168 -24.069158 4.443617 1.2022161 1.0083102
1000 36.429396 -23.978878 7.2603394 1.1966759 1.0027701
1100 34.75827 -22.743232 6.6304628 1.1745152 1.0083102
1200 31.057199 -21.46544 3.7869701 1.1634349 1.0083102
1300 33.127345 -22.426161 5.824726 1.0858726 1.0027701
1400 31.678654 -21.604473 3.2219261 1.0360111 1.0083102
1500 28.345212 -18.030807 0.93335223 1.1191136 1.0027701
1600 26.031412 -15.389052 0.82549542 1.1080332 1.0027701
1700 25.082832 -13.48625 1.0006592 1.0858726 1.0027701
1800 25.673875 -13.965883 0.54607043 1.0692521 1.0027701
1900 26.530842 -13.979318 2.0285449 1.1024931 1.0027701
2000 25.910771 -14.244515 1.9592232 1.1191136 1.0027701
2100 28.505636 -16.220559 1.7154775 1.1191136 1.0027701
2200 28.142753 -15.564302 2.9946076 1.1135734 1.0027701
2300 26.606225 -13.734442 1.4589278 1.0083102 1.0083102
2400 25.664988 -12.389759 1.3450183 1.0360111 1.0027701
2500 25.145328 -11.815173 0.48162788 1.0360111 1.0027701
2600 26.654868 -13.916929 2.8361012 1.0581717 1.0083102
2700 27.3758 -15.495452 4.1206412 1.0360111 1.0027701
2800 23.60864 -14.520038 1.8948923 1.0193906 1.0027701
2900 20.604557 -12.901121 0.17526991 1.0138504 1.0027701
3000 20.852473 -12.756946 -0.44987285 1.0360111 1.0027701
3100 21.934986 -12.797691 0.76186765 1.0415512 1.0027701
3200 23.293263 -12.368233 0.021937309 1.0526316 1.0027701
3300 22.091492 -10.88605 0.013006632 1.0415512 1.0083102
3400 23.535429 -10.937804 2.0738989 1.0360111 1.0027701
3500 24.503573 -12.202994 1.126785 1.0581717 1.0027701
3600 23.54503 -12.745709 0.39022194 1.0858726 1.0027701
3700 22.658187 -10.986188 -0.18869692 1.0692521 1.0027701
3800 21.282045 -9.7879088 -0.061253454 1.0193906 1.0027701
3900 20.571754 -9.1157993 -1.0178917 1.0526316 1.0027701
4000 23.779702 -10.230328 1.0778525 1.0581717 1.0083102
4100 23.675854 -10.63724 0.59402249 1.0415512 1.0027701
4200 24.058963 -11.89505 0.3866378 1.0526316 1.0027701
4300 22.683721 -11.358978 1.8269036 1.0470914 1.0083102
4400 23.002345 -11.081443 0.4529456 1.0415512 1.0027701
4500 21.984542 -10.233276 -0.60718244 1.0415512 1.0083102
4600 22.079237 -9.979061 0.53013572 1.0415512 1.0027701
4700 22.336961 -10.323583 -0.37512832 1.0249307 1.0027701
4800 23.351699 -10.143724 0.95694397 1.0470914 1.0027701
4900 23.643954 -10.687354 1.6062522 1.0858726 1.0083102
5000 25.158132 -11.532398 1.3083639 1.0914127 1.0027701
5100 23.755521 -10.978548 0.60587307 1.0470914 1.0027701
5200 21.842692 -10.443216 -0.41185899 1.0637119 1.0027701
5300 22.828066 -10.871114 1.1754353 1.0470914 1.0027701
5400 24.883977 -12.39165 0.65101173 1.0470914 1.0027701
5500 22.908286 -11.419431 1.4712698 1.0637119 1.0027701
5600 22.718634 -12.083974 1.5706808 1.0526316 1.0027701
5700 23.080763 -11.464882 1.2979578 1.0304709 1.0083102
5800 21.877026 -11.483185 0.279772 1.0360111 1.0027701
5900 22.526809 -10.868636 0.37121786 1.0637119 1.0083102
6000 22.908857 -10.311118 0.58244569 1.0526316 1.0083102
6100 22.399847 -10.222706 0.87875674 1.0858726 1.0027701
6200 22.623463 -10.035541 -0.25811274 1.0304709 1.0027701
6300 21.518006 -10.017552 -0.98187611 1.0470914 1.0083102
6400 21.269816 -11.297716 0.20058535 1.0138504 1.0027701
6500 23.362834 -11.263306 0.47670072 1.0692521 1.0027701
6600 23.705236 -12.358492 -0.63286237 1.0027701 1.0027701
6700 22.410623 -10.849516 0.57027834 1.0581717 1.0083102
6800 21.661639 -9.3981379 0.38726515 1.0470914 1.0027701
6900 21.856521 -8.8451751 0.053822789 1.0304709 1.0027701
7000 21.069495 -8.6443387 -0.10412144 1.0193906 1.0027701
7100 22.305494 -10.098469 -0.22662961 1.0581717 1.0027701
7200 23.52884 -11.055929 -0.099869868 1.0692521 1.0027701
7300 24.042008 -11.411758 2.0528788 1.0415512 1.0027701
7400 22.870777 -12.408763 0.33346225 1.0249307 1.0027701
7500 21.290152 -10.963058 0.26940112 1.0083102 1.0027701
7600 21.702686 -10.36214 0.84057004 1.0083102 1.0027701
7700 22.478034 -10.832724 -0.70855164 1.0747922 1.0027701
7800 22.856853 -11.161008 -0.88354803 1.0083102 1.0083102
7900 22.579842 -10.789899 0.40865274 1.0360111 1.0027701
8000 24.364281 -12.116023 -0.44788445 1.0249307 1.0083102
8100 22.993409 -10.261331 0.44712215 1.0193906 1.0027701
8200 23.006207 -10.723372 1.2357091 1.0415512 1.0083102
8300 23.292233 -10.041314 2.143692 1.0581717 1.0027701
8400 21.658087 -10.089378 -0.25838681 1.0083102 1.0027701
8500 23.268456 -10.356603 0.089787317 1.0526316 1.0083102
8600 22.572019 -10.32801 0.12320758 1.0526316 1.0027701
8700 22.970465 -10.662456 0.57027398 1.0581717 1.0083102
8800 23.515552 -10.415842 1.0048598 1.0138504 1.0083102
8900 22.733961 -10.343495 0.19917627 1.0360111 1.0083102
9000 21.835458 -9.8740971 -1.0653164 1.0193906 1.0027701
9100 22.062821 -9.2303832 0.21428267 1.0415512 1.0083102
9200 23.020404 -10.321542 -0.48757848 1.0193906 1.0083102
9300 22.529362 -9.2916938 0.57056277 1.0415512 1.0027701
9400 23.301911 -10.538876 0.80637627 1.0138504 1.0027701
9500 21.984286 -9.4754676 -0.19048233 1.0193906 1.0027701
9600 23.710224 -10.274983 0.72268146 1.0249307 1.0027701
9700 22.317038 -9.3509008 -0.45727658 1.0360111 1.0027701
9800 23.41615 -10.026331 -0.45909049 1.0415512 1.0027701
9900 22.130299 -11.18528 -0.15359132 1.0747922 1.0027701
10000 23.273859 -11.337403 0.4036321 1.0304709 1.0083102
Loop time of 1.18289 on 2 procs for 10000 steps with 361 atoms
Performance: 3652073.393 tau/day, 8453.874 timesteps/s
97.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25191 | 0.25685 | 0.2618 | 1.0 | 21.71
Bond | 0.097655 | 0.098332 | 0.099009 | 0.2 | 8.31
Neigh | 0.53258 | 0.53993 | 0.54728 | 1.0 | 45.65
Comm | 0.13457 | 0.15372 | 0.17288 | 4.9 | 13.00
Output | 0.0013587 | 0.0016007 | 0.0018427 | 0.6 | 0.14
Modify | 0.074109 | 0.074314 | 0.074518 | 0.1 | 6.28
Other | | 0.05813 | | | 4.91
Nlocal: 180.5 ave 182 max 179 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 172.5 ave 175 max 170 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1421 ave 1488 max 1354 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2842
Ave neighs/atom = 7.87258
Ave special neighs/atom = 5.61773
Neighbor list builds = 4884
Dangerous builds = 0
Total wall time: 0:00:01

242
examples/balance/log.27Nov18.balance.bond.fast.g++.4
View File

@ -1,242 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.00067687 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds many all all 1 1.0 1.5
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 10.0 # because bonds stretch a long ways
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 10
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.141 | 5.174 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
500 37.154928 -24.096946 3.2656177 1.3296399 1.0304709
600 35.059873 -21.524223 2.3729526 1.3296399 1.0083102
700 36.735117 -22.012675 3.266197 1.3296399 1.0083102
800 39.218223 -25.076176 4.7162461 1.4182825 1.0193906
900 38.003628 -24.598176 3.4651756 1.4958449 1.0083102
1000 37.599298 -25.117714 4.6714491 1.2963989 1.0193906
1100 35.587211 -24.476201 4.8766816 1.2077562 1.0083102
1200 33.05745 -21.457847 4.7304313 1.2188366 1.0193906
1300 35.505899 -20.103017 7.0543469 1.1523546 1.0193906
1400 32.687958 -18.411286 2.8022421 1.1523546 1.0083102
1500 30.681103 -13.979491 1.5780815 1.1523546 1.0083102
1600 28.134276 -12.408217 1.4370834 1.2188366 1.0193906
1700 29.150676 -12.486223 1.7118526 1.1745152 1.0083102
1800 29.456937 -11.386522 2.0484739 1.1966759 1.0193906
1900 28.029998 -11.168436 0.38519481 1.1080332 1.0193906
2000 29.476997 -12.337678 1.8878345 1.1523546 1.0083102
2100 30.113294 -12.201714 2.8003366 1.1634349 1.0193906
2200 31.599067 -13.710787 2.5654923 1.2188366 1.0083102
2300 31.333799 -12.269386 1.9573739 1.1412742 1.0193906
2400 28.587094 -10.98229 2.090581 1.1745152 1.0083102
2500 28.012332 -11.416553 2.3293146 1.1855956 1.0083102
2600 28.703189 -13.33369 2.7247345 1.1080332 1.0083102
2700 26.933934 -13.546384 0.71447362 1.0415512 1.0304709
2800 24.556936 -12.231427 0.012081842 1.0526316 1.0193906
2900 24.362943 -10.921093 -0.6063159 1.0858726 1.0193906
3000 24.583358 -10.025143 0.35975315 1.0637119 1.0083102
3100 26.119046 -10.124317 0.75140102 1.0415512 1.0193906
3200 27.665317 -11.418452 0.39942176 1.1301939 1.0083102
3300 27.771434 -9.9777413 0.94693011 1.1080332 1.0083102
3400 25.692188 -9.9016885 2.2582772 1.0415512 1.0083102
3500 27.009276 -10.504438 0.98279258 1.1301939 1.0083102
3600 26.082843 -9.4359595 -0.030819747 1.1301939 1.0083102
3700 23.956851 -8.4601884 -0.45748969 1.0858726 1.0304709
3800 24.92141 -8.3315871 -0.19512647 1.0969529 1.0083102
3900 26.048044 -9.6299934 0.40522014 1.0858726 1.0083102
4000 26.558961 -10.032084 0.56213613 1.1745152 1.0083102
4100 26.949686 -10.133598 1.0140825 1.0747922 1.0083102
4200 25.868196 -9.3971859 1.2758465 1.0969529 1.0083102
4300 24.563369 -9.5992996 0.17389949 1.1191136 1.0193906
4400 24.032818 -10.002668 0.10233743 1.0969529 1.0083102
4500 25.281577 -9.948799 0.7590423 1.1523546 1.0083102
4600 25.010901 -10.195479 -0.24424931 1.0747922 1.0193906
4700 25.062368 -9.2973021 1.1755931 1.0858726 1.0193906
4800 25.70912 -8.890895 1.0780397 1.1080332 1.0193906
4900 26.027757 -10.205469 1.0644859 1.1080332 1.0083102
5000 25.845739 -9.8511049 0.49059257 1.1301939 1.0193906
5100 25.614064 -9.0396911 0.40825814 1.0526316 1.0304709
5200 25.548135 -9.000613 0.81571441 1.1080332 1.0083102
5300 26.592601 -9.2385129 1.4983434 1.0637119 1.0193906
5400 26.230779 -9.8226036 1.0072462 1.0858726 1.0083102
5500 26.809887 -9.9569954 1.4074968 1.0415512 1.0083102
5600 25.722206 -10.240487 -0.5216434 1.0747922 1.0193906
5700 24.973866 -9.0820997 0.92104357 1.0193906 1.0083102
5800 24.257134 -9.5439897 -0.75290789 1.0858726 1.0083102
5900 25.524917 -8.9920216 1.2049479 1.1191136 1.0083102
6000 24.816532 -9.5865764 -0.66634446 1.0637119 1.0193906
6100 27.034385 -9.4017037 1.0769494 1.0969529 1.0083102
6200 24.19144 -8.2292864 0.97913204 1.0415512 1.0193906
6300 26.112877 -9.1531212 0.77578963 1.0526316 1.0193906
6400 25.820541 -9.9662231 -0.092724413 1.0969529 1.0193906
6500 26.181404 -9.5875764 -0.30106405 1.1634349 1.0083102
6600 27.770851 -8.8366116 0.94545206 1.0304709 1.0193906
6700 26.065489 -9.8223382 0.24640067 1.0526316 1.0193906
6800 27.468165 -10.160923 2.7263738 1.0747922 1.0304709
6900 27.317955 -10.356911 1.131609 1.0526316 1.0304709
7000 26.343789 -9.9153453 1.0385354 1.0858726 1.0193906
7100 24.366577 -8.9243936 0.37685043 1.0526316 1.0193906
7200 25.570042 -8.9195237 0.44206575 1.0637119 1.0193906
7300 24.635046 -8.4524117 -0.20581694 1.0193906 1.0193906
7400 27.161863 -7.9885934 1.1323072 1.0858726 1.0193906
7500 26.8044 -9.5703931 0.69476535 1.0858726 1.0193906
7600 27.381006 -10.702178 -0.20230101 1.0526316 1.0083102
7700 26.507406 -9.828117 0.50115907 1.0415512 1.0193906
7800 25.945271 -8.9912842 0.89121191 1.0747922 1.0083102
7900 24.498681 -7.7193231 -0.63874494 1.0858726 1.0083102
8000 24.517408 -7.6046107 -0.91642337 1.0415512 1.0083102
8100 26.388387 -8.1883906 0.093136981 1.1080332 1.0193906
8200 26.261054 -8.7223732 -0.086859057 1.0747922 1.0083102
8300 26.287026 -9.2583895 0.79506804 1.0858726 1.0083102
8400 24.691375 -9.0701909 -0.40058151 1.0637119 1.0193906
8500 25.390612 -7.9499801 0.59874113 1.1412742 1.0193906
8600 26.84383 -8.5520984 0.37618599 1.0637119 1.0083102
8700 25.685137 -7.688836 0.035978149 1.0415512 1.0193906
8800 26.614591 -9.0444146 0.20671465 1.0193906 1.0083102
8900 25.782718 -8.2594705 0.54378816 1.0747922 1.0304709
9000 26.026886 -8.6777252 0.25418163 1.1191136 1.0083102
9100 27.246916 -9.0307861 1.211131 1.0526316 1.0193906
9200 27.282948 -9.180029 -0.0056269613 1.0747922 1.0083102
9300 27.029692 -8.7791461 0.35971649 1.0304709 1.0083102
9400 26.549013 -7.5083174 0.77607249 1.0969529 1.0193906
9500 25.533731 -9.2763668 0.28360762 1.0969529 1.0083102
9600 27.997538 -9.2766769 1.6968428 1.0637119 1.0083102
9700 26.977436 -9.21372 1.8007256 1.0637119 1.0083102
9800 25.547091 -9.1024445 -0.29158273 1.0969529 1.0193906
9900 26.378841 -8.7645665 1.0385835 1.1080332 1.0083102
10000 26.699368 -8.5450739 0.19591452 1.0526316 1.0193906
Loop time of 0.916576 on 4 procs for 10000 steps with 361 atoms
Performance: 4713193.307 tau/day, 10910.170 timesteps/s
92.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10915 | 0.12374 | 0.14167 | 3.5 | 13.50
Bond | 0.047075 | 0.049849 | 0.054161 | 1.2 | 5.44
Neigh | 0.31176 | 0.3246 | 0.3384 | 1.7 | 35.41
Comm | 0.24271 | 0.26717 | 0.30549 | 4.9 | 29.15
Output | 0.0017068 | 0.0021075 | 0.0031145 | 1.3 | 0.23
Modify | 0.064639 | 0.065705 | 0.067641 | 0.5 | 7.17
Other | | 0.08341 | | | 9.10
Nlocal: 90.25 ave 92 max 89 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 248.25 ave 264 max 230 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 569.5 ave 657 max 519 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 2278
Ave neighs/atom = 6.31025
Ave special neighs/atom = 5.61773
Neighbor list builds = 4964
Dangerous builds = 14
Total wall time: 0:00:00

541
examples/balance/log.27Nov18.balance.bond.slow.g++.2
View File

@ -1,541 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.000762701 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds many all all 1 1.0 1.5
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.079 | 7.108 | 7.137 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 0.57437856 0 0.26099453 2 1.0193906
100 0.29756515 0 0.10149401 1.0027701 1.0027701
200 0.35394813 0 0.075159099 1.0027701 1.0083102
300 0.39245849 0 0.033002384 1.0027701 1.0027701
400 0.34078347 0 -0.020825841 1.0083102 1.0027701
500 0.35201095 0 -0.062637506 1.0027701 1.0027701
600 0.34014717 0 -0.11122965 1.0249307 1.0027701
700 0.3323524 0 -0.11598015 1.0083102 1.0027701
800 0.35116047 0 -0.096162395 1.0138504 1.0027701
900 0.35695352 0 -0.01385176 1.0249307 1.0027701
1000 0.36986539 0 0.056772858 1.0027701 1.0027701
1100 0.34584644 0 0.084941323 1.0138504 1.0027701
1200 0.31921435 0 0.10545078 1.0138504 1.0027701
1300 0.32952819 0 0.124902 1.0027701 1.0027701
1400 0.34497365 0 0.12662081 1.0138504 1.0027701
1500 0.33429243 0 0.096230972 1.0193906 1.0027701
1600 0.33765387 0 0.025800542 1.0193906 1.0027701
1700 0.35134464 0 -0.04422593 1.0083102 1.0027701
1800 0.35003859 0 -0.096745576 1.0083102 1.0083102
1900 0.33839618 0 -0.095465943 1.0027701 1.0027701
2000 0.33732078 0 -0.094652802 1.0027701 1.0027701
2100 0.34552238 0 -0.076729261 1.0083102 1.0027701
2200 0.34893142 0 -0.036853228 1.0083102 1.0083102
2300 0.35379341 0 0.021124847 1.0193906 1.0027701
2400 0.34829744 0 0.09230184 1.0027701 1.0027701
2500 0.33038141 0 0.1399855 1.0027701 1.0083102
2600 0.30983019 0 0.12754742 1.0083102 1.0027701
2700 0.32992561 0 0.10485138 1.0193906 1.0027701
2800 0.34604747 0 0.066174138 1.0083102 1.0027701
2900 0.3444791 0 0.036590652 1.0083102 1.0083102
3000 0.34721342 0 -0.023793368 1.0138504 1.0027701
3100 0.33404314 0 -0.08374223 1.0083102 1.0027701
3200 0.33019355 0 -0.12715599 1.0083102 1.0027701
3300 0.33515177 0 -0.12217394 1.0083102 1.0027701
3400 0.33628481 0 -0.070877624 1.0083102 1.0027701
3500 0.34257038 0 -0.021612062 1.0027701 1.0027701
3600 0.32838009 0 0.030131228 1.0027701 1.0027701
3700 0.34462142 0 0.074586378 1.0138504 1.0027701
3800 0.30891825 0 0.10605673 1.0138504 1.0027701
3900 0.33847951 0 0.13956139 1.0027701 1.0027701
4000 0.32952079 0 0.12688129 1.0027701 1.0027701
4100 0.32646772 0 0.081089042 1.0083102 1.0027701
4200 0.35399503 0 0.013422873 1.0027701 1.0027701
4300 0.33154914 0 -0.050919508 1.0027701 1.0083102
4400 0.34113556 0 -0.083171 1.0249307 1.0027701
4500 0.32651708 0 -0.1063133 1.0193906 1.0027701
4600 0.34359609 0 -0.1076395 1.0027701 1.0027701
4700 0.34973537 0 -0.088231606 1.0138504 1.0027701
4800 0.35198515 0 -0.020901044 1.0027701 1.0027701
4900 0.35187284 0 0.043645941 1.0193906 1.0027701
5000 0.34887336 0 0.095698609 1.0027701 1.0027701
5100 0.30308163 0 0.11649328 1.0138504 1.0027701
5200 0.32401285 0 0.12072411 1.0083102 1.0083102
5300 0.33025072 0 0.10933161 1.0138504 1.0027701
5400 0.33288012 0 0.078356448 1.0083102 1.0027701
5500 0.35142492 0 0.036958063 1.0027701 1.0027701
5600 0.35125368 0 -0.041371343 1.0193906 1.0027701
5700 0.34547744 0 -0.096450846 1.0193906 1.0027701
5800 0.30939887 0 -0.12356656 1.0027701 1.0083102
5900 0.32315628 0 -0.11338676 1.0083102 1.0027701
6000 0.34117485 0 -0.066198961 1.0027701 1.0027701
6100 0.35298043 0 -0.016172816 1.0138504 1.0027701
6200 0.35130653 0 0.027660468 1.0027701 1.0027701
6300 0.35398766 0 0.087221238 1.0027701 1.0027701
6400 0.30963379 0 0.11990957 1.0138504 1.0027701
6500 0.3174541 0 0.14103528 1.0083102 1.0083102
6600 0.31989791 0 0.11575506 1.0083102 1.0083102
6700 0.33811477 0 0.060747353 1.0083102 1.0083102
6800 0.3424043 0 0.010357152 1.0083102 1.0027701
6900 0.34804319 0 -0.042621786 1.0083102 1.0027701
7000 0.35357865 0 -0.067248959 1.0027701 1.0027701
7100 0.33556885 0 -0.10983726 1.0083102 1.0027701
7200 0.33531101 0 -0.112179 1.0027701 1.0027701
7300 0.35742607 0 -0.078405267 1.0083102 1.0027701
7400 0.34577559 0 -0.01985432 1.0027701 1.0083102
7500 0.3498641 0 0.052289439 1.0027701 1.0027701
7600 0.33773715 0 0.092939035 1.0027701 1.0027701
7700 0.33093497 0 0.11924405 1.0083102 1.0027701
7800 0.31435814 0 0.12701724 1.0027701 1.0027701
7900 0.33132217 0 0.10793075 1.0083102 1.0027701
8000 0.33451798 0 0.077993125 1.0027701 1.0027701
8100 0.35188371 0 0.019929977 1.0083102 1.0083102
8200 0.33645742 0 -0.039302079 1.0027701 1.0027701
8300 0.3415632 0 -0.098067982 1.0138504 1.0027701
8400 0.30619282 0 -0.12952879 1.0138504 1.0027701
8500 0.34446484 0 -0.098084709 1.0027701 1.0027701
8600 0.33761673 0 -0.07069818 1.0027701 1.0027701
8700 0.34495452 0 -0.022458056 1.0083102 1.0027701
8800 0.33502983 0 0.027742411 1.0027701 1.0027701
8900 0.35418591 0 0.092390134 1.0083102 1.0083102
9000 0.31648387 0 0.12467398 1.0083102 1.0027701
9100 0.33994825 0 0.14460327 1.0138504 1.0027701
9200 0.33822571 0 0.11273284 1.0027701 1.0027701
9300 0.33260773 0 0.060063671 1.0083102 1.0083102
9400 0.36140305 0 0.021427642 1.0138504 1.0027701
9500 0.34273562 0 -0.034064202 1.0083102 1.0027701
9600 0.33867054 0 -0.089076906 1.0138504 1.0027701
9700 0.32088235 0 -0.12027075 1.0138504 1.0083102
9800 0.3320823 0 -0.11602794 1.0138504 1.0027701
9900 0.33916442 0 -0.080281044 1.0083102 1.0027701
10000 0.34852268 0 -0.01000914 1.0083102 1.0083102
10100 0.32955942 0 0.04258493 1.0027701 1.0083102
10200 0.34487898 0 0.086971308 1.0083102 1.0027701
10300 0.32325593 0 0.11558149 1.0138504 1.0027701
10400 0.30927871 0 0.12239437 1.0027701 1.0027701
10500 0.33176799 0 0.12285937 1.0138504 1.0083102
10600 0.35120027 0 0.084897432 1.0027701 1.0027701
10700 0.33129697 0 0.0053089279 1.0138504 1.0027701
10800 0.36028769 0 -0.04280715 1.0083102 1.0027701
10900 0.35552287 0 -0.084955999 1.0138504 1.0027701
11000 0.3406024 0 -0.096554577 1.0027701 1.0027701
11100 0.33041202 0 -0.10703492 1.0138504 1.0027701
11200 0.32442686 0 -0.084328121 1.0193906 1.0027701
11300 0.35952468 0 -0.020191965 1.0083102 1.0027701
11400 0.34610624 0 0.03440148 1.0138504 1.0027701
11500 0.3415612 0 0.1041929 1.0027701 1.0027701
11600 0.34040042 0 0.13215705 1.0138504 1.0027701
11700 0.33555094 0 0.12738686 1.0193906 1.0027701
11800 0.3458647 0 0.10963398 1.0027701 1.0083102
11900 0.33836678 0 0.067253864 1.0138504 1.0027701
12000 0.34853314 0 0.03201448 1.0027701 1.0027701
12100 0.34600048 0 -0.034833402 1.0083102 1.0027701
12200 0.33145631 0 -0.09865675 1.0083102 1.0027701
12300 0.32848884 0 -0.1248489 1.0083102 1.0027701
12400 0.3321344 0 -0.11266575 1.0027701 1.0083102
12500 0.32622305 0 -0.061634993 1.0083102 1.0083102
12600 0.36213537 0 -0.0090593315 1.0138504 1.0027701
12700 0.34673866 0 0.036734645 1.0138504 1.0027701
12800 0.34606618 0 0.086267678 1.0138504 1.0027701
12900 0.34271431 0 0.12415522 1.0027701 1.0027701
13000 0.31993287 0 0.13879926 1.0027701 1.0083102
13100 0.3422918 0 0.11978905 1.0083102 1.0027701
13200 0.33055236 0 0.062620483 1.0083102 1.0027701
13300 0.34652207 0 0.0043833459 1.0138504 1.0027701
13400 0.33574661 0 -0.04691024 1.0027701 1.0027701
13500 0.33940837 0 -0.074241604 1.0027701 1.0083102
13600 0.32093414 0 -0.1078027 1.0138504 1.0083102
13700 0.34336597 0 -0.10544097 1.0027701 1.0027701
13800 0.35806461 0 -0.072531559 1.0027701 1.0027701
13900 0.35209713 0 -0.018851408 1.0083102 1.0083102
14000 0.35702629 0 0.061046366 1.0027701 1.0027701
14100 0.33234093 0 0.094086465 1.0027701 1.0027701
14200 0.3459466 0 0.12186656 1.0027701 1.0027701
14300 0.3327428 0 0.11396572 1.0027701 1.0027701
14400 0.32409443 0 0.10658903 1.0083102 1.0083102
14500 0.35022184 0 0.083558031 1.0083102 1.0083102
14600 0.34823843 0 0.024605569 1.0083102 1.0083102
14700 0.35298973 0 -0.040418888 1.0027701 1.0027701
14800 0.33679845 0 -0.10067728 1.0027701 1.0027701
14900 0.32790966 0 -0.10925568 1.0083102 1.0027701
15000 0.34208495 0 -0.09568004 1.0193906 1.0027701
15100 0.33647529 0 -0.055652929 1.0027701 1.0027701
15200 0.35328398 0 -0.020236536 1.0083102 1.0027701
15300 0.34252669 0 0.026434179 1.0083102 1.0027701
15400 0.34409435 0 0.094410599 1.0027701 1.0027701
15500 0.32288994 0 0.12034455 1.0083102 1.0027701
15600 0.32109689 0 0.13645185 1.0083102 1.0027701
15700 0.33681572 0 0.098607746 1.0083102 1.0027701
15800 0.33635195 0 0.05570715 1.0083102 1.0083102
15900 0.34289757 0 0.013849092 1.0083102 1.0027701
16000 0.34225547 0 -0.035597548 1.0193906 1.0027701
16100 0.33660991 0 -0.076931881 1.0027701 1.0027701
16200 0.32802152 0 -0.12765884 1.0083102 1.0027701
16300 0.3469374 0 -0.10785455 1.0083102 1.0083102
16400 0.34053641 0 -0.070259853 1.0027701 1.0027701
16500 0.34610591 0 -0.014315306 1.0083102 1.0027701
16600 0.35109001 0 0.041251169 1.0138504 1.0027701
16700 0.34336905 0 0.077996627 1.0193906 1.0027701
16800 0.33277414 0 0.11053634 1.0027701 1.0083102
16900 0.32183338 0 0.11680626 1.0027701 1.0027701
17000 0.34044352 0 0.10806555 1.0138504 1.0027701
17100 0.32967873 0 0.067759786 1.0138504 1.0027701
17200 0.36172278 0 -0.0048631904 1.0083102 1.0083102
17300 0.35619435 0 -0.04215545 1.0027701 1.0027701
17400 0.34540936 0 -0.093994174 1.0083102 1.0027701
17500 0.33193585 0 -0.098831315 1.0083102 1.0027701
17600 0.3544756 0 -0.085660403 1.0083102 1.0083102
17700 0.34505209 0 -0.069640515 1.0193906 1.0083102
17800 0.36291124 0 -0.0063088133 1.0027701 1.0027701
17900 0.34255705 0 0.046794555 1.0027701 1.0027701
18000 0.34163238 0 0.11767705 1.0138504 1.0027701
18100 0.3466445 0 0.1351712 1.0193906 1.0083102
18200 0.33037668 0 0.12703659 1.0027701 1.0027701
18300 0.33677404 0 0.10956306 1.0027701 1.0083102
18400 0.34978954 0 0.087193072 1.0027701 1.0027701
18500 0.33354363 0 0.051095814 1.0138504 1.0027701
18600 0.34651729 0 0.0056245561 1.0027701 1.0027701
18700 0.32622232 0 -0.047319269 1.0027701 1.0083102
18800 0.32978847 0 -0.054929416 1.0138504 1.0027701
18900 0.34192451 0 -0.037252471 1.0027701 1.0027701
19000 0.34061294 0 -0.001167235 1.0083102 1.0027701
19100 0.34194478 0 0.016945224 1.0083102 1.0027701
19200 0.33321765 0 0.050665354 1.0193906 1.0027701
19300 0.33197783 0 0.080470585 1.0138504 1.0027701
19400 0.33284715 0 0.12423599 1.0193906 1.0027701
19500 0.33867856 0 0.12689524 1.0027701 1.0027701
19600 0.36092786 0 0.11417704 1.0027701 1.0027701
19700 0.34270183 0 0.069038291 1.0249307 1.0083102
19800 0.34880695 0 0.042483681 1.0083102 1.0083102
19900 0.33903644 0 0.034788638 1.0027701 1.0027701
20000 0.32590125 0 0.011383785 1.0083102 1.0083102
20100 0.30358859 0 0.0030743554 1.0138504 1.0027701
20200 0.31830224 0 0.017637826 1.0027701 1.0027701
20300 0.34195438 0 0.072811099 1.0193906 1.0083102
20400 0.31249563 0 0.10063541 1.0083102 1.0027701
20500 0.31544938 0 0.1405794 1.0027701 1.0027701
20600 0.30071644 0 0.12763486 1.0027701 1.0027701
20700 0.2890265 0 0.1136651 1.0083102 1.0027701
20800 0.28962296 0 0.094481978 1.0083102 1.0027701
20900 0.29447212 0 0.0967165 1.0138504 1.0083102
21000 0.31159961 0 0.067307231 1.0027701 1.0027701
21100 0.30490648 0 0.017689358 1.0027701 1.0083102
21200 0.30687262 0 -0.016055512 1.0027701 1.0083102
21300 0.30083286 0 -0.0014988997 1.0083102 1.0027701
21400 0.32070426 0 0.015960302 1.0083102 1.0083102
21500 0.31439311 0 0.038170385 1.0083102 1.0083102
21600 0.32617832 0 0.043263788 1.0083102 1.0027701
21700 0.35151793 0 0.066302727 1.0083102 1.0083102
21800 0.35912885 0 0.070099103 1.0027701 1.0027701
21900 0.32451958 0 0.068935768 1.0083102 1.0027701
22000 0.35219298 0 0.067161227 1.0138504 1.0083102
22100 0.34857705 0 0.032731746 1.0138504 1.0027701
22200 0.34750227 0 0.0056917695 1.0027701 1.0027701
22300 0.34766017 0 -0.0027090483 1.0027701 1.0083102
22400 0.33426062 0 -0.023196063 1.0027701 1.0083102
22500 0.34174625 0 -0.025019717 1.0083102 1.0027701
22600 0.3356145 0 -0.029707418 1.0138504 1.0027701
22700 0.3362653 0 -0.035815733 1.0083102 1.0027701
22800 0.33973405 0 -0.0024705835 1.0193906 1.0027701
22900 0.33813085 0 0.0077527467 1.0027701 1.0027701
23000 0.33339981 0 0.028340744 1.0027701 1.0027701
23100 0.34079832 0 0.018521302 1.0249307 1.0027701
23200 0.33074548 0 0.032378405 1.0138504 1.0083102
23300 0.32965664 0 0.035989589 1.0138504 1.0027701
23400 0.30927749 0 0.024581106 1.0083102 1.0027701
23500 0.32890632 0 0.01092479 1.0138504 1.0083102
23600 0.34137438 0 0.0094839745 1.0083102 1.0027701
23700 0.34512638 0 -0.012392771 1.0138504 1.0027701
23800 0.31781354 0 -0.012908449 1.0027701 1.0027701
23900 0.32405513 0 -0.015018071 1.0027701 1.0027701
24000 0.33549728 0 -0.012812915 1.0083102 1.0083102
24100 0.31368736 0 -0.020818372 1.0027701 1.0027701
24200 0.33533836 0 0.0056121057 1.0027701 1.0027701
24300 0.32530627 0 0.018183931 1.0249307 1.0027701
24400 0.31930662 0 0.027446878 1.0027701 1.0083102
24500 0.33540302 0 0.040307455 1.0193906 1.0027701
24600 0.34020431 0 0.027403921 1.0027701 1.0027701
24700 0.3291814 0 0.01204865 1.0083102 1.0027701
24800 0.31552604 0 0.019654111 1.0083102 1.0083102
24900 0.34727253 0 0.01670543 1.0027701 1.0027701
25000 0.35120105 0 0.0038617562 1.0083102 1.0027701
25100 0.32706871 0 -0.021196623 1.0193906 1.0083102
25200 0.32915282 0 -0.017146508 1.0083102 1.0027701
25300 0.32577518 0 -0.01312495 1.0083102 1.0027701
25400 0.33286855 0 0.0014726193 1.0138504 1.0027701
25500 0.33002601 0 0.0080974022 1.0083102 1.0027701
25600 0.34127655 0 0.014296091 1.0138504 1.0083102
25700 0.34048065 0 0.022513032 1.0083102 1.0027701
25800 0.33029079 0 0.038733531 1.0138504 1.0027701
25900 0.33031324 0 0.026156982 1.0027701 1.0027701
26000 0.32967371 0 0.028727383 1.0027701 1.0083102
26100 0.33775718 0 0.015607478 1.0027701 1.0083102
26200 0.35097144 0 0.012291703 1.0027701 1.0027701
26300 0.34303792 0 0.00094823191 1.0027701 1.0083102
26400 0.33632665 0 -0.0026904889 1.0027701 1.0083102
26500 0.33580127 0 -0.0074168555 1.0138504 1.0083102
26600 0.33063188 0 -0.020378601 1.0027701 1.0083102
26700 0.33581846 0 -0.00084397268 1.0027701 1.0027701
26800 0.32998532 0 0.015932208 1.0083102 1.0083102
26900 0.33825444 0 0.010428603 1.0193906 1.0027701
27000 0.32081518 0 0.019818223 1.0083102 1.0083102
27100 0.31448098 0 0.020093416 1.0027701 1.0027701
27200 0.32643684 0 0.021934917 1.0083102 1.0027701
27300 0.33289466 0 0.023713072 1.0138504 1.0083102
27400 0.32310744 0 0.024110945 1.0193906 1.0027701
27500 0.33115619 0 0.0025776713 1.0193906 1.0027701
27600 0.33295887 0 -0.010710764 1.0083102 1.0083102
27700 0.32968876 0 -0.0064595905 1.0083102 1.0027701
27800 0.34064581 0 -0.0086519116 1.0027701 1.0027701
27900 0.33559187 0 -0.0055753593 1.0249307 1.0027701
28000 0.32300727 0 -0.0004153384 1.0138504 1.0027701
28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102
28200 0.35532383 0 0.013646951 1.0083102 1.0083102
28300 0.31507942 0 0.026532255 1.0083102 1.0027701
28400 0.32711006 0 0.033214981 1.0083102 1.0027701
28500 0.34472462 0 0.028050837 1.0027701 1.0027701
28600 0.33708059 0 0.019115676 1.0027701 1.0027701
28700 0.34478087 0 0.023743689 1.0193906 1.0027701
28800 0.34546686 0 0.0081772997 1.0083102 1.0027701
28900 0.34004886 0 0.017771865 1.0138504 1.0027701
29000 0.33604232 0 -0.010505671 1.0027701 1.0027701
29100 0.33541374 0 -0.016273261 1.0027701 1.0027701
29200 0.34347489 0 -0.010002306 1.0083102 1.0027701
29300 0.34083904 0 0.0089701784 1.0083102 1.0027701
29400 0.34846892 0 0.020765104 1.0027701 1.0027701
29500 0.3416255 0 0.022650856 1.0083102 1.0027701
29600 0.33725496 0 0.020693083 1.0027701 1.0027701
29700 0.34480638 0 0.024317128 1.0138504 1.0027701
29800 0.31459471 0 0.023097895 1.0027701 1.0027701
29900 0.33014448 0 0.03114046 1.0138504 1.0027701
30000 0.33741498 0 0.015624314 1.0083102 1.0027701
30100 0.32598657 0 -0.0018860541 1.0138504 1.0027701
30200 0.34855815 0 0.0017983372 1.0027701 1.0027701
30300 0.33375921 0 0.0010991235 1.0083102 1.0083102
30400 0.35008944 0 -0.0027316177 1.0027701 1.0027701
30500 0.33279729 0 -0.0035788551 1.0027701 1.0027701
30600 0.33868746 0 -0.0016249482 1.0027701 1.0027701
30700 0.33597034 0 -0.0014524001 1.0193906 1.0083102
30800 0.3227257 0 0.016353457 1.0193906 1.0027701
30900 0.32676516 0 0.027396654 1.0027701 1.0027701
31000 0.34083982 0 0.031606413 1.0138504 1.0083102
31100 0.32165238 0 0.013583368 1.0027701 1.0027701
31200 0.3428492 0 0.020486611 1.0138504 1.0027701
31300 0.32372541 0 0.01215566 1.0027701 1.0027701
31400 0.32734692 0 0.016229397 1.0083102 1.0027701
31500 0.33089262 0 0.0060426618 1.0027701 1.0027701
31600 0.34273493 0 -0.013456537 1.0083102 1.0083102
31700 0.32723905 0 -0.019243766 1.0027701 1.0027701
31800 0.33636488 0 0.0027814902 1.0027701 1.0083102
31900 0.32834805 0 0.00706877 1.0083102 1.0027701
32000 0.33995148 0 0.0018383309 1.0083102 1.0083102
32100 0.33412282 0 0.0076455933 1.0027701 1.0083102
32200 0.34334884 0 0.023586129 1.0083102 1.0027701
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
32400 0.33163443 0 0.038878463 1.0083102 1.0027701
32500 0.32290345 0 0.022247461 1.0027701 1.0027701
32600 0.34113954 0 0.010966365 1.0138504 1.0027701
32700 0.33390633 0 0.0037777555 1.0083102 1.0083102
32800 0.34385341 0 0.010556575 1.0138504 1.0083102
32900 0.32137047 0 0.00022027143 1.0138504 1.0027701
33000 0.32079172 0 -0.017261272 1.0083102 1.0027701
33100 0.33570882 0 -0.0051942206 1.0027701 1.0027701
33200 0.34320894 0 -0.011515281 1.0138504 1.0027701
33300 0.32794746 0 -0.0018153673 1.0027701 1.0027701
33400 0.33060982 0 0.027118146 1.0027701 1.0027701
33500 0.33641809 0 0.02143035 1.0083102 1.0027701
33600 0.33643061 0 0.020833068 1.0083102 1.0027701
33700 0.3485949 0 0.030918751 1.0083102 1.0027701
33800 0.3283985 0 0.01947613 1.0193906 1.0027701
33900 0.31959761 0 0.021128147 1.0027701 1.0027701
34000 0.33897984 0 0.015270986 1.0027701 1.0083102
34100 0.32392267 0 0.0020130852 1.0083102 1.0027701
34200 0.33084514 0 -0.024316708 1.0027701 1.0027701
34300 0.3342259 0 -0.0059047764 1.0138504 1.0027701
34400 0.33385098 0 0.0063818721 1.0027701 1.0027701
34500 0.33255603 0 -0.01023837 1.0027701 1.0083102
34600 0.34766173 0 0.0056703013 1.0083102 1.0027701
34700 0.339822 0 0.0061648559 1.0083102 1.0027701
34800 0.33902329 0 0.030037037 1.0027701 1.0083102
34900 0.3216153 0 0.027996689 1.0027701 1.0027701
35000 0.32701056 0 0.024778517 1.0083102 1.0027701
35100 0.3124942 0 0.011316548 1.0027701 1.0027701
35200 0.34486416 0 0.011670127 1.0027701 1.0027701
35300 0.33275353 0 0.020491246 1.0027701 1.0027701
35400 0.33618763 0 0.014678874 1.0083102 1.0027701
35500 0.32352282 0 -0.018568683 1.0027701 1.0027701
35600 0.32617903 0 -0.012796912 1.0083102 1.0027701
35700 0.32378048 0 -0.021318585 1.0027701 1.0083102
35800 0.3371086 0 -0.0023678632 1.0027701 1.0083102
35900 0.33818476 0 0.011197742 1.0083102 1.0027701
36000 0.35142144 0 0.022520935 1.0083102 1.0027701
36100 0.35147297 0 0.020277852 1.0083102 1.0027701
36200 0.33489465 0 0.014564878 1.0193906 1.0027701
36300 0.33841515 0 0.036439962 1.0027701 1.0027701
36400 0.32301096 0 0.019966746 1.0027701 1.0027701
36500 0.35612028 0 0.036509556 1.0027701 1.0027701
36600 0.33841597 0 -0.0042180605 1.0083102 1.0083102
36700 0.34477654 0 -0.0052770853 1.0193906 1.0083102
36800 0.33804317 0 -0.013751733 1.0027701 1.0027701
36900 0.35003816 0 -0.0021184393 1.0027701 1.0027701
37000 0.32965041 0 -0.020900951 1.0083102 1.0027701
37100 0.34653095 0 -0.013667977 1.0027701 1.0027701
37200 0.35019871 0 -0.0071740923 1.0027701 1.0027701
37300 0.34859745 0 0.02006041 1.0138504 1.0027701
37400 0.35739859 0 0.020892822 1.0083102 1.0027701
37500 0.34128859 0 0.041072111 1.0083102 1.0083102
37600 0.33781905 0 0.023376738 1.0083102 1.0083102
37700 0.32961874 0 0.030953741 1.0138504 1.0027701
37800 0.343987 0 0.029579795 1.0083102 1.0027701
37900 0.33610448 0 0.036836828 1.0138504 1.0027701
38000 0.32757228 0 0.020902031 1.0027701 1.0027701
38100 0.32735808 0 0.019544751 1.0138504 1.0083102
38200 0.35646953 0 0.044607528 1.0027701 1.0083102
38300 0.32509773 0 0.03610738 1.0138504 1.0027701
38400 0.32111741 0 0.034474043 1.0083102 1.0083102
38500 0.30590608 0 0.053461212 1.0083102 1.0027701
38600 0.32322402 0 0.053453832 1.0138504 1.0083102
38700 0.33843057 0 0.076264534 1.0027701 1.0027701
38800 0.31350741 0 0.064733869 1.0083102 1.0027701
38900 0.31943061 0 0.067836769 1.0083102 1.0027701
39000 0.33775583 0 0.0788316 1.0083102 1.0083102
39100 0.34256036 0 0.075874935 1.0027701 1.0027701
39200 0.33128527 0 0.071610976 1.0193906 1.0027701
39300 0.34519653 0 0.046257301 1.0083102 1.0083102
39400 0.34351844 0 0.052422917 1.0027701 1.0027701
39500 0.35716037 0 0.048916058 1.0083102 1.0027701
39600 0.34000737 0 0.016149089 1.0083102 1.0027701
39700 0.34587892 0 0.021619621 1.0083102 1.0083102
39800 0.34878036 0 0.0092881327 1.0083102 1.0027701
39900 0.35225411 0 -0.011341599 1.0083102 1.0027701
40000 0.36309266 0 0.0050869295 1.0304709 1.0027701
Loop time of 1.30389 on 2 procs for 40000 steps with 361 atoms
Performance: 13252650.572 tau/day, 30677.432 timesteps/s
97.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041365 | 0.041785 | 0.042204 | 0.2 | 3.20
Bond | 0.35501 | 0.37082 | 0.38664 | 2.6 | 28.44
Neigh | 0.30901 | 0.31013 | 0.31125 | 0.2 | 23.78
Comm | 0.12939 | 0.15871 | 0.18803 | 7.4 | 12.17
Output | 0.00489 | 0.005671 | 0.0064521 | 1.0 | 0.43
Modify | 0.28208 | 0.28362 | 0.28516 | 0.3 | 21.75
Other | | 0.1332 | | | 10.21
Nlocal: 180.5 ave 181 max 180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 52.5 ave 53 max 52 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0
Total wall time: 0:00:01

541
examples/balance/log.27Nov18.balance.bond.slow.g++.4
View File

@ -1,541 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.000665188 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds many all all 1 1.0 1.5
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.048 | 7.096 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 0.57437856 0 0.26099453 3.2354571 1.0526316
100 0.29756515 0 0.10149401 1.0193906 1.0083102
200 0.35394813 0 0.075159099 1.0304709 1.0193906
300 0.39245849 0 0.033002384 1.0083102 1.0193906
400 0.34078347 0 -0.020825841 1.0304709 1.0083102
500 0.35201095 0 -0.062637506 1.0193906 1.0083102
600 0.34014717 0 -0.11122965 1.0415512 1.0083102
700 0.3323524 0 -0.11598015 1.0193906 1.0083102
800 0.35116047 0 -0.096162395 1.0193906 1.0193906
900 0.35695352 0 -0.01385176 1.0526316 1.0193906
1000 0.36986539 0 0.056772858 1.0083102 1.0083102
1100 0.34584644 0 0.084941323 1.0304709 1.0083102
1200 0.31921435 0 0.10545078 1.0415512 1.0083102
1300 0.32952819 0 0.124902 1.0083102 1.0193906
1400 0.34497365 0 0.12662081 1.0193906 1.0083102
1500 0.33429243 0 0.096230972 1.0193906 1.0193906
1600 0.33765387 0 0.025800542 1.0304709 1.0083102
1700 0.35134464 0 -0.04422593 1.0415512 1.0083102
1800 0.35003859 0 -0.096745576 1.0304709 1.0083102
1900 0.33839618 0 -0.095465943 1.0193906 1.0083102
2000 0.33732078 0 -0.094652802 1.0083102 1.0083102
2100 0.34552238 0 -0.076729261 1.0304709 1.0083102
2200 0.34893142 0 -0.036853228 1.0304709 1.0083102
2300 0.35379341 0 0.021124847 1.0304709 1.0193906
2400 0.34829744 0 0.09230184 1.0304709 1.0083102
2500 0.33038141 0 0.1399855 1.0193906 1.0193906
2600 0.30983019 0 0.12754742 1.0083102 1.0083102
2700 0.32992561 0 0.10485138 1.0415512 1.0083102
2800 0.34604747 0 0.066174138 1.0083102 1.0083102
2900 0.3444791 0 0.036590652 1.0193906 1.0193906
3000 0.34721342 0 -0.023793368 1.0193906 1.0193906
3100 0.33404314 0 -0.08374223 1.0415512 1.0083102
3200 0.33019355 0 -0.12715599 1.0083102 1.0304709
3300 0.33515177 0 -0.12217394 1.0193906 1.0083102
3400 0.33628481 0 -0.070877624 1.0193906 1.0083102
3500 0.34257038 0 -0.021612062 1.0304709 1.0083102
3600 0.32838009 0 0.030131228 1.0083102 1.0083102
3700 0.34462142 0 0.074586378 1.0526316 1.0193906
3800 0.30891825 0 0.10605673 1.0304709 1.0083102
3900 0.33847951 0 0.13956139 1.0083102 1.0083102
4000 0.32952079 0 0.12688129 1.0193906 1.0304709
4100 0.32646772 0 0.081089042 1.0304709 1.0193906
4200 0.35399503 0 0.013422873 1.0083102 1.0083102
4300 0.33154914 0 -0.050919508 1.0193906 1.0193906
4400 0.34113556 0 -0.083171 1.0304709 1.0083102
4500 0.32651708 0 -0.1063133 1.0304709 1.0083102
4600 0.34359609 0 -0.1076395 1.0083102 1.0083102
4700 0.34973537 0 -0.088231606 1.0415512 1.0083102
4800 0.35198515 0 -0.020901044 1.0415512 1.0083102
4900 0.35187284 0 0.043645941 1.0415512 1.0083102
5000 0.34887336 0 0.095698609 1.0193906 1.0083102
5100 0.30308163 0 0.11649328 1.0193906 1.0083102
5200 0.32401285 0 0.12072411 1.0193906 1.0083102
5300 0.33025072 0 0.10933161 1.0193906 1.0083102
5400 0.33288012 0 0.078356448 1.0083102 1.0193906
5500 0.35142492 0 0.036958063 1.0193906 1.0083102
5600 0.35125368 0 -0.041371343 1.0304709 1.0083102
5700 0.34547744 0 -0.096450846 1.0637119 1.0083102
5800 0.30939887 0 -0.12356656 1.0083102 1.0193906
5900 0.32315628 0 -0.11338676 1.0193906 1.0193906
6000 0.34117485 0 -0.066198961 1.0193906 1.0083102
6100 0.35298043 0 -0.016172816 1.0304709 1.0193906
6200 0.35130653 0 0.027660468 1.0415512 1.0083102
6300 0.35398766 0 0.087221238 1.0083102 1.0083102
6400 0.30963379 0 0.11990957 1.0415512 1.0083102
6500 0.3174541 0 0.14103528 1.0193906 1.0193906
6600 0.31989791 0 0.11575506 1.0304709 1.0193906
6700 0.33811477 0 0.060747353 1.0415512 1.0193906
6800 0.3424043 0 0.010357152 1.0193906 1.0083102
6900 0.34804319 0 -0.042621786 1.0193906 1.0083102
7000 0.35357865 0 -0.067248959 1.0083102 1.0083102
7100 0.33556885 0 -0.10983726 1.0193906 1.0083102
7200 0.33531101 0 -0.112179 1.0304709 1.0083102
7300 0.35742607 0 -0.078405267 1.0304709 1.0193906
7400 0.34577559 0 -0.01985432 1.0193906 1.0083102
7500 0.3498641 0 0.052289439 1.0526316 1.0083102
7600 0.33773715 0 0.092939035 1.0083102 1.0193906
7700 0.33093497 0 0.11924405 1.0304709 1.0083102
7800 0.31435814 0 0.12701724 1.0083102 1.0304709
7900 0.33132217 0 0.10793075 1.0083102 1.0083102
8000 0.33451798 0 0.077993125 1.0304709 1.0193906
8100 0.35188371 0 0.019929977 1.0193906 1.0083102
8200 0.33645742 0 -0.039302079 1.0193906 1.0193906
8300 0.3415632 0 -0.098067982 1.0193906 1.0083102
8400 0.30619282 0 -0.12952879 1.0304709 1.0193906
8500 0.34446484 0 -0.098084709 1.0083102 1.0083102
8600 0.33761673 0 -0.07069818 1.0193906 1.0083102
8700 0.34495452 0 -0.022458056 1.0193906 1.0083102
8800 0.33502983 0 0.027742411 1.0193906 1.0083102
8900 0.35418591 0 0.092390134 1.0083102 1.0193906
9000 0.31648387 0 0.12467398 1.0193906 1.0083102
9100 0.33994825 0 0.14460327 1.0193906 1.0083102
9200 0.33822571 0 0.11273284 1.0193906 1.0083102
9300 0.33260773 0 0.060063671 1.0083102 1.0193906
9400 0.36140305 0 0.021427642 1.0193906 1.0083102
9500 0.34273562 0 -0.034064202 1.0193906 1.0083102
9600 0.33867054 0 -0.089076906 1.0193906 1.0083102
9700 0.32088235 0 -0.12027075 1.0193906 1.0083102
9800 0.3320823 0 -0.11602794 1.0415512 1.0083102
9900 0.33916442 0 -0.080281044 1.0083102 1.0083102
10000 0.34852268 0 -0.01000914 1.0193906 1.0083102
10100 0.32955942 0 0.04258493 1.0083102 1.0083102
10200 0.34487898 0 0.086971308 1.0304709 1.0083102
10300 0.32325593 0 0.11558149 1.0304709 1.0193906
10400 0.30927871 0 0.12239437 1.0083102 1.0083102
10500 0.33176799 0 0.12285937 1.0193906 1.0083102
10600 0.35120027 0 0.084897432 1.0415512 1.0083102
10700 0.33129697 0 0.0053089279 1.0193906 1.0193906
10800 0.36028769 0 -0.04280715 1.0193906 1.0083102
10900 0.35552287 0 -0.084955999 1.0193906 1.0193906
11000 0.3406024 0 -0.096554577 1.0083102 1.0083102
11100 0.33041202 0 -0.10703492 1.0304709 1.0193906
11200 0.32442686 0 -0.084328121 1.0304709 1.0193906
11300 0.35952468 0 -0.020191965 1.0304709 1.0083102
11400 0.34610624 0 0.03440148 1.0193906 1.0193906
11500 0.3415612 0 0.1041929 1.0193906 1.0083102
11600 0.34040042 0 0.13215705 1.0304709 1.0083102
11700 0.33555094 0 0.12738686 1.0415512 1.0193906
11800 0.3458647 0 0.10963398 1.0083102 1.0193906
11900 0.33836678 0 0.067253864 1.0193906 1.0193906
12000 0.34853314 0 0.03201448 1.0193906 1.0083102
12100 0.34600048 0 -0.034833402 1.0304709 1.0193906
12200 0.33145631 0 -0.09865675 1.0193906 1.0193906
12300 0.32848884 0 -0.1248489 1.0193906 1.0083102
12400 0.3321344 0 -0.11266575 1.0083102 1.0083102
12500 0.32622305 0 -0.061634993 1.0304709 1.0083102
12600 0.36213537 0 -0.0090593315 1.0526316 1.0083102
12700 0.34673866 0 0.036734645 1.0193906 1.0083102
12800 0.34606618 0 0.086267678 1.0193906 1.0083102
12900 0.34271431 0 0.12415522 1.0193906 1.0083102
13000 0.31993287 0 0.13879926 1.0193906 1.0193906
13100 0.3422918 0 0.11978905 1.0083102 1.0083102
13200 0.33055236 0 0.062620483 1.0083102 1.0083102
13300 0.34652207 0 0.0043833459 1.0304709 1.0083102
13400 0.33574661 0 -0.04691024 1.0304709 1.0083102
13500 0.33940837 0 -0.074241604 1.0304709 1.0083102
13600 0.32093414 0 -0.1078027 1.0193906 1.0083102
13700 0.34336597 0 -0.10544097 1.0193906 1.0083102
13800 0.35806461 0 -0.072531559 1.0193906 1.0083102
13900 0.35209713 0 -0.018851408 1.0193906 1.0083102
14000 0.35702629 0 0.061046366 1.0083102 1.0083102
14100 0.33234093 0 0.094086465 1.0083102 1.0083102
14200 0.3459466 0 0.12186656 1.0193906 1.0193906
14300 0.3327428 0 0.11396572 1.0193906 1.0083102
14400 0.32409443 0 0.10658903 1.0193906 1.0193906
14500 0.35022184 0 0.083558031 1.0083102 1.0083102
14600 0.34823843 0 0.024605569 1.0083102 1.0193906
14700 0.35298973 0 -0.040418888 1.0193906 1.0083102
14800 0.33679845 0 -0.10067728 1.0193906 1.0083102
14900 0.32790966 0 -0.10925568 1.0193906 1.0193906
15000 0.34208495 0 -0.09568004 1.0193906 1.0083102
15100 0.33647529 0 -0.055652929 1.0083102 1.0083102
15200 0.35328398 0 -0.020236536 1.0415512 1.0193906
15300 0.34252669 0 0.026434179 1.0304709 1.0083102
15400 0.34409435 0 0.094410599 1.0304709 1.0083102
15500 0.32288994 0 0.12034455 1.0304709 1.0193906
15600 0.32109689 0 0.13645185 1.0193906 1.0083102
15700 0.33681572 0 0.098607746 1.0415512 1.0193906
15800 0.33635195 0 0.05570715 1.0193906 1.0083102
15900 0.34289757 0 0.013849092 1.0304709 1.0083102
16000 0.34225547 0 -0.035597548 1.0304709 1.0083102
16100 0.33660991 0 -0.076931881 1.0193906 1.0193906
16200 0.32802152 0 -0.12765884 1.0083102 1.0193906
16300 0.3469374 0 -0.10785455 1.0083102 1.0083102
16400 0.34053641 0 -0.070259853 1.0193906 1.0083102
16500 0.34610591 0 -0.014315306 1.0193906 1.0193906
16600 0.35109001 0 0.041251169 1.0304709 1.0083102
16700 0.34336905 0 0.077996627 1.0193906 1.0083102
16800 0.33277414 0 0.11053634 1.0083102 1.0083102
16900 0.32183338 0 0.11680626 1.0193906 1.0083102
17000 0.34044352 0 0.10806555 1.0193906 1.0083102
17100 0.32967873 0 0.067759786 1.0193906 1.0193906
17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102
17300 0.35619435 0 -0.04215545 1.0193906 1.0083102
17400 0.34540936 0 -0.093994174 1.0193906 1.0083102
17500 0.33193585 0 -0.098831315 1.0083102 1.0193906
17600 0.3544756 0 -0.085660403 1.0193906 1.0083102
17700 0.34505209 0 -0.069640515 1.0304709 1.0193906
17800 0.36291124 0 -0.0063088133 1.0083102 1.0193906
17900 0.34255705 0 0.046794555 1.0304709 1.0193906
18000 0.34163238 0 0.11767705 1.0193906 1.0193906
18100 0.3466445 0 0.1351712 1.0415512 1.0193906
18200 0.33037668 0 0.12703659 1.0083102 1.0083102
18300 0.33677404 0 0.10956306 1.0083102 1.0304709
18400 0.34978954 0 0.087193072 1.0193906 1.0193906
18500 0.33354363 0 0.051095814 1.0526316 1.0193906
18600 0.34651729 0 0.0056245561 1.0304709 1.0193906
18700 0.32622232 0 -0.047319269 1.0083102 1.0193906
18800 0.32978847 0 -0.054929416 1.0304709 1.0193906
18900 0.34192451 0 -0.037252471 1.0193906 1.0083102
19000 0.34061294 0 -0.001167235 1.0083102 1.0083102
19100 0.34194478 0 0.016945224 1.0526316 1.0193906
19200 0.33321765 0 0.050665354 1.0526316 1.0083102
19300 0.33197783 0 0.080470585 1.0193906 1.0083102
19400 0.33284715 0 0.12423599 1.0304709 1.0304709
19500 0.33867856 0 0.12689524 1.0083102 1.0083102
19600 0.36092786 0 0.11417704 1.0193906 1.0083102
19700 0.34270183 0 0.069038291 1.0415512 1.0083102
19800 0.34880695 0 0.042483681 1.0193906 1.0083102
19900 0.33903644 0 0.034788638 1.0083102 1.0193906
20000 0.32590125 0 0.011383785 1.0193906 1.0083102
20100 0.30358859 0 0.0030743554 1.0526316 1.0193906
20200 0.31830224 0 0.017637826 1.0193906 1.0193906
20300 0.34195438 0 0.072811099 1.0304709 1.0193906
20400 0.31249563 0 0.10063541 1.0415512 1.0083102
20500 0.31544938 0 0.1405794 1.0083102 1.0083102
20600 0.30071644 0 0.12763486 1.0193906 1.0193906
20700 0.2890265 0 0.1136651 1.0083102 1.0083102
20800 0.28962296 0 0.094481978 1.0193906 1.0083102
20900 0.29447212 0 0.0967165 1.0193906 1.0193906
21000 0.31159961 0 0.067307231 1.0083102 1.0083102
21100 0.30490648 0 0.017689358 1.0083102 1.0304709
21200 0.30687262 0 -0.016055512 1.0193906 1.0193906
21300 0.30083286 0 -0.0014988997 1.0193906 1.0083102
21400 0.32070426 0 0.015960302 1.0083102 1.0083102
21500 0.31439311 0 0.038170385 1.0304709 1.0083102
21600 0.32617832 0 0.043263788 1.0083102 1.0083102
21700 0.35151793 0 0.066302727 1.0193906 1.0083102
21800 0.35912885 0 0.070099103 1.0193906 1.0083102
21900 0.32451958 0 0.068935768 1.0304709 1.0193906
22000 0.35219298 0 0.067161227 1.0193906 1.0193906
22100 0.34857705 0 0.032731746 1.0193906 1.0083102
22200 0.34750227 0 0.0056917695 1.0193906 1.0083102
22300 0.34766017 0 -0.0027090483 1.0193906 1.0083102
22400 0.33426062 0 -0.023196063 1.0304709 1.0083102
22500 0.34174625 0 -0.025019717 1.0083102 1.0083102
22600 0.3356145 0 -0.029707418 1.0304709 1.0193906
22700 0.3362653 0 -0.035815733 1.0193906 1.0193906
22800 0.33973405 0 -0.0024705835 1.0193906 1.0083102
22900 0.33813085 0 0.0077527467 1.0083102 1.0193906
23000 0.33339981 0 0.028340744 1.0193906 1.0083102
23100 0.34079832 0 0.018521302 1.0415512 1.0193906
23200 0.33074548 0 0.032378405 1.0193906 1.0083102
23300 0.32965664 0 0.035989589 1.0193906 1.0083102
23400 0.30927749 0 0.024581106 1.0193906 1.0083102
23500 0.32890632 0 0.01092479 1.0304709 1.0193906
23600 0.34137438 0 0.0094839745 1.0193906 1.0193906
23700 0.34512638 0 -0.012392771 1.0304709 1.0193906
23800 0.31781354 0 -0.012908449 1.0193906 1.0083102
23900 0.32405513 0 -0.015018071 1.0415512 1.0193906
24000 0.33549728 0 -0.012812915 1.0193906 1.0193906
24100 0.31368736 0 -0.020818372 1.0083102 1.0083102
24200 0.33533836 0 0.0056121057 1.0304709 1.0193906
24300 0.32530627 0 0.018183931 1.0415512 1.0083102
24400 0.31930662 0 0.027446878 1.0083102 1.0193906
24500 0.33540302 0 0.040307455 1.0304709 1.0083102
24600 0.34020431 0 0.027403921 1.0083102 1.0083102
24700 0.3291814 0 0.01204865 1.0193906 1.0083102
24800 0.31552604 0 0.019654111 1.0083102 1.0193906
24900 0.34727253 0 0.01670543 1.0193906 1.0083102
25000 0.35120105 0 0.0038617562 1.0193906 1.0083102
25100 0.32706871 0 -0.021196623 1.0415512 1.0193906
25200 0.32915282 0 -0.017146508 1.0083102 1.0193906
25300 0.32577518 0 -0.01312495 1.0193906 1.0083102
25400 0.33286855 0 0.0014726193 1.0415512 1.0193906
25500 0.33002601 0 0.0080974022 1.0193906 1.0083102
25600 0.34127655 0 0.014296091 1.0526316 1.0083102
25700 0.34048065 0 0.022513032 1.0193906 1.0083102
25800 0.33029079 0 0.038733531 1.0526316 1.0083102
25900 0.33031324 0 0.026156982 1.0083102 1.0193906
26000 0.32967371 0 0.028727383 1.0083102 1.0193906
26100 0.33775718 0 0.015607478 1.0083102 1.0193906
26200 0.35097144 0 0.012291703 1.0083102 1.0083102
26300 0.34303792 0 0.00094823191 1.0083102 1.0193906
26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906
26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906
26600 0.33063188 0 -0.020378601 1.0083102 1.0193906
26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906
26800 0.32998532 0 0.015932208 1.0304709 1.0193906
26900 0.33825444 0 0.010428603 1.0304709 1.0083102
27000 0.32081518 0 0.019818223 1.0415512 1.0193906
27100 0.31448098 0 0.020093416 1.0193906 1.0083102
27200 0.32643684 0 0.021934917 1.0193906 1.0083102
27300 0.33289466 0 0.023713072 1.0415512 1.0083102
27400 0.32310744 0 0.024110945 1.0415512 1.0083102
27500 0.33115619 0 0.0025776713 1.0304709 1.0193906
27600 0.33295887 0 -0.010710764 1.0193906 1.0193906
27700 0.32968876 0 -0.0064595905 1.0193906 1.0193906
27800 0.34064581 0 -0.0086519116 1.0193906 1.0083102
27900 0.33559187 0 -0.0055753593 1.0526316 1.0083102
28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102
28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102
28200 0.35532383 0 0.013646951 1.0304709 1.0083102
28300 0.31507942 0 0.026532255 1.0415512 1.0193906
28400 0.32711006 0 0.033214981 1.0193906 1.0083102
28500 0.34472462 0 0.028050837 1.0304709 1.0193906
28600 0.33708059 0 0.019115676 1.0083102 1.0083102
28700 0.34478087 0 0.023743689 1.0304709 1.0083102
28800 0.34546686 0 0.0081772997 1.0304709 1.0083102
28900 0.34004886 0 0.017771865 1.0415512 1.0193906
29000 0.33604232 0 -0.010505671 1.0304709 1.0193906
29100 0.33541374 0 -0.016273261 1.0083102 1.0083102
29200 0.34347489 0 -0.010002306 1.0083102 1.0083102
29300 0.34083904 0 0.0089701784 1.0193906 1.0193906
29400 0.34846892 0 0.020765104 1.0083102 1.0083102
29500 0.3416255 0 0.022650856 1.0304709 1.0083102
29600 0.33725496 0 0.020693083 1.0193906 1.0193906
29700 0.34480638 0 0.024317128 1.0304709 1.0083102
29800 0.31459471 0 0.023097895 1.0083102 1.0083102
29900 0.33014448 0 0.03114046 1.0193906 1.0083102
30000 0.33741498 0 0.015624314 1.0083102 1.0193906
30100 0.32598657 0 -0.0018860541 1.0415512 1.0193906
30200 0.34855815 0 0.0017983372 1.0083102 1.0083102
30300 0.33375921 0 0.0010991235 1.0083102 1.0193906
30400 0.35008944 0 -0.0027316177 1.0193906 1.0083102
30500 0.33279729 0 -0.0035788551 1.0193906 1.0193906
30600 0.33868746 0 -0.0016249482 1.0083102 1.0193906
30700 0.33597034 0 -0.0014524001 1.0193906 1.0193906
30800 0.3227257 0 0.016353457 1.0193906 1.0193906
30900 0.32676516 0 0.027396654 1.0193906 1.0083102
31000 0.34083982 0 0.031606413 1.0415512 1.0193906
31100 0.32165238 0 0.013583368 1.0083102 1.0083102
31200 0.3428492 0 0.020486611 1.0304709 1.0083102
31300 0.32372541 0 0.01215566 1.0083102 1.0083102
31400 0.32734692 0 0.016229397 1.0083102 1.0083102
31500 0.33089262 0 0.0060426618 1.0083102 1.0083102
31600 0.34273493 0 -0.013456537 1.0083102 1.0193906
31700 0.32723905 0 -0.019243766 1.0193906 1.0083102
31800 0.33636488 0 0.0027814902 1.0083102 1.0083102
31900 0.32834805 0 0.00706877 1.0083102 1.0193906
32000 0.33995148 0 0.0018383309 1.0193906 1.0193906
32100 0.33412282 0 0.0076455933 1.0083102 1.0083102
32200 0.34334884 0 0.023586129 1.0083102 1.0083102
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
32400 0.33163443 0 0.038878463 1.0193906 1.0083102
32500 0.32290345 0 0.022247461 1.0193906 1.0083102
32600 0.34113954 0 0.010966365 1.0304709 1.0193906
32700 0.33390633 0 0.0037777555 1.0193906 1.0083102
32800 0.34385341 0 0.010556575 1.0193906 1.0193906
32900 0.32137047 0 0.00022027143 1.0304709 1.0193906
33000 0.32079172 0 -0.017261272 1.0193906 1.0083102
33100 0.33570882 0 -0.0051942206 1.0083102 1.0083102
33200 0.34320894 0 -0.011515281 1.0193906 1.0083102
33300 0.32794746 0 -0.0018153673 1.0083102 1.0193906
33400 0.33060982 0 0.027118146 1.0193906 1.0083102
33500 0.33641809 0 0.02143035 1.0083102 1.0193906
33600 0.33643061 0 0.020833068 1.0304709 1.0083102
33700 0.3485949 0 0.030918751 1.0193906 1.0083102
33800 0.3283985 0 0.01947613 1.0193906 1.0083102
33900 0.31959761 0 0.021128147 1.0083102 1.0304709
34000 0.33897984 0 0.015270986 1.0193906 1.0083102
34100 0.32392267 0 0.0020130852 1.0304709 1.0193906
34200 0.33084514 0 -0.024316708 1.0193906 1.0193906
34300 0.3342259 0 -0.0059047764 1.0193906 1.0304709
34400 0.33385098 0 0.0063818721 1.0193906 1.0083102
34500 0.33255603 0 -0.01023837 1.0083102 1.0304709
34600 0.34766173 0 0.0056703013 1.0193906 1.0083102
34700 0.339822 0 0.0061648559 1.0193906 1.0193906
34800 0.33902329 0 0.030037037 1.0415512 1.0193906
34900 0.3216153 0 0.027996689 1.0083102 1.0083102
35000 0.32701056 0 0.024778517 1.0193906 1.0083102
35100 0.3124942 0 0.011316548 1.0304709 1.0193906
35200 0.34486416 0 0.011670127 1.0083102 1.0083102
35300 0.33275353 0 0.020491246 1.0193906 1.0193906
35400 0.33618763 0 0.014678874 1.0083102 1.0083102
35500 0.32352282 0 -0.018568683 1.0193906 1.0193906
35600 0.32617903 0 -0.012796912 1.0193906 1.0304709
35700 0.32378048 0 -0.021318585 1.0193906 1.0193906
35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906
35900 0.33818476 0 0.011197742 1.0193906 1.0083102
36000 0.35142144 0 0.022520935 1.0083102 1.0193906
36100 0.35147297 0 0.020277852 1.0193906 1.0083102
36200 0.33489465 0 0.014564878 1.0415512 1.0193906
36300 0.33841515 0 0.036439962 1.0193906 1.0083102
36400 0.32301096 0 0.019966746 1.0304709 1.0083102
36500 0.35612028 0 0.036509556 1.0083102 1.0083102
36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906
36700 0.34477654 0 -0.0052770853 1.0193906 1.0083102
36800 0.33804317 0 -0.013751733 1.0083102 1.0083102
36900 0.35003816 0 -0.0021184393 1.0083102 1.0083102
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
37200 0.35019871 0 -0.0071740923 1.0193906 1.0304709
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
37400 0.35739859 0 0.020892822 1.0304709 1.0083102
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
37800 0.343987 0 0.029579795 1.0083102 1.0083102
37900 0.33610448 0 0.036836828 1.0415512 1.0304709
38000 0.32757228 0 0.020902031 1.0193906 1.0193906
38100 0.32735808 0 0.019544751 1.0193906 1.0083102
38200 0.35646953 0 0.044607528 1.0083102 1.0304709
38300 0.32509773 0 0.03610738 1.0193906 1.0083102
38400 0.32111741 0 0.034474043 1.0193906 1.0193906
38500 0.30590608 0 0.053461212 1.0304709 1.0083102
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
39300 0.34519653 0 0.046257301 1.0193906 1.0083102
39400 0.34351844 0 0.052422917 1.0304709 1.0304709
39500 0.35716037 0 0.048916058 1.0304709 1.0083102
39600 0.34000737 0 0.016149089 1.0304709 1.0083102
39700 0.34587892 0 0.021619621 1.0526316 1.0083102
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
39900 0.35225411 0 -0.011341599 1.0083102 1.0193906
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
Loop time of 1.12306 on 4 procs for 40000 steps with 361 atoms
Performance: 15386559.518 tau/day, 35617.036 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.023094 | 0.023348 | 0.023582 | 0.1 | 2.08
Bond | 0.17827 | 0.19268 | 0.21984 | 3.7 | 17.16
Neigh | 0.18144 | 0.18231 | 0.18323 | 0.1 | 16.23
Comm | 0.23759 | 0.28095 | 0.30794 | 5.0 | 25.02
Output | 0.0062952 | 0.013342 | 0.034226 | 10.4 | 1.19
Modify | 0.2379 | 0.24327 | 0.25076 | 0.9 | 21.66
Other | | 0.1871 | | | 16.66
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 59.25 ave 61 max 56 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0
Total wall time: 0:00:01

227
examples/balance/log.27Nov18.balance.clock.dynamic.g++.2
View File

@ -1,227 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000549078 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
Loop time of 3.7099 on 2 procs for 500 steps with 4000 atoms
Performance: 58222.644 tau/day, 134.775 timesteps/s
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5145 | 2.5951 | 2.6756 | 5.0 | 69.95
Neigh | 0.8388 | 0.88634 | 0.93387 | 5.0 | 23.89
Comm | 0.17027 | 0.20258 | 0.23489 | 7.2 | 5.46
Output | 0.00029612 | 0.00032723 | 0.00035834 | 0.0 | 0.01
Modify | 0.016136 | 0.017057 | 0.017979 | 0.7 | 0.46
Other | | 0.008504 | | | 0.23
Nlocal: 2000 ave 2157 max 1843 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10465.5 ave 10840 max 10091 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298070 ave 305706 max 290433 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596139
Ave neighs/atom = 149.035
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.944 | 4.947 | 4.951 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
Loop time of 3.70634 on 2 procs for 500 steps with 4000 atoms
Performance: 58278.514 tau/day, 134.904 timesteps/s
99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5536 | 2.6173 | 2.6811 | 3.9 | 70.62
Neigh | 0.82942 | 0.88683 | 0.94424 | 6.1 | 23.93
Comm | 0.16927 | 0.17474 | 0.1802 | 1.3 | 4.71
Output | 0.00030422 | 0.00033307 | 0.00036192 | 0.0 | 0.01
Modify | 0.016714 | 0.017824 | 0.018933 | 0.8 | 0.48
Other | | 0.009277 | | | 0.25
Nlocal: 2000 ave 2136 max 1864 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10413.5 ave 10877 max 9950 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 300836 ave 312313 max 289358 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 601671
Ave neighs/atom = 150.418
Neighbor list builds = 51
Dangerous builds = 0
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
run 500
Per MPI rank memory allocation (min/avg/max) = 4.951 | 5.142 | 5.334 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418133 4738.2137
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
Loop time of 4.8272 on 2 procs for 500 steps with 4000 atoms
Performance: 44746.478 tau/day, 103.580 timesteps/s
98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9951 | 2.6814 | 3.3676 | 41.9 | 55.55
Neigh | 0.82826 | 0.90961 | 0.99095 | 8.5 | 18.84
Comm | 0.44043 | 1.2083 | 1.9762 | 69.9 | 25.03
Output | 0.00034881 | 0.0003655 | 0.00038218 | 0.0 | 0.01
Modify | 0.016762 | 0.01755 | 0.018337 | 0.6 | 0.36
Other | | 0.01001 | | | 0.21
Nlocal: 2000 ave 2564 max 1436 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10334 ave 10752 max 9916 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 302958 ave 499873 max 106044 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 605917
Ave neighs/atom = 151.479
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.955 | 5.336 | 5.717 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
1550 0.53713591 -6.2504068 0 -5.4449044 -1.7647087 4738.2137
1600 0.5467956 -6.2646482 0 -5.4446599 -1.8115778 4738.2137
1650 0.53806575 -6.2519004 0 -5.4450036 -1.7409135 4738.2137
1700 0.5347949 -6.2468958 0 -5.444904 -1.7162322 4738.2137
1750 0.53714528 -6.2506529 0 -5.4451365 -1.7340402 4738.2137
1800 0.5274989 -6.2358675 0 -5.444817 -1.6874989 4738.2137
1850 0.54585906 -6.2629475 0 -5.4443636 -1.7758918 4738.2137
1900 0.5301071 -6.2387551 0 -5.4437932 -1.6381903 4738.2137
1950 0.54288149 -6.2582818 0 -5.4441632 -1.7367819 4738.2137
2000 0.52766162 -6.2348587 0 -5.4435642 -1.5589151 4738.2137
Loop time of 4.90351 on 2 procs for 500 steps with 4000 atoms
Performance: 44050.062 tau/day, 101.968 timesteps/s
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9937 | 2.6502 | 3.3067 | 40.3 | 54.05
Neigh | 0.81645 | 0.88655 | 0.95664 | 7.4 | 18.08
Comm | 0.61197 | 1.3389 | 2.0659 | 62.8 | 27.31
Output | 0.00036287 | 0.0003773 | 0.00039172 | 0.0 | 0.01
Modify | 0.016585 | 0.017429 | 0.018274 | 0.6 | 0.36
Other | | 0.01003 | | | 0.20
Nlocal: 2000 ave 2564 max 1436 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10256 ave 10620 max 9892 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 303988 ave 502064 max 105911 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 607975
Ave neighs/atom = 151.994
Neighbor list builds = 51
Dangerous builds = 0
Total wall time: 0:00:17

227
examples/balance/log.27Nov18.balance.clock.dynamic.g++.4
View File

@ -1,227 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000421762 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
Loop time of 2.69458 on 4 procs for 500 steps with 4000 atoms
Performance: 80160.913 tau/day, 185.558 timesteps/s
94.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0903 | 1.4509 | 1.7199 | 22.5 | 53.84
Neigh | 0.31688 | 0.47906 | 0.71852 | 24.2 | 17.78
Comm | 0.60463 | 0.72402 | 0.84257 | 12.7 | 26.87
Output | 0.00035119 | 0.00067121 | 0.0015202 | 0.0 | 0.02
Modify | 0.00811 | 0.010936 | 0.014029 | 2.7 | 0.41
Other | | 0.02904 | | | 1.08
Nlocal: 1000 ave 1504 max 634 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8759.25 ave 9896 max 8021 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149308 ave 179946 max 116419 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 597231
Ave neighs/atom = 149.308
Neighbor list builds = 50
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
Loop time of 2.64502 on 4 procs for 500 steps with 4000 atoms
Performance: 81662.873 tau/day, 189.034 timesteps/s
93.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1279 | 1.4127 | 1.6268 | 18.0 | 53.41
Neigh | 0.32225 | 0.49572 | 0.76053 | 26.2 | 18.74
Comm | 0.64504 | 0.6974 | 0.75498 | 5.7 | 26.37
Output | 0.00035477 | 0.00062996 | 0.001343 | 0.0 | 0.02
Modify | 0.0077929 | 0.010538 | 0.013856 | 2.6 | 0.40
Other | | 0.02803 | | | 1.06
Nlocal: 1000 ave 1437 max 597 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 8674 ave 9370 max 8013 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 150170 ave 187030 max 102149 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 600678
Ave neighs/atom = 150.169
Neighbor list builds = 53
Dangerous builds = 0
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
run 500
Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
Loop time of 2.61342 on 4 procs for 500 steps with 4000 atoms
Performance: 82650.254 tau/day, 191.320 timesteps/s
93.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.222 | 1.4442 | 1.5812 | 12.3 | 55.26
Neigh | 0.29672 | 0.48201 | 0.73859 | 27.6 | 18.44
Comm | 0.59138 | 0.65738 | 0.70906 | 6.5 | 25.15
Output | 0.00036502 | 0.00091559 | 0.0020845 | 0.0 | 0.04
Modify | 0.0095406 | 0.012674 | 0.017643 | 2.8 | 0.48
Other | | 0.01621 | | | 0.62
Nlocal: 1000 ave 1446 max 670 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8641 ave 9376 max 8019 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 150494 ave 184085 max 105390 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 601974
Ave neighs/atom = 150.494
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
1550 0.55327018 -6.2750125 0 -5.4453148 -1.9506585 4738.2137
1600 0.5441901 -6.2612622 0 -5.4451811 -1.8559436 4738.2137
1650 0.54710046 -6.2661938 0 -5.4457483 -1.8882766 4738.2137
1700 0.5366569 -6.2504957 0 -5.4457116 -1.8067998 4738.2137
1750 0.5486468 -6.2681121 0 -5.4453476 -1.8662631 4738.2137
1800 0.54476176 -6.2615037 0 -5.4445653 -1.8352743 4738.2137
1850 0.5414305 -6.2555519 0 -5.4436091 -1.8005747 4738.2137
1900 0.53992655 -6.2541344 0 -5.444447 -1.7768718 4738.2137
1950 0.54666071 -6.2640943 0 -5.4443082 -1.7947052 4738.2137
2000 0.54556196 -6.2625262 0 -5.4443879 -1.8071631 4738.2137
Loop time of 2.81593 on 4 procs for 500 steps with 4000 atoms
Performance: 76706.532 tau/day, 177.561 timesteps/s
90.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2508 | 1.4839 | 1.6521 | 13.4 | 52.70
Neigh | 0.34188 | 0.54016 | 0.82358 | 27.6 | 19.18
Comm | 0.70575 | 0.75254 | 0.80167 | 4.6 | 26.72
Output | 0.00041604 | 0.001362 | 0.0041099 | 4.3 | 0.05
Modify | 0.010564 | 0.013653 | 0.018 | 2.7 | 0.48
Other | | 0.02432 | | | 0.86
Nlocal: 1000 ave 1555 max 569 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 8672.75 ave 9821 max 7993 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 151656 ave 164603 max 133455 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 606625
Ave neighs/atom = 151.656
Neighbor list builds = 56
Dangerous builds = 0
Total wall time: 0:00:10

195
examples/balance/log.27Nov18.balance.clock.static.g++.2
View File

@ -1,195 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000517368 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000522375 seconds
iteration count = 1
time weight factor: 1
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162
200 0.536665 -6.2530113 0 -5.448215 -1.933468
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
Loop time of 1.96356 on 2 procs for 250 steps with 4000 atoms
Performance: 55002.186 tau/day, 127.320 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0024 | 1.243 | 1.4835 | 21.6 | 63.30
Neigh | 0.3963 | 0.41601 | 0.43572 | 3.1 | 21.19
Comm | 0.032948 | 0.29324 | 0.55353 | 48.1 | 14.93
Output | 0.00013924 | 0.00014722 | 0.00015521 | 0.0 | 0.01
Modify | 0.0072696 | 0.0073524 | 0.0074351 | 0.1 | 0.37
Other | | 0.003842 | | | 0.20
Nlocal: 2000 ave 2051 max 1949 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10443 ave 10506 max 10380 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 363449 max 233215 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 24
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
rebalancing time: 0.000424623 seconds
iteration count = 3
time weight factor: 1
initial/final max load/proc = 1.91926 1.6972
initial/final imbalance factor = 1.15689 1.02304
x cuts: 0 0.4375 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.685 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
Loop time of 1.84751 on 2 procs for 250 steps with 4000 atoms
Performance: 58457.127 tau/day, 135.317 timesteps/s
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1214 | 1.2291 | 1.3368 | 9.7 | 66.53
Neigh | 0.37418 | 0.41926 | 0.46434 | 7.0 | 22.69
Comm | 0.033842 | 0.18738 | 0.34091 | 35.5 | 10.14
Output | 0.00016665 | 0.00018752 | 0.00020838 | 0.0 | 0.01
Modify | 0.0062993 | 0.0072798 | 0.0082603 | 1.1 | 0.39
Other | | 0.00428 | | | 0.23
Nlocal: 2000 ave 2284 max 1716 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10450 ave 10742 max 10158 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298063 ave 326003 max 270123 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596126
Ave neighs/atom = 149.031
Neighbor list builds = 25
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
rebalancing time: 0.000502825 seconds
iteration count = 3
time weight factor: 1
initial/final max load/proc = 1.80118 1.79434
initial/final imbalance factor = 1.0927 1.08854
x cuts: 0 0.507812 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523
Loop time of 2.03694 on 2 procs for 250 steps with 4000 atoms
Performance: 53020.655 tau/day, 122.733 timesteps/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.92132 | 1.2301 | 1.5389 | 27.8 | 60.39
Neigh | 0.3924 | 0.42313 | 0.45386 | 4.7 | 20.77
Comm | 0.032816 | 0.37246 | 0.71211 | 55.7 | 18.29
Output | 0.00013733 | 0.00014532 | 0.0001533 | 0.0 | 0.01
Modify | 0.0069692 | 0.0072372 | 0.0075052 | 0.3 | 0.36
Other | | 0.003856 | | | 0.19
Nlocal: 2000 ave 2097 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10439.5 ave 10561 max 10318 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 299628 ave 378859 max 220397 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 599256
Ave neighs/atom = 149.814
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:05

195
examples/balance/log.27Nov18.balance.clock.static.g++.4
View File

@ -1,195 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000427961 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000848055 seconds
iteration count = 2
time weight factor: 1
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.713 | 4.188 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
Loop time of 1.50594 on 4 procs for 250 steps with 4000 atoms
Performance: 71716.080 tau/day, 166.009 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34764 | 0.66777 | 1.2288 | 43.4 | 44.34
Neigh | 0.1594 | 0.20524 | 0.2451 | 7.5 | 13.63
Comm | 0.039175 | 0.62421 | 0.93047 | 45.4 | 41.45
Output | 0.00015855 | 0.00024235 | 0.00047231 | 0.0 | 0.02
Modify | 0.0028908 | 0.0039527 | 0.0049407 | 1.2 | 0.26
Other | | 0.004522 | | | 0.30
Nlocal: 1000 ave 1263 max 712 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 8711.5 ave 9045 max 8325 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 149325 ave 275165 max 77227 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 597299
Ave neighs/atom = 149.325
Neighbor list builds = 23
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
rebalancing time: 0.000421047 seconds
iteration count = 4
time weight factor: 1
initial/final max load/proc = 1.45871 0.956175
initial/final imbalance factor = 1.6709 1.09526
x cuts: 0 0.296875 0.453125 0.628906 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.787 | 3.907 | 4.192 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
Loop time of 1.24397 on 4 procs for 250 steps with 4000 atoms
Performance: 86819.073 tau/day, 200.970 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4612 | 0.67729 | 0.88321 | 20.9 | 54.45
Neigh | 0.14175 | 0.20919 | 0.28903 | 13.7 | 16.82
Comm | 0.19855 | 0.34785 | 0.48428 | 18.8 | 27.96
Output | 0.00016665 | 0.00030792 | 0.00066757 | 0.0 | 0.02
Modify | 0.0027177 | 0.0053391 | 0.010109 | 4.1 | 0.43
Other | | 0.003992 | | | 0.32
Nlocal: 1000 ave 1462 max 652 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8657 ave 9421 max 7969 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 149356 ave 195930 max 106343 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 597424
Ave neighs/atom = 149.356
Neighbor list builds = 24
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
rebalancing time: 0.000288963 seconds
iteration count = 5
time weight factor: 1
initial/final max load/proc = 1.03814 0.978524
initial/final imbalance factor = 1.17108 1.10383
x cuts: 0 0.301758 0.448242 0.60144 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.804 | 3.927 | 4.209 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
Loop time of 1.14445 on 4 procs for 250 steps with 4000 atoms
Performance: 94368.537 tau/day, 218.446 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 | 0.52287 | 0.67351 | 0.79602 | 13.2 | 58.85
Neigh | 0.14306 | 0.21848 | 0.31638 | 16.2 | 19.09
Comm | 0.19457 | 0.24404 | 0.29562 | 7.2 | 21.32
Output | 0.00016236 | 0.00029993 | 0.00065851 | 0.0 | 0.03
Modify | 0.0024104 | 0.0038835 | 0.0057485 | 2.3 | 0.34
Other | | 0.004232 | | | 0.37
Nlocal: 1000 ave 1522 max 593 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8754 ave 9866 max 8002 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149124 ave 182694 max 120516 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 596497
Ave neighs/atom = 149.124
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:03

209
examples/balance/log.27Nov18.balance.g++.2
View File

@ -1,209 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.000478506 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.061 | 3.065 | 3.07 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -29.143179 -1.2407285 2 1.0193906
100 26.269576 -29.713313 7.9052334 1.1135734 1.0027701
200 26.368336 -29.809962 1.6412462 1.0803324 1.0027701
300 26.479082 -29.920083 2.3678653 1.1578947 1.0083102
400 26.522239 -29.965537 6.6787858 1.1578947 1.0083102
500 25.725591 -29.168034 0.67065285 1.1024931 1.0083102
600 26.247693 -29.692706 7.9887712 1.1301939 1.0027701
700 26.237368 -29.676926 1.5987214 1.1578947 1.0027701
800 25.889643 -29.431589 4.6160859 1.1523546 1.0027701
900 23.635295 -27.372963 9.029962 1.1468144 1.0027701
1000 22.571904 -25.87422 1.8936085 1.1191136 1.0083102
1100 17.493795 -21.447274 9.502619 1.0747922 1.0027701
1200 17.214459 -20.726965 6.3578919 1.0193906 1.0083102
1300 16.424217 -19.757401 3.9026861 1.0083102 1.0027701
1400 15.051731 -18.13464 1.7558146 1.0249307 1.0027701
1500 13.966718 -17.051915 1.4843674 1.0470914 1.0027701
1600 13.615641 -16.582695 1.7845355 1.0415512 1.0027701
1700 13.278822 -16.278248 1.8263176 1.0470914 1.0083102
1800 12.680841 -15.81089 2.0096239 1.0415512 1.0027701
1900 12.039167 -14.99225 1.4379549 1.0360111 1.0027701
2000 12.298923 -15.188233 1.6287319 1.0249307 1.0027701
2100 12.048347 -14.947484 1.0583787 1.0304709 1.0027701
2200 12.024664 -14.91864 1.0617555 1.0304709 1.0027701
2300 11.878263 -14.769923 1.2892425 1.0360111 1.0027701
2400 11.578448 -14.525725 1.2925126 1.0083102 1.0027701
2500 11.948793 -14.736647 1.5473169 1.0249307 1.0027701
2600 11.933924 -14.725605 1.3673896 1.0249307 1.0027701
2700 11.622855 -14.414518 1.3035925 1.0304709 1.0083102
2800 10.600538 -13.451379 1.3422508 1.0138504 1.0027701
2900 10.404739 -13.242902 1.3070821 1.0083102 1.0027701
3000 10.73199 -13.60699 0.92518136 1.0138504 1.0027701
3100 10.807664 -13.624775 1.3037969 1.0193906 1.0027701
3200 10.393964 -13.212022 0.72081929 1.0027701 1.0027701
3300 9.8733371 -12.65719 1.1606833 1.0138504 1.0027701
3400 9.6206594 -12.349773 0.69859994 1.0138504 1.0027701
3500 9.5882688 -12.32291 1.0028888 1.0138504 1.0027701
3600 9.693129 -12.441628 0.94751509 1.0193906 1.0083102
3700 9.3727837 -12.162354 1.9639195 1.0027701 1.0027701
3800 9.1011581 -11.860999 1.0253876 1.0083102 1.0027701
3900 8.6637799 -11.44226 1.4848652 1.0027701 1.0027701
4000 9.0454579 -11.770928 0.82719098 1.0083102 1.0083102
4100 8.5574492 -11.30614 0.82422479 1.0193906 1.0027701
4200 8.5903538 -11.322978 0.45091349 1.0027701 1.0027701
4300 8.540208 -11.282844 0.55403945 1.0027701 1.0027701
4400 7.7043293 -10.372194 0.80170046 1.0027701 1.0027701
4500 7.3429905 -9.9970461 0.77097228 1.0193906 1.0027701
4600 7.35485 -9.9992837 0.66531873 1.0027701 1.0027701
4700 7.3278467 -9.9885021 0.99577458 1.0193906 1.0027701
4800 7.8179777 -10.468758 0.56434522 1.0138504 1.0083102
4900 7.571002 -10.215558 0.81064116 1.0138504 1.0027701
5000 7.5326417 -10.224594 0.86387082 1.0083102 1.0027701
5100 7.8120521 -10.468885 0.86739094 1.0027701 1.0027701
5200 7.2949975 -10.041278 1.0298349 1.0027701 1.0027701
5300 7.6564811 -10.297993 0.71060925 1.0027701 1.0083102
5400 7.7359804 -10.373635 0.61872932 1.0027701 1.0083102
5500 7.6511513 -10.279058 0.87569767 1.0027701 1.0027701
5600 7.2927879 -9.9378811 1.1573049 1.0083102 1.0083102
5700 7.1836162 -9.8357325 0.43012076 1.0083102 1.0083102
5800 7.3405818 -9.9780947 0.69346928 1.0083102 1.0027701
5900 7.6636501 -10.323536 0.82554433 1.0027701 1.0027701
6000 7.3515582 -9.9803466 1.09521 1.0138504 1.0027701
6100 7.0275875 -9.6739554 0.48460922 1.0027701 1.0027701
6200 7.1449226 -9.7541904 0.83007096 1.0193906 1.0083102
6300 7.036185 -9.6445595 1.0982599 1.0193906 1.0027701
6400 7.1288989 -9.7501637 1.0103414 1.0138504 1.0027701
6500 6.6559525 -9.256798 0.58741228 1.0027701 1.0027701
6600 7.0559949 -9.6563848 0.53504661 1.0027701 1.0027701
6700 7.124289 -9.7613906 0.70816625 1.0027701 1.0027701
6800 7.0141849 -9.6298357 0.55987809 1.0083102 1.0027701
6900 6.8617323 -9.4376408 0.62371253 1.0193906 1.0083102
7000 6.7496366 -9.3379578 0.83540012 1.0027701 1.0083102
7100 7.0418565 -9.664915 0.68231111 1.0083102 1.0027701
7200 6.6175362 -9.2066737 0.31371885 1.0138504 1.0027701
7300 7.076179 -9.6917457 1.0827515 1.0083102 1.0027701
7400 6.5263123 -9.1321276 1.1892921 1.0027701 1.0027701
7500 6.8072952 -9.3976358 0.60458526 1.0138504 1.0027701
7600 6.610006 -9.1934492 0.54359615 1.0193906 1.0027701
7700 6.3533198 -8.943515 0.91970357 1.0138504 1.0027701
7800 6.7226774 -9.3164434 0.81151352 1.0027701 1.0083102
7900 6.2329222 -8.8531998 0.59439797 1.0083102 1.0027701
8000 6.5818943 -9.2025911 0.66303132 1.0083102 1.0027701
8100 6.372739 -8.9403406 0.81325975 1.0138504 1.0027701
8200 6.462003 -9.0346265 0.54917879 1.0083102 1.0027701
8300 6.5947825 -9.2171877 0.9005455 1.0027701 1.0027701
8400 6.7803374 -9.4179158 0.37270772 1.0027701 1.0027701
8500 6.7122886 -9.3363107 0.77011047 1.0083102 1.0027701
8600 6.8286386 -9.4264779 0.35815593 1.0027701 1.0027701
8700 6.4796483 -9.0676554 0.84568363 1.0138504 1.0027701
8800 6.551896 -9.1793668 1.0319947 1.0083102 1.0027701
8900 6.1879163 -8.7590749 0.34445309 1.0027701 1.0027701
9000 6.2374494 -8.7872159 0.46749314 1.0027701 1.0027701
9100 6.3605933 -8.9335681 0.86786624 1.0027701 1.0027701
9200 6.4387791 -9.0144583 0.56089061 1.0083102 1.0027701
9300 6.2745383 -8.9019836 0.58565081 1.0083102 1.0027701
9400 6.1957924 -8.7638279 0.65785826 1.0027701 1.0083102
9500 6.079287 -8.6556289 0.47532552 1.0083102 1.0027701
9600 6.7679205 -9.3427341 0.48539851 1.0083102 1.0027701
9700 6.4007616 -8.9753463 0.58689382 1.0138504 1.0027701
9800 6.2137021 -8.7670545 0.80327882 1.0249307 1.0027701
9900 6.063559 -8.6359278 0.34977555 1.0083102 1.0027701
10000 6.5604562 -9.1417599 0.49589297 1.0083102 1.0027701
Loop time of 0.469504 on 2 procs for 10000 steps with 361 atoms
Performance: 9201197.252 tau/day, 21299.068 timesteps/s
94.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13648 | 0.14553 | 0.15459 | 2.4 | 31.00
Neigh | 0.13867 | 0.14128 | 0.1439 | 0.7 | 30.09
Comm | 0.05533 | 0.06494 | 0.07455 | 3.8 | 13.83
Output | 0.0012147 | 0.0013802 | 0.0015457 | 0.4 | 0.29
Modify | 0.071393 | 0.071421 | 0.07145 | 0.0 | 15.21
Other | | 0.04494 | | | 9.57
Nlocal: 180.5 ave 181 max 180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 30 ave 34 max 26 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 579.5 ave 644 max 515 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 1159
Ave neighs/atom = 3.21053
Neighbor list builds = 3510
Dangerous builds = 0
Total wall time: 0:00:00

209
examples/balance/log.27Nov18.balance.g++.4
View File

@ -1,209 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.000404358 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.041 | 3.047 | 3.059 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
500 25.725591 -29.168034 0.67065285 1.2520776 1.0193906
600 26.247693 -29.692706 7.9887712 1.3074792 1.0193906
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
1200 17.214459 -20.726965 6.3578918 1.0304709 1.0083102
1300 16.42412 -19.757358 3.9027527 1.1191136 1.0193906
1400 15.030721 -18.114099 1.7564242 1.1523546 1.0193906
1500 13.81681 -16.902783 1.1577715 1.0858726 1.0083102
1600 13.686443 -16.661545 1.5415714 1.0969529 1.0083102
1700 13.019794 -16.066239 2.0360985 1.0526316 1.0083102
1800 12.297559 -15.3505 2.3411708 1.0858726 1.0083102
1900 12.279142 -15.287559 1.6641576 1.0415512 1.0083102
2000 12.230052 -15.192836 1.0975388 1.0415512 1.0193906
2100 11.697549 -14.599737 1.6237216 1.0969529 1.0083102
2200 11.682062 -14.610972 1.4641234 1.0747922 1.0083102
2300 11.075799 -13.986408 1.3034228 1.0637119 1.0083102
2400 11.362073 -14.290331 1.4934327 1.0304709 1.0083102
2500 11.100258 -14.006922 1.5476543 1.0415512 1.0193906
2600 11.12995 -14.013738 1.648208 1.0526316 1.0193906
2700 10.709161 -13.560172 1.396234 1.0193906 1.0083102
2800 10.827433 -13.654426 1.0691842 1.0304709 1.0083102
2900 10.653946 -13.622298 1.0985321 1.0304709 1.0083102
3000 10.277755 -13.110194 0.80184675 1.0304709 1.0083102
3100 9.9099809 -12.702359 1.0351594 1.0304709 1.0193906
3200 9.7539825 -12.558768 0.54465848 1.0526316 1.0083102
3300 10.126666 -12.949441 0.64914734 1.0304709 1.0083102
3400 9.5324496 -12.338741 1.2896056 1.0193906 1.0193906
3500 9.4041639 -12.170248 0.72157285 1.0304709 1.0083102
3600 9.2601291 -12.094438 1.1638062 1.0415512 1.0193906
3700 9.7052324 -12.503428 1.0681965 1.0193906 1.0193906
3800 9.1757619 -11.95576 1.2517655 1.0637119 1.0083102
3900 9.2622488 -12.036744 0.49874718 1.0193906 1.0083102
4000 8.8510215 -11.634558 1.0887428 1.0415512 1.0193906
4100 8.3821331 -11.145234 0.91008971 1.0193906 1.0083102
4200 8.2295054 -10.970304 0.5181043 1.0304709 1.0083102
4300 8.2161013 -10.942353 0.42128421 1.0304709 1.0193906
4400 7.7366945 -10.4592 0.79646198 1.0304709 1.0193906
4500 7.6089407 -10.446852 1.0059975 1.0083102 1.0193906
4600 7.6662499 -10.406613 1.7369986 1.0193906 1.0083102
4700 7.9515739 -10.665324 0.73173058 1.0193906 1.0083102
4800 7.7580664 -10.520311 1.1065958 1.0304709 1.0083102
4900 7.561205 -10.291568 0.97923495 1.0083102 1.0193906
5000 7.4169102 -10.130439 1.1566293 1.0193906 1.0193906
5100 7.5994418 -10.310725 1.1081236 1.0193906 1.0193906
5200 7.4637026 -10.211945 0.46308591 1.0193906 1.0083102
5300 7.5864081 -10.289039 0.55146387 1.0415512 1.0083102
5400 7.2190688 -9.8943729 0.56255805 1.0193906 1.0193906
5500 7.3953465 -10.112294 0.49166363 1.0193906 1.0193906
5600 7.3584536 -10.027488 0.69227871 1.0193906 1.0193906
5700 6.932639 -9.6121874 0.67344283 1.0304709 1.0083102
5800 7.088604 -9.7715725 0.20307999 1.0193906 1.0193906
5900 6.9761247 -9.6446998 0.90406994 1.0083102 1.0083102
6000 6.8763621 -9.5236579 0.57873884 1.0415512 1.0083102
6100 6.939987 -9.5929188 0.36904108 1.0304709 1.0083102
6200 6.820038 -9.4635599 0.63193653 1.0304709 1.0083102
6300 6.8288347 -9.4833639 0.41971515 1.0415512 1.0304709
6400 6.8690672 -9.5446244 1.0201589 1.0415512 1.0193906
6500 6.4727631 -9.1148404 0.80775699 1.0193906 1.0193906
6600 6.7113328 -9.3554765 0.61684835 1.0083102 1.0083102
6700 6.5896516 -9.2696941 0.58593745 1.0526316 1.0193906
6800 6.5609717 -9.2314045 1.2897992 1.0193906 1.0083102
6900 6.6225137 -9.2809347 0.47677707 1.0415512 1.0083102
7000 6.6617661 -9.3147214 0.72415312 1.0304709 1.0193906
7100 6.5773856 -9.2843036 0.7800794 1.0304709 1.0083102
7200 6.7300254 -9.4233488 0.73403634 1.0193906 1.0193906
7300 6.8497011 -9.4992354 0.97755826 1.0304709 1.0193906
7400 6.5848304 -9.2649536 0.89449647 1.0526316 1.0193906
7500 6.6468599 -9.3004561 0.53259674 1.0304709 1.0083102
7600 6.7096387 -9.3824628 0.40095675 1.0193906 1.0083102
7700 6.6205931 -9.2612947 0.44113095 1.0083102 1.0083102
7800 6.444935 -9.073124 0.47355329 1.0193906 1.0083102
7900 6.6143353 -9.2763501 0.57936627 1.0193906 1.0083102
8000 6.5718284 -9.2099799 0.88048189 1.0637119 1.0083102
8100 6.9155381 -9.5644544 0.36029314 1.0415512 1.0083102
8200 6.4217261 -9.0582117 0.4577164 1.0193906 1.0193906
8300 6.4639521 -9.0911283 0.50560328 1.0193906 1.0193906
8400 6.2047897 -8.8357836 0.71150301 1.0083102 1.0083102
8500 6.5688691 -9.2701491 0.5963871 1.0193906 1.0083102
8600 6.6803448 -9.3311473 0.47008064 1.0304709 1.0083102
8700 6.4794219 -9.1136868 0.97764575 1.0193906 1.0193906
8800 6.3899651 -9.0655629 0.72557611 1.0083102 1.0193906
8900 6.4446062 -9.1121453 0.53050589 1.0193906 1.0083102
9000 6.7012614 -9.3365992 0.63041848 1.0415512 1.0083102
9100 6.3982388 -9.0510004 0.34575359 1.0415512 1.0083102
9200 6.9775773 -9.6647109 0.97993232 1.0304709 1.0193906
9300 6.5504231 -9.2113542 0.58697844 1.0193906 1.0193906
9400 6.6900283 -9.3954145 0.40867465 1.0083102 1.0193906
9500 6.3553229 -8.9965934 0.60133843 1.0526316 1.0193906
9600 6.4861076 -9.1404384 1.0033387 1.0193906 1.0193906
9700 6.469481 -9.1202491 0.85523385 1.0083102 1.0193906
9800 6.5508552 -9.188341 0.6068644 1.0304709 1.0083102
9900 6.4355199 -9.1044882 0.83288252 1.0304709 1.0193906
10000 6.4850092 -9.1433721 0.58691238 1.0193906 1.0193906
Loop time of 0.418243 on 4 procs for 10000 steps with 361 atoms
Performance: 10328920.895 tau/day, 23909.539 timesteps/s
87.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.062269 | 0.073833 | 0.096031 | 4.9 | 17.65
Neigh | 0.066658 | 0.072882 | 0.084956 | 2.7 | 17.43
Comm | 0.10814 | 0.13013 | 0.14677 | 4.4 | 31.11
Output | 0.0015733 | 0.0017747 | 0.0023153 | 0.7 | 0.42
Modify | 0.060045 | 0.060904 | 0.061674 | 0.3 | 14.56
Other | | 0.07872 | | | 18.82
Nlocal: 90.25 ave 92 max 89 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 33.25 ave 57 max 13 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 309.25 ave 496 max 125 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1237
Ave neighs/atom = 3.42659
Neighbor list builds = 3620
Dangerous builds = 0
Total wall time: 0:00:00

110
examples/balance/log.27Nov18.balance.group.dynamic.g++.2
View File

@ -1,110 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000552893 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000512123 seconds
iteration count = 1
group weights: fast=1 slow=1
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor}
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.628 | 4.819 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
Loop time of 1.95661 on 2 procs for 250 steps with 4000 atoms
Performance: 55197.383 tau/day, 127.772 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0628 | 1.263 | 1.4632 | 17.8 | 64.55
Neigh | 0.42332 | 0.43486 | 0.44639 | 1.7 | 22.22
Comm | 0.033167 | 0.2449 | 0.45664 | 42.8 | 12.52
Output | 0.00015879 | 0.00017142 | 0.00018406 | 0.0 | 0.01
Modify | 0.010039 | 0.010042 | 0.010045 | 0.0 | 0.51
Other | | 0.003658 | | | 0.19
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 10441 ave 10457 max 10425 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 349156 max 247508 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:01

110
examples/balance/log.27Nov18.balance.group.dynamic.g++.4
View File

@ -1,110 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000427008 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000735044 seconds
iteration count = 2
group weights: fast=1 slow=1
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor}
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 3.566 | 3.947 | 4.329 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
Loop time of 1.48981 on 4 procs for 250 steps with 4000 atoms
Performance: 72492.623 tau/day, 167.807 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22803 | 0.67101 | 1.1622 | 43.7 | 45.04
Neigh | 0.20611 | 0.2259 | 0.23756 | 2.5 | 15.16
Comm | 0.085412 | 0.58198 | 1.045 | 47.7 | 39.06
Output | 0.00016332 | 0.00028861 | 0.0006516 | 0.0 | 0.02
Modify | 0.0069213 | 0.0070978 | 0.0072331 | 0.1 | 0.48
Other | | 0.003534 | | | 0.24
Nlocal: 1000 ave 1001 max 999 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 8727 ave 8761 max 8674 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 149349 ave 260848 max 51191 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 597396
Ave neighs/atom = 149.349
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:01

146
examples/balance/log.27Nov18.balance.group.static.g++.2
View File

@ -1,146 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00050807 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
balance 1.0 shift x 5 1.1 # out unweighted.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000545979 seconds
iteration count = 1
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
rebalancing time: 0.000159502 seconds
iteration count = 0
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
variable weight atom (type==1)*1.0+(type==2)*v_factor
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
rebalancing time: 0.000320673 seconds
iteration count = 1
weight variable: weight
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
rebalancing time: 0.000132561 seconds
iteration count = 0
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
rebalancing time: 0.000235796 seconds
iteration count = 1
group weights: fast=1 slow=1
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162
200 0.536665 -6.2530113 0 -5.448215 -1.933468
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
Loop time of 1.99136 on 2 procs for 250 steps with 4000 atoms
Performance: 54234.216 tau/day, 125.542 timesteps/s
99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0081 | 1.262 | 1.5159 | 22.6 | 63.37
Neigh | 0.40357 | 0.41713 | 0.43069 | 2.1 | 20.95
Comm | 0.033287 | 0.30076 | 0.56822 | 48.8 | 15.10
Output | 0.00014162 | 0.00015128 | 0.00016093 | 0.0 | 0.01
Modify | 0.0072243 | 0.0073462 | 0.007468 | 0.1 | 0.37
Other | | 0.003961 | | | 0.20
Nlocal: 2000 ave 2051 max 1949 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10443 ave 10506 max 10380 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 363449 max 233215 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:02

146
examples/balance/log.27Nov18.balance.group.static.g++.4
View File

@ -1,146 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000426769 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
balance 1.0 shift x 5 1.1 # out unweighted.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000867605 seconds
iteration count = 2
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
rebalancing time: 0.000295401 seconds
iteration count = 0
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.75 1
y cuts: 0 1
z cuts: 0 1
variable weight atom (type==1)*1.0+(type==2)*v_factor
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
rebalancing time: 0.000428915 seconds
iteration count = 2
weight variable: weight
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
rebalancing time: 0.000236273 seconds
iteration count = 0
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.75 1
y cuts: 0 1
z cuts: 0 1
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
rebalancing time: 0.000319958 seconds
iteration count = 2
group weights: fast=1 slow=1
initial/final max load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.713 | 4.188 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
Loop time of 1.45972 on 4 procs for 250 steps with 4000 atoms
Performance: 73986.752 tau/day, 171.266 timesteps/s
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34936 | 0.66325 | 1.1729 | 40.9 | 45.44
Neigh | 0.15811 | 0.20835 | 0.24806 | 7.4 | 14.27
Comm | 0.04955 | 0.57875 | 0.86745 | 43.6 | 39.65
Output | 0.00015831 | 0.00028872 | 0.00064492 | 0.0 | 0.02
Modify | 0.0030367 | 0.0040676 | 0.0050561 | 1.1 | 0.28
Other | | 0.005014 | | | 0.34
Nlocal: 1000 ave 1263 max 712 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 8711.5 ave 9045 max 8325 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 149325 ave 275165 max 77227 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 597299
Ave neighs/atom = 149.325
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:00:01

117
examples/balance/log.27Nov18.balance.kspace.g++.2
View File

@ -1,117 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
#atom_style charge
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000510931 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
#set type 1:2 charge 0.0
velocity all create 1.0 87287
pair_style lj/long/coul/long long off 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
kspace_style pppm/disp 1.0e-4
kspace_modify gewald/disp 0.1
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
fix 0 all balance 20 1.0 shift x 5 1.0 weight group 2 fast 1.0 slow 2.0 weight time 0.66
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
PPPMDisp initialization ...
Dispersion G vector (1/distance) = 0.1
Dispersion grid = 2 2 2
Dispersion stencil order = 5
Dispersion estimated absolute RMS force accuracy = 1.01251
Dispersion estimated absolute real space RMS force accuracy = 1.01251
Dispersion estimated absolute kspace RMS force accuracy = 7.29446e-07
Disperion estimated relative force accuracy = 1.01251
using double precision FFTs
3d grid and FFT values/proc dispersion = 294 4
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/long/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.846 | 5.014 | 5.182 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 52.148338 0 53.647963 94.09503 4738.2137
50 17.747599 42.836975 0 69.451719 143.44398 4738.2137
100 9.0390947 49.78615 0 63.341402 117.79296 4738.2137
150 13.456072 47.810527 0 67.989589 140.52068 4738.2137
200 11.358932 52.542448 0 69.576586 142.87196 4738.2137
250 13.204593 48.601437 0 68.403375 134.97484 4738.2137
300 12.061996 50.642194 0 68.730665 133.27077 4738.2137
350 14.107163 50.201375 0 71.356829 143.54662 4738.2137
400 12.053939 50.221116 0 68.297504 132.01999 4738.2137
450 13.523963 50.829687 0 71.11056 143.8183 4738.2137
500 13.135822 50.150114 0 69.848921 137.26364 4738.2137
Loop time of 6.95261 on 2 procs for 500 steps with 4000 atoms
Performance: 31067.471 tau/day, 71.915 timesteps/s
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8521 | 3.0997 | 3.3472 | 14.1 | 44.58
Kspace | 1.1859 | 1.303 | 1.4202 | 10.3 | 18.74
Neigh | 2.2324 | 2.387 | 2.5417 | 10.0 | 34.33
Comm | 0.1003 | 0.12513 | 0.14996 | 7.0 | 1.80
Output | 0.00033641 | 0.00036693 | 0.00039744 | 0.0 | 0.01
Modify | 0.026408 | 0.02737 | 0.028331 | 0.6 | 0.39
Other | | 0.009989 | | | 0.14
Nlocal: 2000 ave 2316 max 1684 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 9543.5 ave 9675 max 9412 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 254445 ave 276022 max 232868 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 508890
Ave neighs/atom = 127.222
Neighbor list builds = 124
Dangerous builds = 97
Total wall time: 0:00:06

117
examples/balance/log.27Nov18.balance.kspace.g++.4
View File

@ -1,117 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
#atom_style charge
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000432491 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
#set type 1:2 charge 0.0
velocity all create 1.0 87287
pair_style lj/long/coul/long long off 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
kspace_style pppm/disp 1.0e-4
kspace_modify gewald/disp 0.1
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
fix 0 all balance 20 1.0 shift x 5 1.0 weight group 2 fast 1.0 slow 2.0 weight time 0.66
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
PPPMDisp initialization ...
Dispersion G vector (1/distance) = 0.1
Dispersion grid = 2 2 2
Dispersion stencil order = 5
Dispersion estimated absolute RMS force accuracy = 1.01251
Dispersion estimated absolute real space RMS force accuracy = 1.01251
Dispersion estimated absolute kspace RMS force accuracy = 7.29446e-07
Disperion estimated relative force accuracy = 1.01251
using double precision FFTs
3d grid and FFT values/proc dispersion = 294 4
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/long/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.291 | 4.423 | 4.656 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 52.148338 0 53.647963 94.09503 4738.2137
50 17.850656 42.620113 0 69.389403 142.80556 4738.2137
100 9.4607189 49.700118 0 63.887649 117.51739 4738.2137
150 13.992056 47.731988 0 68.714825 140.56926 4738.2137
200 11.617635 52.509394 0 69.93149 142.6933 4738.2137
250 13.536287 48.33108 0 68.630434 133.91794 4738.2137
300 12.619985 50.328139 0 69.253384 132.46719 4738.2137
350 14.497923 50.092405 0 71.833853 143.39356 4738.2137
400 12.228079 50.202361 0 68.539894 131.75614 4738.2137
450 14.01349 50.908526 0 71.923506 144.25732 4738.2137
500 13.277341 50.381613 0 70.292644 137.20282 4738.2137
Loop time of 6.17838 on 4 procs for 500 steps with 4000 atoms
Performance: 34960.628 tau/day, 80.927 timesteps/s
93.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.74813 | 1.6453 | 2.5052 | 65.7 | 26.63
Kspace | 1.036 | 2.9098 | 4.5974 | 94.8 | 47.10
Neigh | 0.27464 | 1.2099 | 2.4155 | 84.8 | 19.58
Comm | 0.1711 | 0.36843 | 0.5217 | 25.2 | 5.96
Output | 0.00052595 | 0.0053349 | 0.0074508 | 3.8 | 0.09
Modify | 0.023363 | 0.027308 | 0.032521 | 2.3 | 0.44
Other | | 0.01228 | | | 0.20
Nlocal: 1000 ave 2002 max 241 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 7608 ave 9312 max 5850 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 127345 ave 211903 max 47616 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 509381
Ave neighs/atom = 127.345
Neighbor list builds = 124
Dangerous builds = 97
Total wall time: 0:00:06

228
examples/balance/log.27Nov18.balance.neigh.dynamic.g++.2
View File

@ -1,228 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000553608 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT
compute p all property/atom d_WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
thermo 50
run 500
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
Loop time of 3.92718 on 2 procs for 500 steps with 4000 atoms
Performance: 55001.290 tau/day, 127.318 timesteps/s
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2902 | 2.6102 | 2.9303 | 19.8 | 66.47
Neigh | 0.89715 | 0.89718 | 0.8972 | 0.0 | 22.85
Comm | 0.074355 | 0.39408 | 0.7138 | 50.9 | 10.03
Output | 0.0003202 | 0.00035989 | 0.00039959 | 0.0 | 0.01
Modify | 0.016438 | 0.016832 | 0.017226 | 0.3 | 0.43
Other | | 0.008523 | | | 0.22
Nlocal: 2000 ave 2056 max 1944 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10457.5 ave 10508 max 10407 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298070 ave 333007 max 263132 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596139
Ave neighs/atom = 149.035
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
Loop time of 3.83028 on 2 procs for 500 steps with 4000 atoms
Performance: 56392.741 tau/day, 130.539 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.263 | 2.5605 | 2.858 | 18.6 | 66.85
Neigh | 0.8789 | 0.88341 | 0.88791 | 0.5 | 23.06
Comm | 0.068052 | 0.36076 | 0.65347 | 48.7 | 9.42
Output | 0.0003016 | 0.0003438 | 0.000386 | 0.0 | 0.01
Modify | 0.016381 | 0.016829 | 0.017277 | 0.3 | 0.44
Other | | 0.008426 | | | 0.22
Nlocal: 2000 ave 2049 max 1951 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10389 ave 10436 max 10342 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 300836 ave 335987 max 265684 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 601671
Ave neighs/atom = 150.418
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
Loop time of 3.81946 on 2 procs for 500 steps with 4000 atoms
Performance: 56552.445 tau/day, 130.908 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2594 | 2.5549 | 2.8504 | 18.5 | 66.89
Neigh | 0.86746 | 0.87203 | 0.8766 | 0.5 | 22.83
Comm | 0.06715 | 0.36699 | 0.66684 | 49.5 | 9.61
Output | 0.00029325 | 0.00033867 | 0.00038409 | 0.0 | 0.01
Modify | 0.016529 | 0.016817 | 0.017105 | 0.2 | 0.44
Other | | 0.008371 | | | 0.22
Nlocal: 2000 ave 2034 max 1966 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10386 ave 10936 max 9836 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 302958 ave 337188 max 268729 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 605917
Ave neighs/atom = 151.479
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
1550 0.53713593 -6.2504069 0 -5.4449044 -1.764709 4738.2137
1600 0.54679556 -6.2646482 0 -5.4446599 -1.8115775 4738.2137
1650 0.53806577 -6.2519006 0 -5.4450037 -1.7409142 4738.2137
1700 0.5347951 -6.2468962 0 -5.4449041 -1.7162331 4738.2137
1750 0.53714568 -6.2506577 0 -5.4451406 -1.7340499 4738.2137
1800 0.52749839 -6.2358664 0 -5.4448167 -1.6874961 4738.2137
1850 0.54585956 -6.2629394 0 -5.4443547 -1.7758764 4738.2137
1900 0.53010831 -6.2387561 0 -5.4437925 -1.6381825 4738.2137
1950 0.54288557 -6.2583073 0 -5.4441826 -1.7368524 4738.2137
2000 0.52765923 -6.2348572 0 -5.4435663 -1.5588839 4738.2137
Loop time of 3.78423 on 2 procs for 500 steps with 4000 atoms
Performance: 57078.976 tau/day, 132.127 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2449 | 2.5388 | 2.8328 | 18.4 | 67.09
Neigh | 0.85527 | 0.85828 | 0.86129 | 0.3 | 22.68
Comm | 0.065453 | 0.36215 | 0.65885 | 49.3 | 9.57
Output | 0.00030518 | 0.00032794 | 0.00035071 | 0.0 | 0.01
Modify | 0.016444 | 0.016597 | 0.01675 | 0.1 | 0.44
Other | | 0.008044 | | | 0.21
Nlocal: 2000 ave 2031 max 1969 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10334 ave 10921 max 9747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 303988 ave 338808 max 269168 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 607976
Ave neighs/atom = 151.994
Neighbor list builds = 51
Dangerous builds = 0
Total wall time: 0:00:15

228
examples/balance/log.27Nov18.balance.neigh.dynamic.g++.4
View File

@ -1,228 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000430107 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT
compute p all property/atom d_WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
thermo 50
run 500
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
Loop time of 2.45924 on 4 procs for 500 steps with 4000 atoms
Performance: 87831.985 tau/day, 203.315 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1372 | 1.4179 | 1.6656 | 18.1 | 57.66
Neigh | 0.30681 | 0.46841 | 0.69372 | 24.1 | 19.05
Comm | 0.46019 | 0.55206 | 0.6052 | 7.7 | 22.45
Output | 0.00034404 | 0.0005753 | 0.001132 | 0.0 | 0.02
Modify | 0.007339 | 0.0099927 | 0.013719 | 2.7 | 0.41
Other | | 0.01029 | | | 0.42
Nlocal: 1000 ave 1549 max 605 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8755 ave 9851 max 8071 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149308 ave 164554 max 128538 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 597231
Ave neighs/atom = 149.308
Neighbor list builds = 50
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
Loop time of 2.389 on 4 procs for 500 steps with 4000 atoms
Performance: 90414.542 tau/day, 209.293 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 | 1.2112 | 1.381 | 1.5214 | 11.0 | 57.81
Neigh | 0.29746 | 0.48382 | 0.74669 | 27.5 | 20.25
Comm | 0.40449 | 0.50032 | 0.57922 | 9.4 | 20.94
Output | 0.00033617 | 0.00064272 | 0.0013907 | 0.0 | 0.03
Modify | 0.0070128 | 0.010942 | 0.015494 | 3.7 | 0.46
Other | | 0.01223 | | | 0.51
Nlocal: 1000 ave 1569 max 595 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8715.25 ave 9779 max 8018 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 150170 ave 163282 max 132114 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 600678
Ave neighs/atom = 150.169
Neighbor list builds = 53
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
Loop time of 2.45895 on 4 procs for 500 steps with 4000 atoms
Performance: 87842.291 tau/day, 203.339 timesteps/s
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2592 | 1.4017 | 1.5327 | 11.0 | 57.01
Neigh | 0.28831 | 0.47661 | 0.75988 | 28.7 | 19.38
Comm | 0.41426 | 0.54907 | 0.6044 | 10.6 | 22.33
Output | 0.0003705 | 0.00060898 | 0.0012109 | 0.0 | 0.02
Modify | 0.014004 | 0.016774 | 0.020669 | 1.9 | 0.68
Other | | 0.01415 | | | 0.58
Nlocal: 1000 ave 1543 max 605 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8704.5 ave 9803 max 7983 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 150494 ave 166334 max 129306 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 601974
Ave neighs/atom = 150.494
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
1550 0.55327018 -6.2750126 0 -5.4453148 -1.9506585 4738.2137
1600 0.54419004 -6.2612622 0 -5.4451812 -1.8559437 4738.2137
1650 0.54710034 -6.2661938 0 -5.4457484 -1.8882763 4738.2137
1700 0.53665691 -6.2504958 0 -5.4457117 -1.8068009 4738.2137
1750 0.5486471 -6.2681127 0 -5.4453478 -1.8662656 4738.2137
1800 0.54476222 -6.2615086 0 -5.4445695 -1.8352838 4738.2137
1850 0.54143048 -6.2555517 0 -5.443609 -1.8005726 4738.2137
1900 0.53992511 -6.254136 0 -5.4444508 -1.7768715 4738.2137
1950 0.54665895 -6.2640958 0 -5.4443124 -1.7946993 4738.2137
2000 0.5455751 -6.2625337 0 -5.4443756 -1.8072242 4738.2137
Loop time of 2.42708 on 4 procs for 500 steps with 4000 atoms
Performance: 88995.678 tau/day, 206.009 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2482 | 1.3902 | 1.5329 | 10.6 | 57.28
Neigh | 0.31099 | 0.50813 | 0.78451 | 28.1 | 20.94
Comm | 0.37293 | 0.5011 | 0.58684 | 11.2 | 20.65
Output | 0.00033593 | 0.00060582 | 0.0012991 | 0.0 | 0.02
Modify | 0.007091 | 0.0097566 | 0.013303 | 2.7 | 0.40
Other | | 0.01727 | | | 0.71
Nlocal: 1000 ave 1539 max 607 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8677 ave 9837 max 7981 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 151655 ave 168263 max 129443 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 606619
Ave neighs/atom = 151.655
Neighbor list builds = 56
Dangerous builds = 0
Total wall time: 0:00:09

141
examples/balance/log.27Nov18.balance.neigh.rcb.g++.2
View File

@ -1,141 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000511885 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
comm_style tiled
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
compute p all property/atom d_WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.329 | 4.52 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
Loop time of 1.80309 on 2 procs for 250 steps with 4000 atoms
Performance: 59897.213 tau/day, 138.651 timesteps/s
97.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2185 | 1.2646 | 1.3106 | 4.1 | 70.13
Neigh | 0.43131 | 0.43248 | 0.43365 | 0.2 | 23.99
Comm | 0.045418 | 0.090311 | 0.1352 | 14.9 | 5.01
Output | 0.00017476 | 0.00021195 | 0.00024915 | 0.0 | 0.01
Modify | 0.011012 | 0.01103 | 0.011048 | 0.0 | 0.61
Other | | 0.004476 | | | 0.25
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 10412.5 ave 10414 max 10411 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 299797 max 296867 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 25
Dangerous builds = 0
run 250
Per MPI rank memory allocation (min/avg/max) = 4.929 | 4.929 | 4.93 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
Loop time of 1.77097 on 2 procs for 250 steps with 4000 atoms
Performance: 60983.669 tau/day, 141.166 timesteps/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2353 | 1.2515 | 1.2678 | 1.5 | 70.67
Neigh | 0.44235 | 0.44303 | 0.44371 | 0.1 | 25.02
Comm | 0.045978 | 0.061555 | 0.077133 | 6.3 | 3.48
Output | 0.0001564 | 0.00016713 | 0.00017786 | 0.0 | 0.01
Modify | 0.010305 | 0.01031 | 0.010315 | 0.0 | 0.58
Other | | 0.004365 | | | 0.25
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 10466.5 ave 10470 max 10463 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298070 ave 349236 max 246903 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596139
Ave neighs/atom = 149.035
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:03

141
examples/balance/log.27Nov18.balance.neigh.rcb.g++.4
View File

@ -1,141 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000440836 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
comm_style tiled
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
compute p all property/atom d_WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
Per MPI rank memory allocation (min/avg/max) = 3.917 | 3.927 | 3.945 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
Loop time of 1.0693 on 4 procs for 250 steps with 4000 atoms
Performance: 101000.295 tau/day, 233.797 timesteps/s
89.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.58255 | 0.65493 | 0.72281 | 8.3 | 61.25
Neigh | 0.214 | 0.22344 | 0.23158 | 1.4 | 20.90
Comm | 0.10451 | 0.17801 | 0.25967 | 17.3 | 16.65
Output | 0.00015521 | 0.00020903 | 0.00034142 | 0.0 | 0.02
Modify | 0.007113 | 0.0073407 | 0.0076027 | 0.2 | 0.69
Other | | 0.005369 | | | 0.50
Nlocal: 1000 ave 1005 max 996 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 7674 ave 7679 max 7670 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 149349 ave 149991 max 147960 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 597396
Ave neighs/atom = 149.349
Neighbor list builds = 25
Dangerous builds = 0
run 250
Per MPI rank memory allocation (min/avg/max) = 3.922 | 4.004 | 4.078 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
Loop time of 0.999028 on 4 procs for 250 steps with 4000 atoms
Performance: 108105.088 tau/day, 250.243 timesteps/s
93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60256 | 0.6507 | 0.68091 | 3.8 | 65.13
Neigh | 0.21602 | 0.21945 | 0.22516 | 0.8 | 21.97
Comm | 0.087366 | 0.11787 | 0.16957 | 9.6 | 11.80
Output | 0.00016737 | 0.00028127 | 0.00057006 | 0.0 | 0.03
Modify | 0.0065138 | 0.0066211 | 0.0067828 | 0.1 | 0.66
Other | | 0.004103 | | | 0.41
Nlocal: 1000 ave 1005 max 994 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 7675.75 ave 7703 max 7648 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 149308 ave 173909 max 124842 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 597231
Ave neighs/atom = 149.308
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:02

211
examples/balance/log.27Nov18.balance.neigh.static.g++.2
View File

@ -1,211 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000495195 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
rebalancing time: 0.000623703 seconds
iteration count = 1
neigh weight factor: 0.8
initial/final max load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162
200 0.536665 -6.2530113 0 -5.448215 -1.933468
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
Loop time of 1.97176 on 2 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8
rebalancing time: 0.000482321 seconds
iteration count = 10
neigh weight factor: 0.8
initial/final max load/proc = 290759 262123
initial/final imbalance factor = 1.10982 1.00052
x cuts: 0 0.45166 1
y cuts: 0 1
z cuts: 0 1
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 4.304 | 4.492 | 4.681 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
Loop time of 1.77716 on 2 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8
rebalancing time: 0.000497341 seconds
iteration count = 10
neigh weight factor: 0.8
initial/final max load/proc = 296648 269016
initial/final imbalance factor = 1.10642 1.00336
x cuts: 0 0.501461 1
y cuts: 0 1
z cuts: 0 1
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523
Loop time of 2.0039 on 2 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
rebalancing time: 0.000368118 seconds
iteration count = 10
neigh weight factor: 0.8
time weight factor: 0.6
initial/final max load/proc = 168.493 167.093
initial/final imbalance factor = 1.00948 1.00109
x cuts: 0 0.499991 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes
Step Temp E_pair E_mol TotEng Press
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624
Loop time of 2.0382 on 2 procs for 250 steps with 4000 atoms
Performance: 52987.998 tau/day, 122.657 timesteps/s
98.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.96918 | 1.257 | 1.5449 | 25.7 | 61.67
Neigh | 0.40421 | 0.42672 | 0.44923 | 3.4 | 20.94
Comm | 0.032542 | 0.34306 | 0.65358 | 53.0 | 16.83
Output | 0.00014377 | 0.00015366 | 0.00016356 | 0.0 | 0.01
Modify | 0.0070617 | 0.007337 | 0.0076122 | 0.3 | 0.36
Other | | 0.003878 | | | 0.19
Nlocal: 2000 ave 2056 max 1944 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10403.5 ave 10525 max 10282 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 300836 ave 365656 max 236015 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 601671
Ave neighs/atom = 150.418
Neighbor list builds = 25
Dangerous builds = 0
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
rebalancing time: 0.000344753 seconds
iteration count = 10
neigh weight factor: 0.8
time weight factor: 0.6
initial/final max load/proc = 170.235 168.809
initial/final imbalance factor = 1.01037 1.00191
x cuts: 0 0.49755 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134
Loop time of 2.01086 on 2 procs for 250 steps with 4000 atoms
Performance: 53708.387 tau/day, 124.325 timesteps/s
98.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0037 | 1.2615 | 1.5192 | 23.0 | 62.73
Neigh | 0.40846 | 0.4277 | 0.44695 | 2.9 | 21.27
Comm | 0.033029 | 0.31012 | 0.5872 | 49.8 | 15.42
Output | 0.00014424 | 0.00015259 | 0.00016093 | 0.0 | 0.01
Modify | 0.007298 | 0.0074347 | 0.0075715 | 0.2 | 0.37
Other | | 0.003999 | | | 0.20
Nlocal: 2000 ave 2038 max 1962 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10391 ave 10489 max 10293 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 301104 ave 358264 max 243943 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 602207
Ave neighs/atom = 150.552
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:09

211
examples/balance/log.27Nov18.balance.neigh.static.g++.4
View File

@ -1,211 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000429153 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
rebalancing time: 0.000684023 seconds
iteration count = 3
neigh weight factor: 0.8
initial/final max load/proc = 1200 1000
initial/final imbalance factor = 1.2 1
x cuts: 0 0.25 0.5 0.71875 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.802 | 4.188 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
Loop time of 1.44749 on 4 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8
rebalancing time: 0.000543356 seconds
iteration count = 10
neigh weight factor: 0.8
initial/final max load/proc = 220132 125739
initial/final imbalance factor = 1.75833 1.00436
x cuts: 0 0.304443 0.450928 0.626678 1
y cuts: 0 1
z cuts: 0 1
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 3.814 | 3.999 | 4.192 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
Loop time of 1.19834 on 4 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8
rebalancing time: 0.000308752 seconds
iteration count = 10
neigh weight factor: 0.8
initial/final max load/proc = 147109 128929
initial/final imbalance factor = 1.14487 1.00338
x cuts: 0 0.304873 0.449926 0.59527 1
y cuts: 0 1
z cuts: 0 1
run 250 post no
Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.018 | 4.209 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
Loop time of 1.23246 on 4 procs for 250 steps with 4000 atoms
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
rebalancing time: 0.000306845 seconds
iteration count = 10
neigh weight factor: 0.8
time weight factor: 0.6
initial/final max load/proc = 114.116 101.665
initial/final imbalance factor = 1.12567 1.00285
x cuts: 0 0.30983 0.449501 0.588031 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.018 | 4.209 Mbytes
Step Temp E_pair E_mol TotEng Press
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466
Loop time of 1.13265 on 4 procs for 250 steps with 4000 atoms
Performance: 95351.673 tau/day, 220.721 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.64092 | 0.67347 | 0.70289 | 3.5 | 59.46
Neigh | 0.11654 | 0.22172 | 0.35287 | 22.2 | 19.58
Comm | 0.068215 | 0.22827 | 0.36221 | 28.0 | 20.15
Output | 0.00016975 | 0.00031555 | 0.00065875 | 0.0 | 0.03
Modify | 0.00214 | 0.004007 | 0.0062947 | 3.0 | 0.35
Other | | 0.004862 | | | 0.43
Nlocal: 1000 ave 1651 max 529 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8692.5 ave 9709 max 8037 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 150170 ave 154877 max 145634 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 600681
Ave neighs/atom = 150.17
Neighbor list builds = 25
Dangerous builds = 0
balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
rebalancing time: 0.000319719 seconds
iteration count = 10
neigh weight factor: 0.8
time weight factor: 0.6
initial/final max load/proc = 102.192 99.2749
initial/final imbalance factor = 1.03206 1.0026
x cuts: 0 0.312695 0.449907 0.587625 1
y cuts: 0 1
z cuts: 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.019 | 4.209 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797
Loop time of 1.16447 on 4 procs for 250 steps with 4000 atoms
Performance: 92745.661 tau/day, 214.689 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 | 0.61612 | 0.67903 | 0.73112 | 5.1 | 58.31
Neigh | 0.11722 | 0.22257 | 0.35236 | 22.3 | 19.11
Comm | 0.099441 | 0.25198 | 0.42338 | 28.4 | 21.64
Output | 0.00018501 | 0.0012686 | 0.0040495 | 4.5 | 0.11
Modify | 0.0020952 | 0.0044899 | 0.0086782 | 4.0 | 0.39
Other | | 0.005134 | | | 0.44
Nlocal: 1000 ave 1631 max 523 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 8693.75 ave 9752 max 8002 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149995 ave 161500 max 141963 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 599979
Ave neighs/atom = 149.995
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:06

257
examples/balance/log.27Nov18.balance.var.dynamic.g++.2
View File

@ -1,257 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000491142 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.000805378 seconds
iteration count = 10
group weights: fast=0.8 slow=2.5
storing weight in atom property d_WEIGHT
initial/final max load/proc = 2960 3120
initial/final imbalance factor = 1.06093 1.11828
x cuts: 0 0.449707 1
y cuts: 0 1
z cuts: 0 1
variable lastweight atom c_p
fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Per MPI rank memory allocation (min/avg/max) = 4.708 | 4.876 | 5.044 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
Loop time of 5.01752 on 2 procs for 500 steps with 4000 atoms
Performance: 43049.176 tau/day, 99.651 timesteps/s
98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4325 | 2.6317 | 3.8309 | 73.9 | 52.45
Neigh | 0.72307 | 0.89995 | 1.0768 | 18.6 | 17.94
Comm | 0.08143 | 1.4587 | 2.836 | 114.0 | 29.07
Output | 0.00034356 | 0.00034773 | 0.00035191 | 0.0 | 0.01
Modify | 0.015713 | 0.017661 | 0.01961 | 1.5 | 0.35
Other | | 0.009141 | | | 0.18
Nlocal: 2000 ave 2500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10457 ave 11055 max 9859 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298070 ave 483758 max 112381 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596139
Ave neighs/atom = 149.035
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 5.092 | 5.269 | 5.445 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
Loop time of 5.38962 on 2 procs for 500 steps with 4000 atoms
Performance: 40077.052 tau/day, 92.771 timesteps/s
98.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93627 | 2.5477 | 4.1591 | 101.0 | 47.27
Neigh | 0.61458 | 0.87078 | 1.127 | 27.5 | 16.16
Comm | 0.072418 | 1.9424 | 3.8124 | 134.2 | 36.04
Output | 0.00034833 | 0.00035048 | 0.00035262 | 0.0 | 0.01
Modify | 0.014652 | 0.018169 | 0.021687 | 2.6 | 0.34
Other | | 0.01024 | | | 0.19
Nlocal: 2000 ave 2561 max 1439 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10257 ave 11109 max 9405 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 300836 ave 498670 max 103001 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 601671
Ave neighs/atom = 150.418
Neighbor list builds = 51
Dangerous builds = 0
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
rebalancing time: 0.000744104 seconds
iteration count = 10
group weights: fast=0.8 slow=2.5
storing weight in atom property d_WEIGHT
initial/final max load/proc = 4428.8 2798.1
initial/final imbalance factor = 1.58738 1.0029
x cuts: 0 0.45485 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
run 500
Per MPI rank memory allocation (min/avg/max) = 5.098 | 5.464 | 5.83 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
Loop time of 5.50675 on 2 procs for 500 steps with 4000 atoms
Performance: 39224.584 tau/day, 90.798 timesteps/s
98.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1091 | 2.6165 | 4.124 | 93.2 | 47.51
Neigh | 0.49666 | 0.88338 | 1.2701 | 41.1 | 16.04
Comm | 0.079062 | 1.9768 | 3.8745 | 135.0 | 35.90
Output | 0.00032926 | 0.00041151 | 0.00049376 | 0.0 | 0.01
Modify | 0.012776 | 0.018102 | 0.023428 | 4.0 | 0.33
Other | | 0.01156 | | | 0.21
Nlocal: 2000 ave 3010 max 990 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10343 ave 12129 max 8557 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 302958 ave 519016 max 86901 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 605917
Ave neighs/atom = 151.479
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 5.847 | 5.872 | 5.897 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
1550 0.5371361 -6.250403 0 -5.4449003 -1.7647032 4738.2137
1600 0.54679571 -6.2646443 0 -5.4446558 -1.8115722 4738.2137
1650 0.53806587 -6.2519009 0 -5.4450039 -1.7409152 4738.2137
1700 0.53479436 -6.2469032 0 -5.4449122 -1.7162441 4738.2137
1750 0.53714071 -6.2506513 0 -5.4451416 -1.7340205 4738.2137
1800 0.52750533 -6.2358819 0 -5.4448217 -1.687537 4738.2137
1850 0.54585346 -6.262937 0 -5.4443615 -1.7758597 4738.2137
1900 0.53011247 -6.2387653 0 -5.4437954 -1.6382086 4738.2137
1950 0.54287683 -6.2583097 0 -5.4441981 -1.7367469 4738.2137
2000 0.52771288 -6.2349676 0 -5.4435962 -1.5593804 4738.2137
Loop time of 5.80884 on 2 procs for 500 steps with 4000 atoms
Performance: 37184.695 tau/day, 86.076 timesteps/s
97.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71314 | 2.5435 | 4.3738 | 114.8 | 43.79
Neigh | 0.39935 | 0.85806 | 1.3168 | 49.5 | 14.77
Comm | 0.082629 | 2.3761 | 4.6695 | 148.8 | 40.90
Output | 0.00034571 | 0.00044024 | 0.00053477 | 0.0 | 0.01
Modify | 0.011643 | 0.018227 | 0.024811 | 4.9 | 0.31
Other | | 0.01257 | | | 0.22
Nlocal: 2000 ave 3032 max 968 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10266 ave 12245 max 8287 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 303998 ave 525128 max 82868 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 607996
Ave neighs/atom = 151.999
Neighbor list builds = 51
Dangerous builds = 0
Total wall time: 0:00:21

257
examples/balance/log.27Nov18.balance.var.dynamic.g++.4
View File

@ -1,257 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000424862 secs
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
rebalancing time: 0.00115108 seconds
iteration count = 10
group weights: fast=0.8 slow=2.5
storing weight in atom property d_WEIGHT
initial/final max load/proc = 2160 1620
initial/final imbalance factor = 1.54839 1.16129
x cuts: 0 0.300049 0.449951 0.599854 1
y cuts: 0 1
z cuts: 0 1
variable lastweight atom c_p
fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Per MPI rank memory allocation (min/avg/max) = 4.132 | 4.192 | 4.274 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
Loop time of 2.66424 on 4 procs for 500 steps with 4000 atoms
Performance: 81073.650 tau/day, 187.670 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1083 | 1.3909 | 1.7318 | 24.2 | 52.21
Neigh | 0.19732 | 0.45425 | 0.7722 | 38.2 | 17.05
Comm | 0.24921 | 0.79627 | 1.3351 | 60.3 | 29.89
Output | 0.00041294 | 0.00065368 | 0.0011899 | 0.0 | 0.02
Modify | 0.0071657 | 0.010935 | 0.015748 | 3.6 | 0.41
Other | | 0.01124 | | | 0.42
Nlocal: 1000 ave 1870 max 299 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 8679.25 ave 10190 max 7374 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 149308 ave 215125 max 81132 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 597231
Ave neighs/atom = 149.308
Neighbor list builds = 50
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.134 | 4.387 | 4.664 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
Loop time of 3.02509 on 4 procs for 500 steps with 4000 atoms
Performance: 71402.836 tau/day, 165.284 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.6808 | 1.3385 | 1.959 | 52.5 | 44.25
Neigh | 0.13127 | 0.4678 | 0.86924 | 48.5 | 15.46
Comm | 0.19735 | 1.1921 | 2.1903 | 85.9 | 39.41
Output | 0.00045371 | 0.00090569 | 0.0013952 | 0.0 | 0.03
Modify | 0.0062041 | 0.011167 | 0.01691 | 4.5 | 0.37
Other | | 0.01462 | | | 0.48
Nlocal: 1000 ave 1935 max 262 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 8739.75 ave 10498 max 7333 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 150170 ave 231608 max 72161 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 600678
Ave neighs/atom = 150.169
Neighbor list builds = 53
Dangerous builds = 0
balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
rebalancing time: 0.000575304 seconds
iteration count = 10
group weights: fast=0.8 slow=2.5
storing weight in atom property d_WEIGHT
initial/final max load/proc = 2318.1 1408.1
initial/final imbalance factor = 1.66172 1.00939
x cuts: 0 0.337054 0.454419 0.59556 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
run 500
Per MPI rank memory allocation (min/avg/max) = 4.136 | 4.393 | 4.673 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
1300 0.54134321 -6.2590728 0 -5.447261 -1.917027 4738.2137
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
1400 0.53726925 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
1450 0.54525929 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137
Loop time of 3.07108 on 4 procs for 500 steps with 4000 atoms
Performance: 70333.514 tau/day, 162.809 timesteps/s
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77463 | 1.3897 | 2.1328 | 51.3 | 45.25
Neigh | 0.13416 | 0.45546 | 0.80534 | 46.9 | 14.83
Comm | 0.17763 | 1.2036 | 2.1448 | 83.6 | 39.19
Output | 0.00039482 | 0.00067067 | 0.0013118 | 0.0 | 0.02
Modify | 0.0058403 | 0.010695 | 0.015841 | 4.5 | 0.35
Other | | 0.01099 | | | 0.36
Nlocal: 1000 ave 1955 max 199 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 8729 ave 10472 max 7399 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 150494 ave 251670 max 54664 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 601974
Ave neighs/atom = 150.494
Neighbor list builds = 51
Dangerous builds = 0
run 500
Per MPI rank memory allocation (min/avg/max) = 4.136 | 4.393 | 4.673 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137
1550 0.55327047 -6.2750129 0 -5.4453147 -1.9506601 4738.2137
1600 0.54419056 -6.2612631 0 -5.4451813 -1.8559469 4738.2137
1650 0.54710007 -6.2661977 0 -5.4457528 -1.8882828 4738.2137
1700 0.53665429 -6.250492 0 -5.4457118 -1.8067907 4738.2137
1750 0.54864943 -6.2681198 0 -5.4453514 -1.8662924 4738.2137
1800 0.54477002 -6.2615118 0 -5.4445611 -1.835304 4738.2137
1850 0.54143129 -6.2555621 0 -5.4436182 -1.8005839 4738.2137
1900 0.53994573 -6.254175 0 -5.4444588 -1.7770422 4738.2137
1950 0.54665379 -6.2640981 0 -5.4443224 -1.7946205 4738.2137
2000 0.54548501 -6.2623919 0 -5.4443689 -1.8063177 4738.2137
Loop time of 3.48709 on 4 procs for 500 steps with 4000 atoms
Performance: 61942.848 tau/day, 143.386 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42099 | 1.3571 | 2.3564 | 80.4 | 38.92
Neigh | 0.083965 | 0.4942 | 0.96204 | 58.6 | 14.17
Comm | 0.25895 | 1.6131 | 2.9631 | 106.2 | 46.26
Output | 0.00042915 | 0.00068706 | 0.0012567 | 0.0 | 0.02
Modify | 0.0051193 | 0.010964 | 0.017898 | 5.5 | 0.31
Other | | 0.01109 | | | 0.32
Nlocal: 1000 ave 2036 max 127 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 8722.75 ave 10448 max 7456 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 151642 ave 269558 max 35372 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 606566
Ave neighs/atom = 151.642
Neighbor list builds = 56
Dangerous builds = 0
Total wall time: 0:00:12

255
examples/balance/log.3Nov23.balance.bond.fast.g++.2 Normal file
View File

@ -0,0 +1,255 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
create_bonds many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
6 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 10.0 # because bonds stretch a long ways
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 10
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.157 | 5.167 | 5.178 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -2.2032569 3.1039469 2 1.0193906
100 25.57187 -2.2902218 2.9990153 1.0193906 1.0027701
200 25.532511 -2.5273097 2.8286231 1.0304709 1.0027701
300 25.860246 -3.0674998 2.6725358 1.0138504 1.0027701
400 26.628011 -4.394738 2.6618897 1.0138504 1.0083102
500 27.627309 -6.2305012 2.6564278 1.0138504 1.0027701
600 28.881803 -8.2757766 2.8249236 1.0138504 1.0027701
700 29.941402 -9.9816088 2.9828232 1.0138504 1.0027701
800 31.118457 -12.199787 3.2044549 1.0249307 1.0083102
900 32.393498 -14.204491 2.9496587 1.0304709 1.0027701
1000 33.392657 -15.747519 3.1613807 1.0249307 1.0027701
1100 34.671769 -17.728904 3.019138 1.0193906 1.0083102
1200 35.632627 -19.846347 3.1061176 1.0193906 1.0083102
1300 36.77272 -21.156179 3.2353009 1.0415512 1.0027701
1400 38.241608 -22.744765 4.1163075 1.0193906 1.0027701
1500 40.072478 -25.139827 5.3032535 1.0304709 1.0027701
1600 40.665382 -25.901697 5.4330761 1.0304709 1.0027701
1700 40.957034 -26.28667 7.1881521 1.0360111 1.0027701
1800 41.536831 -27.393841 6.6814405 1.0470914 1.0027701
1900 41.952676 -28.123051 7.4683871 1.0360111 1.0027701
2000 42.201937 -28.685743 7.4624285 1.0304709 1.0027701
2100 41.509082 -27.909225 6.8666951 1.0304709 1.0083102
2200 40.794911 -27.085519 5.2599455 1.0415512 1.0027701
2300 38.74971 -25.146012 4.2936194 1.0360111 1.0083102
2400 38.418073 -24.593601 3.1418121 1.0470914 1.0027701
2500 36.932581 -23.407617 1.9397617 1.0304709 1.0027701
2600 35.979152 -23.066707 2.1676871 1.0415512 1.0027701
2700 35.848339 -22.556586 2.079815 1.0526316 1.0027701
2800 35.796197 -22.092919 2.6843042 1.0470914 1.0027701
2900 35.752758 -21.6603 2.4924275 1.0360111 1.0083102
3000 36.548479 -21.940002 2.8478206 1.0304709 1.0027701
3100 36.74473 -22.072441 3.7028736 1.0193906 1.0027701
3200 36.633543 -22.568923 3.7319143 1.0249307 1.0083102
3300 37.175051 -23.069268 3.5045201 1.0193906 1.0027701
3400 36.942892 -23.480254 3.1212991 1.0193906 1.0027701
3500 37.813564 -24.659011 3.6045332 1.0138504 1.0027701
3600 37.856787 -24.954353 4.3062815 1.0249307 1.0027701
3700 38.543481 -25.054481 4.7177629 1.0304709 1.0027701
3800 39.011196 -25.760455 4.9664492 1.0304709 1.0027701
3900 38.784228 -25.618896 4.944851 1.0304709 1.0027701
4000 39.348833 -26.615389 4.8191233 1.0304709 1.0027701
4100 39.242191 -26.754066 4.7960336 1.0249307 1.0027701
4200 38.989902 -26.741978 3.7980048 1.0415512 1.0027701
4300 38.726515 -25.916493 3.7176038 1.0304709 1.0027701
4400 38.720441 -25.549542 3.3956415 1.0470914 1.0027701
4500 38.22257 -25.122141 4.5771547 1.0304709 1.0083102
4600 38.217511 -25.390842 4.4896706 1.0360111 1.0027701
4700 39.121636 -26.227786 4.9811267 1.0415512 1.0083102
4800 39.306166 -26.700977 4.9963051 1.0249307 1.0027701
4900 38.909059 -25.799524 6.1957543 1.0692521 1.0027701
5000 38.778196 -26.491002 5.6393984 1.0526316 1.0027701
5100 38.587868 -27.253335 5.5460314 1.0415512 1.0027701
5200 38.686438 -27.40612 5.5186442 1.0249307 1.0027701
5300 37.986414 -26.049806 5.3696903 1.0304709 1.0027701
5400 37.111804 -26.019738 4.2114526 1.0415512 1.0083102
5500 36.62295 -25.592884 5.1349 1.0415512 1.0027701
5600 36.087987 -25.398454 4.4963434 1.0249307 1.0083102
5700 34.435409 -24.548062 3.5310124 1.0249307 1.0027701
5800 33.18681 -22.76355 3.2061242 1.0470914 1.0027701
5900 32.57428 -21.832024 3.2865828 1.0193906 1.0027701
6000 30.557555 -20.714816 4.2280358 1.0304709 1.0083102
6100 31.893092 -21.235479 4.5931729 1.0304709 1.0027701
6200 31.577761 -21.222778 4.1847871 1.0415512 1.0027701
6300 32.003743 -20.825156 5.6968257 1.0526316 1.0027701
6400 32.073012 -20.877815 7.3062956 1.0360111 1.0027701
6500 31.588306 -21.556202 5.7846536 1.0138504 1.0027701
6600 32.453985 -21.478064 4.8089249 1.0083102 1.0027701
6700 31.269576 -21.24005 4.0540095 1.0193906 1.0027701
6800 31.548438 -21.335039 3.767158 1.0138504 1.0027701
6900 31.249216 -20.689547 4.5435057 1.0083102 1.0027701
7000 31.72893 -20.373971 6.0204212 1.0249307 1.0027701
7100 30.888569 -19.028984 5.2458824 1.0027701 1.0027701
7200 30.747229 -19.579694 3.2582453 1.0138504 1.0083102
7300 28.339584 -19.225504 3.1235472 1.0193906 1.0027701
7400 26.754307 -18.557545 1.3860606 1.0193906 1.0083102
7500 26.559389 -17.395026 1.7206081 1.0138504 1.0083102
7600 26.227728 -16.755138 2.1148459 1.0193906 1.0027701
7700 26.361463 -15.711397 2.5458994 1.0138504 1.0027701
7800 26.081484 -16.032712 0.70050048 1.0138504 1.0027701
7900 24.660082 -15.079215 1.1999533 1.0138504 1.0027701
8000 24.448184 -14.668849 0.63886653 1.0138504 1.0083102
8100 24.198589 -15.157555 0.12256041 1.0027701 1.0027701
8200 24.764129 -14.876966 0.97060609 1.0249307 1.0083102
8300 25.33268 -14.891698 1.6089548 1.0083102 1.0027701
8400 24.992342 -14.652659 1.3317376 1.0138504 1.0027701
8500 25.115045 -14.683247 0.98361969 1.0138504 1.0027701
8600 24.954894 -14.451543 1.2228755 1.0083102 1.0027701
8700 24.51303 -14.159235 0.75345783 1.0249307 1.0083102
8800 22.697326 -13.254743 1.2913804 1.0138504 1.0027701
8900 22.868775 -13.677092 -0.048154854 1.0083102 1.0027701
9000 25.269332 -13.649225 1.0337367 1.0083102 1.0083102
9100 24.184813 -12.826606 1.1160895 1.0360111 1.0027701
9200 23.664589 -13.449013 0.031451624 1.0193906 1.0083102
9300 23.944566 -13.401803 0.20095909 1.0193906 1.0027701
9400 24.146696 -12.879011 0.89518549 1.0249307 1.0027701
9500 25.383214 -13.411768 0.95798595 1.0304709 1.0027701
9600 25.248933 -13.838658 0.45253554 1.0304709 1.0027701
9700 24.38613 -13.123006 1.5446061 1.0138504 1.0027701
9800 25.743921 -13.610838 1.2556191 1.0083102 1.0027701
9900 26.468479 -13.72971 2.3998562 1.0249307 1.0027701
10000 26.338099 -14.82183 1.5233934 1.0193906 1.0027701
Loop time of 0.372607 on 2 procs for 10000 steps with 361 atoms
Performance: 2318795.909 tau/day, 26837.916 timesteps/s, 9.688 Matom-step/s
96.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13582 | 0.14029 | 0.14475 | 1.2 | 37.65
Bond | 0.035027 | 0.035038 | 0.035049 | 0.0 | 9.40
Neigh | 0.085828 | 0.08675 | 0.087673 | 0.3 | 23.28
Comm | 0.05562 | 0.05851 | 0.061399 | 1.2 | 15.70
Output | 0.0010102 | 0.0011746 | 0.0013391 | 0.5 | 0.32
Modify | 0.029008 | 0.02926 | 0.029512 | 0.1 | 7.85
Other | | 0.02159 | | | 5.79
Nlocal: 180.5 ave 181 max 180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 166.5 ave 170 max 163 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1628.5 ave 1652 max 1605 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 3257
Ave neighs/atom = 9.0221607
Ave special neighs/atom = 5.6177285
Neighbor list builds = 1208
Dangerous builds = 0
Total wall time: 0:00:00

255
examples/balance/log.3Nov23.balance.bond.fast.g++.4 Normal file
View File

@ -0,0 +1,255 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
create_bonds many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
6 = max # of 1-2 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 10.0 # because bonds stretch a long ways
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 10
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.123 | 5.142 | 5.176 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
100 25.57187 -2.2902218 2.9990153 1.0526316 1.0193906
200 25.532511 -2.5273097 2.8286231 1.0526316 1.0083102
300 25.860246 -3.0674998 2.6725358 1.0415512 1.0083102
400 26.628011 -4.394738 2.6618897 1.0526316 1.0083102
500 27.627309 -6.2305012 2.6564278 1.0415512 1.0083102
600 28.881803 -8.2757766 2.8249236 1.0526316 1.0083102
700 29.941402 -9.9816088 2.9828232 1.0526316 1.0083102
800 31.118457 -12.199787 3.2044549 1.0304709 1.0083102
900 32.393498 -14.204491 2.9496587 1.0747922 1.0193906
1000 33.392657 -15.747519 3.1613807 1.0637119 1.0193906
1100 34.671769 -17.728904 3.019138 1.0526316 1.0193906
1200 35.632627 -19.846347 3.1061176 1.0637119 1.0193906
1300 36.77272 -21.156179 3.2353009 1.0415512 1.0193906
1400 38.241608 -22.744765 4.1163075 1.0637119 1.0083102
1500 40.072478 -25.139827 5.3032535 1.0415512 1.0193906
1600 40.665382 -25.901697 5.4330761 1.0858726 1.0083102
1700 40.957034 -26.28667 7.1881521 1.1080332 1.0083102
1800 41.536831 -27.393841 6.6814405 1.0969529 1.0193906
1900 41.952676 -28.123051 7.4683871 1.0858726 1.0193906
2000 42.201937 -28.685743 7.4624284 1.0747922 1.0083102
2100 41.509082 -27.909225 6.8666955 1.0969529 1.0083102
2200 40.794912 -27.085519 5.259945 1.0415512 1.0083102
2300 38.749709 -25.14601 4.2936222 1.0526316 1.0083102
2400 38.418065 -24.593596 3.1418049 1.1191136 1.0083102
2500 36.932588 -23.407613 1.9397982 1.0637119 1.0083102
2600 35.979181 -23.066748 2.1678902 1.0637119 1.0193906
2700 35.84858 -22.55645 2.0798013 1.0858726 1.0193906
2800 35.795795 -22.092149 2.6849882 1.0637119 1.0193906
2900 35.754958 -21.662138 2.4892921 1.0526316 1.0083102
3000 36.548644 -21.943203 2.8497192 1.0747922 1.0083102
3100 36.755531 -22.081384 3.6960187 1.0858726 1.0193906
3200 36.606921 -22.538438 3.7047874 1.0415512 1.0193906
3300 37.185396 -23.077004 3.4202006 1.0858726 1.0083102
3400 37.136687 -23.617745 2.9763794 1.0858726 1.0083102
3500 37.908279 -24.364631 3.5155218 1.0304709 1.0083102
3600 38.459203 -25.01024 4.3313693 1.0747922 1.0083102
3700 39.108683 -25.636756 4.4707992 1.0415512 1.0083102
3800 38.67059 -25.126486 5.3753987 1.0747922 1.0083102
3900 38.395639 -25.140269 5.1661495 1.0858726 1.0193906
4000 38.552057 -24.871721 5.0206769 1.0747922 1.0083102
4100 39.065683 -25.344035 4.4042913 1.0858726 1.0083102
4200 37.714294 -24.728278 5.1978439 1.0304709 1.0083102
4300 38.785555 -25.380643 3.7033369 1.0304709 1.0193906
4400 38.341445 -25.13442 3.4298833 1.1191136 1.0193906
4500 37.720522 -24.702087 3.4450752 1.0637119 1.0083102
4600 37.509806 -24.477444 3.6155741 1.0858726 1.0083102
4700 37.319957 -23.722654 4.7111338 1.0526316 1.0193906
4800 38.233154 -24.653472 4.25263 1.0637119 1.0083102
4900 37.309164 -24.21353 4.8513758 1.0637119 1.0193906
5000 37.559292 -24.720651 5.409312 1.0415512 1.0193906
5100 37.449783 -25.21538 6.0099692 1.0747922 1.0083102
5200 38.187982 -25.16709 6.1425844 1.0415512 1.0083102
5300 36.91668 -24.616017 4.7873357 1.0304709 1.0083102
5400 35.103465 -23.85158 5.1950262 1.0304709 1.0193906
5500 35.299351 -23.946174 4.8038223 1.0526316 1.0083102
5600 35.713482 -24.962908 3.5111314 1.0193906 1.0193906
5700 33.740794 -23.77699 4.5783011 1.0304709 1.0193906
5800 33.791635 -23.536627 3.1317306 1.0415512 1.0193906
5900 34.039769 -23.068008 4.0189755 1.0415512 1.0083102
6000 32.809103 -22.085195 4.0827943 1.0637119 1.0193906
6100 32.522642 -21.979287 4.1437901 1.0637119 1.0083102
6200 32.347924 -21.661359 4.1436759 1.0526316 1.0193906
6300 32.099974 -21.114688 5.5745084 1.0193906 1.0193906
6400 33.767704 -23.489786 4.1038662 1.0526316 1.0193906
6500 32.283906 -22.076822 7.2664805 1.0526316 1.0083102
6600 33.25146 -23.191973 6.01093 1.0526316 1.0083102
6700 31.7665 -22.1476 6.4256074 1.0747922 1.0193906
6800 30.775727 -21.513059 5.1709188 1.0304709 1.0083102
6900 30.964501 -21.153634 5.1077701 1.0193906 1.0193906
7000 31.292268 -20.800916 3.6047789 1.0193906 1.0193906
7100 31.460811 -20.280043 3.2369395 1.0193906 1.0083102
7200 30.871387 -19.340893 2.9615798 1.0193906 1.0083102
7300 28.983475 -18.709174 3.1686601 1.0304709 1.0083102
7400 28.032829 -18.200801 1.8738157 1.0304709 1.0193906
7500 28.088176 -17.117863 3.5604961 1.0304709 1.0083102
7600 27.456327 -17.011025 1.7822114 1.0526316 1.0304709
7700 26.483887 -16.024179 1.258431 1.0415512 1.0193906
7800 26.023393 -15.532176 1.3663841 1.0304709 1.0083102
7900 26.154386 -14.738286 1.5214339 1.0415512 1.0193906
8000 25.755121 -14.487715 1.0185064 1.0415512 1.0304709
8100 25.468927 -14.273205 1.3553057 1.0526316 1.0304709
8200 25.74216 -14.606852 0.13693979 1.0193906 1.0083102
8300 24.457219 -14.529941 -0.0032579349 1.0304709 1.0193906
8400 24.054076 -13.704387 0.80714443 1.0193906 1.0193906
8500 23.742098 -13.699968 0.41096573 1.0304709 1.0193906
8600 24.060806 -13.289555 0.22489663 1.0193906 1.0083102
8700 23.831533 -13.025052 -0.090244538 1.0304709 1.0193906
8800 23.823082 -13.407662 -0.28029605 1.0304709 1.0083102
8900 23.982182 -12.862338 0.50556065 1.0193906 1.0193906
9000 24.876045 -13.400416 1.1475671 1.0415512 1.0193906
9100 25.018155 -13.625286 0.74749825 1.0304709 1.0083102
9200 25.671195 -13.850993 0.88340554 1.0526316 1.0083102
9300 26.076502 -13.935292 1.2705214 1.0526316 1.0083102
9400 25.847786 -13.626034 1.5676611 1.0415512 1.0193906
9500 25.963986 -14.23672 1.4791684 1.0304709 1.0083102
9600 26.58066 -14.74703 1.3431841 1.0526316 1.0083102
9700 27.401448 -14.568412 2.4488742 1.0747922 1.0083102
9800 27.927894 -15.254362 2.8516414 1.0415512 1.0083102
9900 28.204891 -15.219892 3.0631109 1.0415512 1.0083102
10000 27.30902 -14.939134 2.8235246 1.0304709 1.0083102
Loop time of 0.317224 on 4 procs for 10000 steps with 361 atoms
Performance: 2723630.892 tau/day, 31523.506 timesteps/s, 11.380 Matom-step/s
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.066318 | 0.073612 | 0.081352 | 2.6 | 23.21
Bond | 0.01886 | 0.020483 | 0.022893 | 1.1 | 6.46
Neigh | 0.051128 | 0.052747 | 0.054345 | 0.5 | 16.63
Comm | 0.093881 | 0.11329 | 0.13156 | 4.2 | 35.71
Output | 0.0011573 | 0.0013205 | 0.0016444 | 0.5 | 0.42
Modify | 0.025957 | 0.026647 | 0.027249 | 0.3 | 8.40
Other | | 0.02913 | | | 9.18
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 260.75 ave 265 max 256 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 889.5 ave 1035 max 794 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 3558
Ave neighs/atom = 9.8559557
Ave special neighs/atom = 5.6177285
Neighbor list builds = 1192
Dangerous builds = 0
Total wall time: 0:00:00

550
examples/balance/log.3Nov23.balance.bond.slow.g++.2 Normal file
View File

@ -0,0 +1,550 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
special bonds CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 40000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.08 | 7.108 | 7.137 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 0.57437856 0 0.26099453 2 1.0193906
100 0.36302846 0 0.17339851 1.0027701 1.0027701
200 0.19645077 0 0.087800915 1.0027701 1.0027701
300 0.32061117 0 0.11295723 1.0027701 1.0027701
400 0.32854136 0 0.11325585 1.0027701 1.0027701
500 0.29754179 0 0.10150632 1.0083102 1.0027701
600 0.37384867 0 0.11949784 1.0027701 1.0027701
700 0.33202319 0 0.092871339 1.0027701 1.0083102
800 0.28340637 0 0.065861565 1.0027701 1.0027701
900 0.36250157 0 0.085896287 1.0083102 1.0027701
1000 0.35402718 0 0.07519914 1.0027701 1.0083102
1100 0.31576357 0 0.050253636 1.0083102 1.0027701
1200 0.35727572 0 0.05153538 1.0027701 1.0027701
1300 0.34322607 0 0.036115722 1.0027701 1.0027701
1400 0.34007557 0 0.025378602 1.0027701 1.0083102
1500 0.39242551 0 0.033002212 1.0027701 1.0027701
1600 0.35679049 0 0.010101576 1.0027701 1.0027701
1700 0.31293001 0 -0.013791036 1.0027701 1.0027701
1800 0.34767962 0 -0.0065490806 1.0027701 1.0027701
1900 0.34721592 0 -0.010055082 1.0027701 1.0083102
2000 0.34074949 0 -0.020822697 1.0027701 1.0027701
2100 0.37195615 0 -0.024943134 1.0027701 1.0027701
2200 0.35367164 0 -0.047369336 1.0027701 1.0027701
2300 0.32088735 0 -0.069724381 1.0027701 1.0027701
2400 0.34291945 0 -0.065470223 1.0027701 1.0027701
2500 0.35204641 0 -0.062631879 1.0027701 1.0027701
2600 0.32762755 0 -0.075128824 1.0027701 1.0083102
2700 0.32042617 0 -0.086259498 1.0083102 1.0027701
2800 0.32747171 0 -0.094775765 1.0027701 1.0027701
2900 0.33544664 0 -0.10376048 1.0027701 1.0027701
3000 0.34015845 0 -0.1112134 1.0083102 1.0027701
3100 0.34425802 0 -0.11413914 1.0027701 1.0083102
3200 0.34158654 0 -0.1164643 1.0027701 1.0027701
3300 0.32525955 0 -0.12206636 1.0027701 1.0083102
3400 0.32183965 0 -0.12186353 1.0083102 1.0027701
3500 0.3323435 0 -0.11597815 1.0027701 1.0027701
3600 0.34124638 0 -0.11177335 1.0083102 1.0083102
3700 0.3404339 0 -0.11235575 1.0027701 1.0027701
3800 0.32736123 0 -0.11610108 1.0027701 1.0027701
3900 0.32897993 0 -0.11138151 1.0027701 1.0027701
4000 0.35111095 0 -0.096171644 1.0083102 1.0027701
4100 0.34682622 0 -0.087507472 1.0027701 1.0027701
4200 0.3307829 0 -0.079759555 1.0027701 1.0027701
4300 0.35057085 0 -0.055194355 1.0027701 1.0027701
4400 0.36389071 0 -0.02963313 1.0027701 1.0083102
4500 0.35694456 0 -0.013842583 1.0027701 1.0027701
4600 0.3472078 0 -0.0048118723 1.0083102 1.0027701
4700 0.31734514 0 -0.0032417081 1.0027701 1.0027701
4800 0.32419237 0 0.01409306 1.0027701 1.0027701
4900 0.36939799 0 0.045351789 1.0027701 1.0083102
5000 0.36998276 0 0.056830437 1.0027701 1.0027701
5100 0.33969031 0 0.051833536 1.0027701 1.0027701
5200 0.33910288 0 0.055544085 1.0027701 1.0027701
5300 0.34641009 0 0.0651487 1.0027701 1.0027701
5400 0.34469325 0 0.074538093 1.0027701 1.0027701
5500 0.34582041 0 0.084940845 1.0027701 1.0027701
5600 0.33471774 0 0.090102411 1.0027701 1.0083102
5700 0.32667873 0 0.09528948 1.0083102 1.0027701
5800 0.33762496 0 0.10545364 1.0027701 1.0027701
5900 0.33285742 0 0.10816506 1.0027701 1.0027701
6000 0.31920877 0 0.10547467 1.0027701 1.0027701
6100 0.31933081 0 0.10610684 1.0027701 1.0027701
6200 0.3152523 0 0.10651599 1.0083102 1.0083102
6300 0.32548074 0 0.11405234 1.0027701 1.0027701
6400 0.33851595 0 0.12389967 1.0027701 1.0027701
6500 0.32957825 0 0.12493331 1.0027701 1.0027701
6600 0.32319786 0 0.12404318 1.0027701 1.0027701
6700 0.3223738 0 0.12418108 1.0083102 1.0027701
6800 0.32390959 0 0.12576314 1.0027701 1.0027701
6900 0.34414413 0 0.1318456 1.0027701 1.0027701
7000 0.34508922 0 0.12669741 1.0027701 1.0083102
7100 0.31655025 0 0.10869109 1.0027701 1.0027701
7200 0.31997193 0 0.10305508 1.0027701 1.0027701
7300 0.33199085 0 0.10377052 1.0027701 1.0027701
7400 0.32146221 0 0.097589803 1.0027701 1.0027701
7500 0.33416843 0 0.096202638 1.0027701 1.0027701
7600 0.35297124 0 0.092441999 1.0027701 1.0027701
7700 0.34494663 0 0.075206332 1.0027701 1.0027701
7800 0.34010702 0 0.056336074 1.0083102 1.0027701
7900 0.343424 0 0.040946914 1.0027701 1.0027701
8000 0.33772245 0 0.025817271 1.0027701 1.0027701
8100 0.34463909 0 0.017237548 1.0083102 1.0083102
8200 0.36052034 0 0.010393623 1.0027701 1.0027701
8300 0.36083091 0 -0.0053933186 1.0027701 1.0027701
8400 0.35378067 0 -0.02600248 1.0027701 1.0027701
8500 0.35133887 0 -0.044211483 1.0027701 1.0027701
8600 0.34559937 0 -0.060861345 1.0027701 1.0027701
8700 0.33724119 0 -0.075776058 1.0027701 1.0027701
8800 0.33337192 0 -0.087098937 1.0027701 1.0027701
8900 0.33533081 0 -0.094631485 1.0027701 1.0083102
9000 0.34994303 0 -0.096758052 1.0083102 1.0083102
9100 0.34448227 0 -0.10330192 1.0083102 1.0083102
9200 0.32675792 0 -0.11000278 1.0083102 1.0083102
9300 0.33814013 0 -0.10358181 1.0027701 1.0027701
9400 0.34457419 0 -0.096896951 1.0027701 1.0027701
9500 0.33834959 0 -0.09547729 1.0027701 1.0027701
9600 0.33204582 0 -0.097694622 1.0027701 1.0027701
9700 0.31152805 0 -0.10637377 1.0083102 1.0027701
9800 0.31637311 0 -0.1053323 1.0027701 1.0027701
9900 0.33416162 0 -0.097857158 1.0027701 1.0083102
10000 0.33731767 0 -0.094656227 1.0027701 1.0027701
10100 0.34565093 0 -0.090199556 1.0083102 1.0083102
10200 0.34549074 0 -0.088914471 1.0083102 1.0027701
10300 0.33545625 0 -0.09066219 1.0027701 1.0083102
10400 0.33649703 0 -0.086437886 1.0027701 1.0027701
10500 0.34549848 0 -0.0767365 1.0027701 1.0027701
10600 0.34222917 0 -0.069368792 1.0027701 1.0027701
10700 0.34262469 0 -0.060550996 1.0027701 1.0027701
10800 0.34859129 0 -0.050692625 1.0027701 1.0027701
10900 0.34850448 0 -0.043627505 1.0027701 1.0027701
11000 0.34887257 0 -0.036859125 1.0027701 1.0083102
11100 0.34171718 0 -0.032690742 1.0083102 1.0027701
11200 0.329808 0 -0.02793377 1.0027701 1.0027701
11300 0.34490203 0 -0.010278222 1.0027701 1.0027701
11400 0.36226391 0 0.010141624 1.0027701 1.0083102
11500 0.35392138 0 0.021188939 1.0027701 1.0027701
11600 0.34378732 0 0.031423313 1.0083102 1.0083102
11700 0.33606385 0 0.043944374 1.0083102 1.0027701
11800 0.33212482 0 0.058629338 1.0027701 1.0027701
11900 0.34547313 0 0.078112959 1.0027701 1.0083102
12000 0.34840957 0 0.092356502 1.0083102 1.0027701
12100 0.34146853 0 0.10236492 1.0027701 1.0027701
12200 0.34591494 0 0.11620659 1.0027701 1.0027701
12300 0.33290894 0 0.12437245 1.0027701 1.0027701
12400 0.32423652 0 0.13191976 1.0083102 1.0083102
12500 0.33031748 0 0.13999363 1.0083102 1.0083102
12600 0.31927087 0 0.13776242 1.0083102 1.0027701
12700 0.30865965 0 0.13340787 1.0027701 1.0027701
12800 0.32542691 0 0.13690449 1.0027701 1.0083102
12900 0.32453244 0 0.13376127 1.0027701 1.0027701
13000 0.30974678 0 0.12749869 1.0027701 1.0027701
13100 0.32402285 0 0.13240572 1.0027701 1.0083102
13200 0.32896987 0 0.13257567 1.0083102 1.0027701
13300 0.32939197 0 0.12690791 1.0027701 1.0027701
13400 0.33966453 0 0.12036916 1.0027701 1.0027701
13500 0.33012942 0 0.10496127 1.0027701 1.0027701
13600 0.32363377 0 0.091763332 1.0083102 1.0083102
13700 0.33427955 0 0.087928243 1.0027701 1.0027701
13800 0.33457885 0 0.08191828 1.0027701 1.0027701
13900 0.33819924 0 0.074487337 1.0027701 1.0027701
14000 0.34611002 0 0.066256529 1.0083102 1.0027701
14100 0.33224254 0 0.052608223 1.0027701 1.0027701
14200 0.33796934 0 0.049677792 1.0027701 1.0027701
14300 0.36216731 0 0.055173039 1.0027701 1.0083102
14400 0.35140789 0 0.047322221 1.0027701 1.0027701
14500 0.34425046 0 0.036527245 1.0027701 1.0083102
14600 0.3604575 0 0.0294772 1.0083102 1.0083102
14700 0.3433878 0 0.0096774422 1.0083102 1.0083102
14800 0.3287069 0 -0.0079768782 1.0027701 1.0027701
14900 0.34978607 0 -0.01178453 1.0027701 1.0027701
15000 0.34749548 0 -0.023685074 1.0027701 1.0027701
15100 0.33474304 0 -0.040569945 1.0027701 1.0027701
15200 0.35036594 0 -0.048341599 1.0027701 1.0027701
15300 0.35686042 0 -0.058664905 1.0027701 1.0027701
15400 0.34041567 0 -0.074858327 1.0027701 1.0027701
15500 0.33397773 0 -0.083782088 1.0027701 1.0027701
15600 0.3420119 0 -0.084635487 1.0083102 1.0027701
15700 0.345487 0 -0.088137628 1.0027701 1.0027701
15800 0.33494392 0 -0.10083064 1.0027701 1.0027701
15900 0.32675175 0 -0.11620387 1.0027701 1.0027701
16000 0.33011636 0 -0.12713401 1.0027701 1.0027701
16100 0.32443118 0 -0.13685913 1.0027701 1.0027701
16200 0.31608392 0 -0.14164152 1.0027701 1.0083102
16300 0.33293965 0 -0.13335387 1.0027701 1.0027701
16400 0.34462807 0 -0.12471686 1.0027701 1.0027701
16500 0.33528082 0 -0.12211554 1.0027701 1.0027701
16600 0.34250121 0 -0.11228169 1.0027701 1.0027701
16700 0.35342336 0 -0.099226948 1.0027701 1.0027701
16800 0.33730938 0 -0.093581966 1.0027701 1.0027701
16900 0.3275761 0 -0.085163356 1.0027701 1.0027701
17000 0.33624873 0 -0.070896594 1.0083102 1.0027701
17100 0.34339177 0 -0.057731935 1.0027701 1.0027701
17200 0.34874414 0 -0.046575228 1.0027701 1.0027701
17300 0.33950911 0 -0.041862179 1.0027701 1.0027701
17400 0.33100286 0 -0.036618199 1.0027701 1.0027701
17500 0.34238095 0 -0.021681436 1.0027701 1.0027701
17600 0.35476614 0 -0.0032568304 1.0027701 1.0027701
17700 0.35452053 0 0.011863966 1.0027701 1.0027701
17800 0.35423934 0 0.024753043 1.0083102 1.0027701
17900 0.35001044 0 0.031647802 1.0083102 1.0083102
18000 0.32867773 0 0.030261102 1.0027701 1.0027701
18100 0.32730114 0 0.037627319 1.0027701 1.0027701
18200 0.35786038 0 0.057653258 1.0027701 1.0027701
18300 0.35598175 0 0.065533711 1.0027701 1.0027701
18400 0.33913202 0 0.066186406 1.0027701 1.0027701
18500 0.34449656 0 0.074575322 1.0027701 1.0027701
18600 0.34792041 0 0.083818651 1.0027701 1.0027701
18700 0.33910599 0 0.089751723 1.0027701 1.0027701
18800 0.33627789 0 0.097491916 1.0027701 1.0083102
18900 0.32937699 0 0.10350872 1.0083102 1.0027701
19000 0.30908702 0 0.10610099 1.0027701 1.0027701
19100 0.31033435 0 0.1168178 1.0027701 1.0027701
19200 0.32011336 0 0.12898885 1.0027701 1.0027701
19300 0.31851339 0 0.13398981 1.0027701 1.0027701
19400 0.33289985 0 0.1401039 1.0027701 1.0027701
19500 0.3387096 0 0.13971063 1.0027701 1.0027701
19600 0.31475734 0 0.12963499 1.0027701 1.0083102
19700 0.31971554 0 0.13189606 1.0083102 1.0083102
19800 0.33096999 0 0.13636987 1.0083102 1.0027701
19900 0.31601688 0 0.12889803 1.0027701 1.0027701
20000 0.32916469 0 0.12683491 1.0027701 1.0027701
20100 0.34355734 0 0.12251501 1.0027701 1.0027701
20200 0.33029721 0 0.10833335 1.0083102 1.0027701
20300 0.34079176 0 0.10305862 1.0027701 1.0027701
20400 0.35196716 0 0.098386494 1.0027701 1.0027701
20500 0.32687648 0 0.081202778 1.0083102 1.0027701
20600 0.33371658 0 0.074287923 1.0027701 1.0083102
20700 0.36625228 0 0.073768436 1.0083102 1.0027701
20800 0.35824217 0 0.054876358 1.0027701 1.0027701
20900 0.34861601 0 0.031603534 1.0027701 1.0027701
21000 0.35396698 0 0.013464537 1.0027701 1.0027701
21100 0.33592449 0 -0.0096173026 1.0027701 1.0027701
21200 0.327063 0 -0.025970252 1.0027701 1.0027701
21300 0.34418745 0 -0.030446162 1.0027701 1.0027701
21400 0.34181459 0 -0.039942616 1.0027701 1.0027701
21500 0.3315724 0 -0.05089285 1.0027701 1.0027701
21600 0.35674681 0 -0.047926263 1.0083102 1.0083102
21700 0.37320044 0 -0.047190592 1.0027701 1.0027701
21800 0.34626293 0 -0.063211549 1.0083102 1.0027701
21900 0.32941853 0 -0.078034339 1.0083102 1.0027701
22000 0.34102577 0 -0.083179211 1.0027701 1.0027701
22100 0.33614888 0 -0.091647522 1.0083102 1.0083102
22200 0.3339762 0 -0.09744915 1.0083102 1.0027701
22300 0.33867021 0 -0.10026932 1.0027701 1.0027701
22400 0.31974078 0 -0.10896583 1.0027701 1.0027701
22500 0.3261442 0 -0.10644809 1.0027701 1.0027701
22600 0.35128159 0 -0.097711062 1.0027701 1.0027701
22700 0.33133845 0 -0.10656571 1.0027701 1.0027701
22800 0.31730555 0 -0.11420891 1.0027701 1.0027701
22900 0.34720941 0 -0.10586647 1.0083102 1.0027701
23000 0.34418922 0 -0.10745826 1.0027701 1.0027701
23100 0.32342851 0 -0.11384766 1.0027701 1.0027701
23200 0.3408144 0 -0.10631064 1.0027701 1.0027701
23300 0.33006722 0 -0.1070084 1.0027701 1.0027701
23400 0.31578528 0 -0.10711608 1.0027701 1.0027701
23500 0.34908788 0 -0.088441889 1.0027701 1.0027701
23600 0.35801835 0 -0.075953983 1.0027701 1.0027701
23700 0.33573037 0 -0.072357745 1.0027701 1.0083102
23800 0.34435835 0 -0.055470682 1.0083102 1.0027701
23900 0.35307683 0 -0.036076205 1.0027701 1.0027701
24000 0.35184599 0 -0.020939815 1.0027701 1.0027701
24100 0.35687079 0 -0.0063601457 1.0027701 1.0027701
24200 0.33612385 0 -0.0014613923 1.0027701 1.0027701
24300 0.32234106 0 0.006750452 1.0027701 1.0027701
24400 0.34852008 0 0.029170079 1.0027701 1.0027701
24500 0.35224811 0 0.043783151 1.0027701 1.0027701
24600 0.34160459 0 0.05294313 1.0027701 1.0027701
24700 0.35616752 0 0.069291509 1.0027701 1.0027701
24800 0.34984726 0 0.076650029 1.0027701 1.0027701
24900 0.33337969 0 0.080083735 1.0027701 1.0027701
25000 0.34846751 0 0.095559187 1.0027701 1.0027701
25100 0.34495541 0 0.10558042 1.0027701 1.0083102
25200 0.32630088 0 0.10897783 1.0083102 1.0027701
25300 0.33651146 0 0.11888202 1.0027701 1.0027701
25400 0.32194445 0 0.11826793 1.0027701 1.0027701
25500 0.30295352 0 0.11641357 1.0027701 1.0027701
25600 0.33485387 0 0.13204258 1.0027701 1.0027701
25700 0.34407287 0 0.13738986 1.0027701 1.0027701
25800 0.32421817 0 0.12822703 1.0083102 1.0083102
25900 0.32463356 0 0.12403448 1.0027701 1.0027701
26000 0.32431468 0 0.12087994 1.0027701 1.0083102
26100 0.31886825 0 0.11741621 1.0083102 1.0027701
26200 0.32607823 0 0.1180517 1.0083102 1.0027701
26300 0.32511255 0 0.11479741 1.0027701 1.0083102
26400 0.32336124 0 0.11055002 1.0027701 1.0027701
26500 0.33026321 0 0.10934888 1.0027701 1.0027701
26600 0.32604491 0 0.10480442 1.0027701 1.0027701
26700 0.33764955 0 0.10458959 1.0027701 1.0027701
26800 0.35202544 0 0.10295075 1.0027701 1.0027701
26900 0.33382028 0 0.088148483 1.0027701 1.0027701
27000 0.33252808 0 0.078275659 1.0027701 1.0027701
27100 0.35433636 0 0.076729989 1.0083102 1.0027701
27200 0.34824881 0 0.065720375 1.0083102 1.0027701
27300 0.33525644 0 0.051611147 1.0027701 1.0027701
27400 0.34685762 0 0.045597284 1.0027701 1.0027701
27500 0.35181712 0 0.037076034 1.0027701 1.0027701
27600 0.34541685 0 0.022287411 1.0027701 1.0027701
27700 0.34559823 0 0.0056480168 1.0027701 1.0083102
27800 0.33646375 0 -0.015571541 1.0027701 1.0027701
27900 0.33681932 0 -0.031777883 1.0083102 1.0027701
28000 0.35093514 0 -0.041519343 1.0027701 1.0027701
28100 0.34345697 0 -0.057623438 1.0027701 1.0027701
28200 0.33655073 0 -0.072228985 1.0027701 1.0027701
28300 0.34428448 0 -0.080015243 1.0027701 1.0027701
28400 0.34089922 0 -0.089955339 1.0027701 1.0027701
28500 0.34522966 0 -0.096529413 1.0083102 1.0027701
28600 0.34713819 0 -0.10221712 1.0083102 1.0083102
28700 0.33692049 0 -0.10868625 1.0027701 1.0027701
28800 0.34522852 0 -0.10679446 1.0027701 1.0083102
28900 0.33956477 0 -0.1105454 1.0083102 1.0027701
29000 0.30989301 0 -0.12332622 1.0083102 1.0083102
29100 0.32373738 0 -0.11985261 1.0027701 1.0027701
29200 0.35156812 0 -0.10956099 1.0027701 1.0027701
29300 0.33938829 0 -0.11259535 1.0027701 1.0027701
29400 0.32401178 0 -0.11664978 1.0083102 1.0083102
29500 0.32320492 0 -0.11336533 1.0027701 1.0027701
29600 0.32928877 0 -0.10404547 1.0027701 1.0027701
29700 0.3436911 0 -0.089845529 1.0027701 1.0027701
29800 0.34194019 0 -0.081660797 1.0027701 1.0027701
29900 0.32909826 0 -0.07807778 1.0027701 1.0083102
30000 0.34092826 0 -0.06626489 1.0027701 1.0027701
30100 0.34763086 0 -0.055589635 1.0027701 1.0027701
30200 0.34479984 0 -0.047402672 1.0083102 1.0083102
30300 0.34783224 0 -0.036371931 1.0083102 1.0027701
30400 0.34525176 0 -0.027246663 1.0027701 1.0027701
30500 0.35266364 0 -0.016275033 1.0027701 1.0027701
30600 0.35792479 0 -0.007158119 1.0083102 1.0083102
30700 0.33607567 0 -0.0064391529 1.0027701 1.0027701
30800 0.34311607 0 0.005382948 1.0083102 1.0027701
30900 0.37218574 0 0.025004945 1.0027701 1.0027701
31000 0.35196541 0 0.027902483 1.0027701 1.0027701
31100 0.33533693 0 0.032349025 1.0083102 1.0083102
31200 0.34382193 0 0.046631454 1.0083102 1.0027701
31300 0.32886237 0 0.05405956 1.0027701 1.0027701
31400 0.32738754 0 0.066295734 1.0027701 1.0027701
31500 0.35367575 0 0.087140904 1.0027701 1.0027701
31600 0.33756811 0 0.092135887 1.0027701 1.0027701
31700 0.31701631 0 0.094576339 1.0027701 1.0027701
31800 0.34217612 0 0.11195071 1.0027701 1.0027701
31900 0.33725187 0 0.11924087 1.0027701 1.0083102
32000 0.30966055 0 0.1199329 1.0027701 1.0027701
32100 0.32771084 0 0.13627552 1.0027701 1.0027701
32200 0.3400914 0 0.14816015 1.0027701 1.0027701
32300 0.32210513 0 0.14569378 1.0027701 1.0027701
32400 0.32096229 0 0.14515284 1.0027701 1.0083102
32500 0.31781969 0 0.14124479 1.0083102 1.0083102
32600 0.3146986 0 0.13616644 1.0083102 1.0083102
32700 0.33526021 0 0.13913538 1.0027701 1.0027701
32800 0.33561156 0 0.13481353 1.0027701 1.0027701
32900 0.31418235 0 0.12161202 1.0027701 1.0027701
33000 0.31952054 0 0.11558871 1.0083102 1.0083102
33100 0.33437451 0 0.11011602 1.0083102 1.0083102
33200 0.33381704 0 0.096535424 1.0027701 1.0027701
33300 0.33786259 0 0.08382113 1.0027701 1.0027701
33400 0.34590937 0 0.073879824 1.0027701 1.0027701
33500 0.33844204 0 0.060854835 1.0083102 1.0083102
33600 0.33845544 0 0.052237152 1.0027701 1.0027701
33700 0.35419837 0 0.048922784 1.0027701 1.0027701
33800 0.3485977 0 0.036886422 1.0027701 1.0083102
33900 0.33816081 0 0.021599335 1.0083102 1.0083102
34000 0.34241389 0 0.010436074 1.0083102 1.0027701
34100 0.33934235 0 -0.002581075 1.0027701 1.0083102
34200 0.34579204 0 -0.011373729 1.0027701 1.0027701
34300 0.35778336 0 -0.018118327 1.0083102 1.0083102
34400 0.35522938 0 -0.030427967 1.0027701 1.0027701
34500 0.34820709 0 -0.042562699 1.0027701 1.0027701
34600 0.35026547 0 -0.047488326 1.0027701 1.0027701
34700 0.35221351 0 -0.050832178 1.0027701 1.0027701
34800 0.33043515 0 -0.062718859 1.0027701 1.0027701
34900 0.32750488 0 -0.068765033 1.0027701 1.0027701
35000 0.35323787 0 -0.067326627 1.0027701 1.0027701
35100 0.34732304 0 -0.080326407 1.0083102 1.0027701
35200 0.3248439 0 -0.099312427 1.0027701 1.0027701
35300 0.32854244 0 -0.10509437 1.0027701 1.0027701
35400 0.33511384 0 -0.10605662 1.0027701 1.0027701
35500 0.33532722 0 -0.10993967 1.0027701 1.0027701
35600 0.33523312 0 -0.11653983 1.0027701 1.0083102
35700 0.32405906 0 -0.12564005 1.0083102 1.0083102
35800 0.32914902 0 -0.12476137 1.0083102 1.0027701
35900 0.34093492 0 -0.11716996 1.0027701 1.0027701
36000 0.33557882 0 -0.11216382 1.0027701 1.0027701
36100 0.3342841 0 -0.10445781 1.0027701 1.0027701
36200 0.33557348 0 -0.0983036 1.0027701 1.0027701
36300 0.33052024 0 -0.097594107 1.0027701 1.0027701
36400 0.34570912 0 -0.089010349 1.0083102 1.0083102
36500 0.35735704 0 -0.078483059 1.0083102 1.0027701
36600 0.33199022 0 -0.079452064 1.0083102 1.0083102
36700 0.3191692 0 -0.074378584 1.0083102 1.0027701
36800 0.34473865 0 -0.052467819 1.0027701 1.0027701
36900 0.35012922 0 -0.034841373 1.0027701 1.0027701
37000 0.34543508 0 -0.019956141 1.0083102 1.0083102
37100 0.36637971 0 0.0034123108 1.0027701 1.0027701
37200 0.36008557 0 0.016667331 1.0083102 1.0083102
37300 0.34027931 0 0.024177377 1.0083102 1.0027701
37400 0.35097853 0 0.041160628 1.0027701 1.0027701
37500 0.35024671 0 0.052433671 1.0027701 1.0027701
37600 0.33483801 0 0.05655083 1.0027701 1.0027701
37700 0.3402098 0 0.067222448 1.0083102 1.0083102
37800 0.33859985 0 0.075720813 1.0083102 1.0083102
37900 0.32323549 0 0.079678841 1.0083102 1.0027701
38000 0.33701532 0 0.092666162 1.0027701 1.0027701
38100 0.3424632 0 0.10094611 1.0027701 1.0027701
38200 0.32167421 0 0.099350179 1.0027701 1.0083102
38300 0.32540911 0 0.10664752 1.0027701 1.0027701
38400 0.33574781 0 0.11614552 1.0027701 1.0027701
38500 0.33125908 0 0.11940265 1.0027701 1.0027701
38600 0.33885801 0 0.12616083 1.0027701 1.0027701
38700 0.33813506 0 0.1298943 1.0027701 1.0027701
38800 0.31888318 0 0.1260135 1.0027701 1.0027701
38900 0.31006429 0 0.12450345 1.0027701 1.0027701
39000 0.31407783 0 0.12693078 1.0083102 1.0083102
39100 0.33078021 0 0.13111094 1.0027701 1.0083102
39200 0.34311375 0 0.12937945 1.0027701 1.0083102
39300 0.33594172 0 0.11839992 1.0027701 1.0027701
39400 0.32763204 0 0.10898509 1.0083102 1.0083102
39500 0.33114946 0 0.10782558 1.0083102 1.0027701
39600 0.32905328 0 0.10631627 1.0027701 1.0027701
39700 0.32416114 0 0.10142386 1.0083102 1.0027701
39800 0.32709132 0 0.096046083 1.0027701 1.0027701
39900 0.32910896 0 0.087876394 1.0027701 1.0027701
40000 0.33462908 0 0.07810396 1.0027701 1.0027701
Loop time of 0.503795 on 2 procs for 40000 steps with 361 atoms
Performance: 6859934.469 tau/day, 79397.390 timesteps/s, 28.662 Matom-step/s
95.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016365 | 0.01652 | 0.016675 | 0.1 | 3.28
Bond | 0.15864 | 0.16196 | 0.16529 | 0.8 | 32.15
Neigh | 0.05169 | 0.051701 | 0.051711 | 0.0 | 10.26
Comm | 0.076385 | 0.091917 | 0.10745 | 5.1 | 18.24
Output | 0.0032235 | 0.0038308 | 0.004438 | 1.0 | 0.76
Modify | 0.11757 | 0.11844 | 0.1193 | 0.3 | 23.51
Other | | 0.05943 | | | 11.80
Nlocal: 180.5 ave 181 max 180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 53.5 ave 54 max 53 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 31.024931
Neighbor list builds = 800
Dangerous builds = 0
Total wall time: 0:00:00

550
examples/balance/log.3Nov23.balance.bond.slow.g++.4 Normal file
View File

@ -0,0 +1,550 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command create_bonds, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
special bonds CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 40000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.05 | 7.102 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 0.57437856 0 0.26099453 3.2354571 1.0526316
100 0.36302846 0 0.17339851 1.0083102 1.0193906
200 0.19645077 0 0.087800915 1.0083102 1.0083102
300 0.32061117 0 0.11295723 1.0193906 1.0193906
400 0.32854136 0 0.11325585 1.0083102 1.0083102
500 0.29754179 0 0.10150632 1.0193906 1.0083102
600 0.37384867 0 0.11949784 1.0083102 1.0083102
700 0.33202319 0 0.092871339 1.0083102 1.0193906
800 0.28340637 0 0.065861565 1.0083102 1.0083102
900 0.36250157 0 0.085896287 1.0193906 1.0083102
1000 0.35402718 0 0.07519914 1.0083102 1.0193906
1100 0.31576357 0 0.050253636 1.0193906 1.0083102
1200 0.35727572 0 0.05153538 1.0083102 1.0083102
1300 0.34322607 0 0.036115722 1.0083102 1.0083102
1400 0.34007557 0 0.025378602 1.0083102 1.0193906
1500 0.39242551 0 0.033002212 1.0083102 1.0193906
1600 0.35679049 0 0.010101576 1.0083102 1.0193906
1700 0.31293001 0 -0.013791036 1.0193906 1.0193906
1800 0.34767962 0 -0.0065490806 1.0193906 1.0193906
1900 0.34721592 0 -0.010055082 1.0193906 1.0083102
2000 0.34074949 0 -0.020822697 1.0083102 1.0083102
2100 0.37195615 0 -0.024943134 1.0193906 1.0083102
2200 0.35367164 0 -0.047369336 1.0193906 1.0083102
2300 0.32088735 0 -0.069724381 1.0083102 1.0083102
2400 0.34291945 0 -0.065470223 1.0193906 1.0083102
2500 0.35204641 0 -0.062631879 1.0083102 1.0083102
2600 0.32762755 0 -0.075128824 1.0083102 1.0083102
2700 0.32042617 0 -0.086259498 1.0193906 1.0083102
2800 0.32747171 0 -0.094775765 1.0083102 1.0083102
2900 0.33544664 0 -0.10376048 1.0193906 1.0083102
3000 0.34015845 0 -0.1112134 1.0193906 1.0083102
3100 0.34425802 0 -0.11413914 1.0083102 1.0193906
3200 0.34158654 0 -0.1164643 1.0083102 1.0083102
3300 0.32525955 0 -0.12206636 1.0083102 1.0193906
3400 0.32183965 0 -0.12186353 1.0193906 1.0083102
3500 0.3323435 0 -0.11597815 1.0083102 1.0083102
3600 0.34124638 0 -0.11177335 1.0193906 1.0193906
3700 0.3404339 0 -0.11235575 1.0083102 1.0193906
3800 0.32736123 0 -0.11610108 1.0083102 1.0193906
3900 0.32897993 0 -0.11138151 1.0193906 1.0083102
4000 0.35111095 0 -0.096171644 1.0193906 1.0193906
4100 0.34682622 0 -0.087507472 1.0193906 1.0193906
4200 0.3307829 0 -0.079759555 1.0193906 1.0083102
4300 0.35057085 0 -0.055194355 1.0193906 1.0083102
4400 0.36389071 0 -0.02963313 1.0193906 1.0193906
4500 0.35694456 0 -0.013842583 1.0193906 1.0193906
4600 0.3472078 0 -0.0048118723 1.0083102 1.0083102
4700 0.31734514 0 -0.0032417081 1.0083102 1.0083102
4800 0.32419237 0 0.01409306 1.0083102 1.0193906
4900 0.36939799 0 0.045351789 1.0193906 1.0193906
5000 0.36998276 0 0.056830437 1.0083102 1.0083102
5100 0.33969031 0 0.051833536 1.0083102 1.0083102
5200 0.33910288 0 0.055544085 1.0083102 1.0083102
5300 0.34641009 0 0.0651487 1.0083102 1.0083102
5400 0.34469325 0 0.074538093 1.0083102 1.0083102
5500 0.34582041 0 0.084940845 1.0193906 1.0083102
5600 0.33471774 0 0.090102411 1.0083102 1.0193906
5700 0.32667873 0 0.09528948 1.0083102 1.0193906
5800 0.33762496 0 0.10545364 1.0083102 1.0083102
5900 0.33285742 0 0.10816506 1.0083102 1.0083102
6000 0.31920877 0 0.10547467 1.0083102 1.0193906
6100 0.31933081 0 0.10610684 1.0083102 1.0193906
6200 0.3152523 0 0.10651599 1.0193906 1.0083102
6300 0.32548074 0 0.11405234 1.0083102 1.0193906
6400 0.33851595 0 0.12389967 1.0193906 1.0193906
6500 0.32957825 0 0.12493331 1.0083102 1.0083102
6600 0.32319786 0 0.12404318 1.0083102 1.0083102
6700 0.3223738 0 0.12418108 1.0304709 1.0304709
6800 0.32390959 0 0.12576314 1.0193906 1.0083102
6900 0.34414413 0 0.1318456 1.0193906 1.0193906
7000 0.34508922 0 0.12669741 1.0083102 1.0083102
7100 0.31655025 0 0.10869109 1.0083102 1.0193906
7200 0.31997193 0 0.10305508 1.0083102 1.0193906
7300 0.33199085 0 0.10377052 1.0083102 1.0083102
7400 0.32146221 0 0.097589803 1.0193906 1.0193906
7500 0.33416843 0 0.096202638 1.0083102 1.0193906
7600 0.35297124 0 0.092441999 1.0193906 1.0083102
7700 0.34494663 0 0.075206332 1.0083102 1.0193906
7800 0.34010702 0 0.056336074 1.0193906 1.0083102
7900 0.343424 0 0.040946914 1.0193906 1.0193906
8000 0.33772245 0 0.025817271 1.0083102 1.0083102
8100 0.34463909 0 0.017237548 1.0193906 1.0304709
8200 0.36052034 0 0.010393623 1.0083102 1.0083102
8300 0.36083091 0 -0.0053933186 1.0083102 1.0083102
8400 0.35378067 0 -0.02600248 1.0083102 1.0083102
8500 0.35133887 0 -0.044211483 1.0083102 1.0083102
8600 0.34559937 0 -0.060861345 1.0083102 1.0083102
8700 0.33724119 0 -0.075776058 1.0083102 1.0193906
8800 0.33337192 0 -0.087098937 1.0193906 1.0193906
8900 0.33533081 0 -0.094631485 1.0193906 1.0304709
9000 0.34994303 0 -0.096758052 1.0193906 1.0083102
9100 0.34448227 0 -0.10330192 1.0193906 1.0193906
9200 0.32675792 0 -0.11000278 1.0193906 1.0193906
9300 0.33814013 0 -0.10358181 1.0083102 1.0193906
9400 0.34457419 0 -0.096896951 1.0083102 1.0083102
9500 0.33834959 0 -0.09547729 1.0083102 1.0083102
9600 0.33204582 0 -0.097694622 1.0193906 1.0083102
9700 0.31152805 0 -0.10637377 1.0193906 1.0083102
9800 0.31637311 0 -0.1053323 1.0083102 1.0083102
9900 0.33416162 0 -0.097857158 1.0083102 1.0083102
10000 0.33731767 0 -0.094656227 1.0083102 1.0083102
10100 0.34565093 0 -0.090199556 1.0193906 1.0193906
10200 0.34549074 0 -0.088914471 1.0193906 1.0083102
10300 0.33545625 0 -0.09066219 1.0083102 1.0083102
10400 0.33649703 0 -0.086437886 1.0083102 1.0083102
10500 0.34549848 0 -0.0767365 1.0193906 1.0193906
10600 0.34222917 0 -0.069368792 1.0083102 1.0083102
10700 0.34262469 0 -0.060550996 1.0193906 1.0083102
10800 0.34859129 0 -0.050692625 1.0193906 1.0193906
10900 0.34850448 0 -0.043627505 1.0193906 1.0193906
11000 0.34887257 0 -0.036859125 1.0193906 1.0193906
11100 0.34171718 0 -0.032690742 1.0193906 1.0083102
11200 0.329808 0 -0.02793377 1.0083102 1.0083102
11300 0.34490203 0 -0.010278222 1.0083102 1.0083102
11400 0.36226391 0 0.010141624 1.0193906 1.0193906
11500 0.35392138 0 0.021188939 1.0193906 1.0193906
11600 0.34378732 0 0.031423313 1.0304709 1.0193906
11700 0.33606385 0 0.043944374 1.0193906 1.0193906
11800 0.33212482 0 0.058629338 1.0193906 1.0193906
11900 0.34547313 0 0.078112959 1.0193906 1.0083102
12000 0.34840957 0 0.092356502 1.0083102 1.0083102
12100 0.34146853 0 0.10236492 1.0193906 1.0193906
12200 0.34591494 0 0.11620659 1.0193906 1.0083102
12300 0.33290894 0 0.12437245 1.0083102 1.0193906
12400 0.32423652 0 0.13191976 1.0193906 1.0193906
12500 0.33031748 0 0.13999363 1.0193906 1.0193906
12600 0.31927087 0 0.13776242 1.0083102 1.0193906
12700 0.30865965 0 0.13340787 1.0193906 1.0083102
12800 0.32542691 0 0.13690449 1.0083102 1.0083102
12900 0.32453244 0 0.13376127 1.0083102 1.0083102
13000 0.30974678 0 0.12749869 1.0083102 1.0083102
13100 0.32402285 0 0.13240572 1.0083102 1.0193906
13200 0.32896987 0 0.13257567 1.0193906 1.0083102
13300 0.32939197 0 0.12690791 1.0083102 1.0083102
13400 0.33966453 0 0.12036916 1.0083102 1.0083102
13500 0.33012942 0 0.10496127 1.0083102 1.0304709
13600 0.32363377 0 0.091763332 1.0304709 1.0304709
13700 0.33427955 0 0.087928243 1.0193906 1.0193906
13800 0.33457885 0 0.08191828 1.0083102 1.0083102
13900 0.33819924 0 0.074487337 1.0193906 1.0083102
14000 0.34611002 0 0.066256529 1.0083102 1.0083102
14100 0.33224254 0 0.052608223 1.0083102 1.0083102
14200 0.33796934 0 0.049677792 1.0083102 1.0083102
14300 0.36216731 0 0.055173039 1.0083102 1.0083102
14400 0.35140789 0 0.047322221 1.0193906 1.0193906
14500 0.34425046 0 0.036527245 1.0193906 1.0193906
14600 0.3604575 0 0.0294772 1.0083102 1.0083102
14700 0.3433878 0 0.0096774422 1.0083102 1.0083102
14800 0.3287069 0 -0.0079768782 1.0083102 1.0083102
14900 0.34978607 0 -0.01178453 1.0083102 1.0083102
15000 0.34749548 0 -0.023685074 1.0193906 1.0193906
15100 0.33474304 0 -0.040569945 1.0083102 1.0083102
15200 0.35036594 0 -0.048341599 1.0083102 1.0083102
15300 0.35686042 0 -0.058664905 1.0193906 1.0083102
15400 0.34041567 0 -0.074858327 1.0083102 1.0083102
15500 0.33397773 0 -0.083782088 1.0083102 1.0083102
15600 0.3420119 0 -0.084635487 1.0193906 1.0083102
15700 0.345487 0 -0.088137628 1.0193906 1.0083102
15800 0.33494392 0 -0.10083064 1.0083102 1.0083102
15900 0.32675175 0 -0.11620387 1.0083102 1.0083102
16000 0.33011636 0 -0.12713401 1.0083102 1.0304709
16100 0.32443118 0 -0.13685913 1.0193906 1.0193906
16200 0.31608392 0 -0.14164152 1.0193906 1.0193906
16300 0.33293965 0 -0.13335387 1.0083102 1.0083102
16400 0.34462807 0 -0.12471686 1.0083102 1.0083102
16500 0.33528082 0 -0.12211554 1.0083102 1.0083102
16600 0.34250121 0 -0.11228169 1.0083102 1.0083102
16700 0.35342336 0 -0.099226948 1.0083102 1.0083102
16800 0.33730938 0 -0.093581966 1.0083102 1.0193906
16900 0.3275761 0 -0.085163356 1.0083102 1.0083102
17000 0.33624873 0 -0.070896594 1.0193906 1.0083102
17100 0.34339177 0 -0.057731935 1.0083102 1.0083102
17200 0.34874414 0 -0.046575228 1.0083102 1.0083102
17300 0.33950911 0 -0.041862179 1.0083102 1.0083102
17400 0.33100286 0 -0.036618199 1.0193906 1.0083102
17500 0.34238095 0 -0.021681436 1.0193906 1.0083102
17600 0.35476614 0 -0.0032568304 1.0083102 1.0083102
17700 0.35452053 0 0.011863966 1.0083102 1.0304709
17800 0.35423934 0 0.024753043 1.0193906 1.0193906
17900 0.35001044 0 0.031647802 1.0193906 1.0193906
18000 0.32867773 0 0.030261102 1.0083102 1.0083102
18100 0.32730114 0 0.037627319 1.0083102 1.0083102
18200 0.35786038 0 0.057653258 1.0083102 1.0083102
18300 0.35598175 0 0.065533711 1.0083102 1.0304709
18400 0.33913202 0 0.066186406 1.0083102 1.0083102
18500 0.34449656 0 0.074575322 1.0083102 1.0193906
18600 0.34792041 0 0.083818651 1.0304709 1.0193906
18700 0.33910599 0 0.089751723 1.0193906 1.0193906
18800 0.33627789 0 0.097491916 1.0304709 1.0083102
18900 0.32937699 0 0.10350872 1.0193906 1.0083102
19000 0.30908702 0 0.10610099 1.0083102 1.0083102
19100 0.31033435 0 0.1168178 1.0083102 1.0083102
19200 0.32011336 0 0.12898885 1.0083102 1.0083102
19300 0.31851339 0 0.13398981 1.0083102 1.0083102
19400 0.33289985 0 0.1401039 1.0083102 1.0083102
19500 0.3387096 0 0.13971063 1.0083102 1.0083102
19600 0.31475734 0 0.12963499 1.0083102 1.0193906
19700 0.31971554 0 0.13189606 1.0083102 1.0193906
19800 0.33096999 0 0.13636987 1.0193906 1.0083102
19900 0.31601688 0 0.12889803 1.0083102 1.0083102
20000 0.32916469 0 0.12683491 1.0083102 1.0304709
20100 0.34355734 0 0.12251501 1.0083102 1.0083102
20200 0.33029721 0 0.10833335 1.0193906 1.0083102
20300 0.34079176 0 0.10305862 1.0083102 1.0083102
20400 0.35196716 0 0.098386494 1.0083102 1.0083102
20500 0.32687648 0 0.081202778 1.0193906 1.0193906
20600 0.33371658 0 0.074287923 1.0083102 1.0193906
20700 0.36625228 0 0.073768436 1.0083102 1.0083102
20800 0.35824217 0 0.054876358 1.0193906 1.0193906
20900 0.34861601 0 0.031603534 1.0083102 1.0083102
21000 0.35396698 0 0.013464537 1.0083102 1.0083102
21100 0.33592449 0 -0.0096173026 1.0083102 1.0083102
21200 0.327063 0 -0.025970252 1.0083102 1.0083102
21300 0.34418745 0 -0.030446162 1.0083102 1.0083102
21400 0.34181459 0 -0.039942616 1.0083102 1.0083102
21500 0.3315724 0 -0.05089285 1.0083102 1.0083102
21600 0.35674681 0 -0.047926263 1.0083102 1.0083102
21700 0.37320044 0 -0.047190592 1.0083102 1.0083102
21800 0.34626293 0 -0.063211549 1.0193906 1.0083102
21900 0.32941853 0 -0.078034339 1.0083102 1.0083102
22000 0.34102577 0 -0.083179211 1.0083102 1.0083102
22100 0.33614888 0 -0.091647522 1.0083102 1.0083102
22200 0.3339762 0 -0.09744915 1.0083102 1.0083102
22300 0.33867021 0 -0.10026932 1.0083102 1.0083102
22400 0.31974078 0 -0.10896583 1.0083102 1.0193906
22500 0.3261442 0 -0.10644809 1.0193906 1.0083102
22600 0.35128159 0 -0.097711062 1.0083102 1.0083102
22700 0.33133845 0 -0.10656571 1.0083102 1.0083102
22800 0.31730555 0 -0.11420891 1.0193906 1.0083102
22900 0.34720941 0 -0.10586647 1.0083102 1.0083102
23000 0.34418922 0 -0.10745826 1.0083102 1.0083102
23100 0.32342851 0 -0.11384766 1.0083102 1.0083102
23200 0.3408144 0 -0.10631064 1.0083102 1.0083102
23300 0.33006722 0 -0.1070084 1.0083102 1.0083102
23400 0.31578528 0 -0.10711608 1.0193906 1.0193906
23500 0.34908788 0 -0.088441889 1.0193906 1.0083102
23600 0.35801835 0 -0.075953983 1.0083102 1.0083102
23700 0.33573037 0 -0.072357745 1.0083102 1.0193906
23800 0.34435835 0 -0.055470682 1.0193906 1.0083102
23900 0.35307683 0 -0.036076205 1.0193906 1.0193906
24000 0.35184599 0 -0.020939815 1.0083102 1.0083102
24100 0.35687079 0 -0.0063601457 1.0083102 1.0083102
24200 0.33612385 0 -0.0014613923 1.0083102 1.0083102
24300 0.32234106 0 0.006750452 1.0083102 1.0083102
24400 0.34852008 0 0.029170079 1.0083102 1.0083102
24500 0.35224811 0 0.043783151 1.0083102 1.0083102
24600 0.34160459 0 0.05294313 1.0083102 1.0083102
24700 0.35616752 0 0.069291509 1.0083102 1.0083102
24800 0.34984726 0 0.076650029 1.0193906 1.0193906
24900 0.33337969 0 0.080083735 1.0193906 1.0083102
25000 0.34846751 0 0.095559187 1.0083102 1.0083102
25100 0.34495541 0 0.10558042 1.0193906 1.0083102
25200 0.32630088 0 0.10897783 1.0193906 1.0083102
25300 0.33651146 0 0.11888202 1.0083102 1.0083102
25400 0.32194445 0 0.11826793 1.0083102 1.0083102
25500 0.30295352 0 0.11641357 1.0083102 1.0083102
25600 0.33485387 0 0.13204258 1.0083102 1.0083102
25700 0.34407287 0 0.13738986 1.0083102 1.0083102
25800 0.32421817 0 0.12822703 1.0083102 1.0083102
25900 0.32463356 0 0.12403448 1.0193906 1.0193906
26000 0.32431468 0 0.12087994 1.0193906 1.0083102
26100 0.31886825 0 0.11741621 1.0193906 1.0083102
26200 0.32607823 0 0.1180517 1.0083102 1.0083102
26300 0.32511255 0 0.11479741 1.0304709 1.0193906
26400 0.32336124 0 0.11055002 1.0083102 1.0083102
26500 0.33026321 0 0.10934888 1.0083102 1.0083102
26600 0.32604491 0 0.10480442 1.0083102 1.0193906
26700 0.33764955 0 0.10458959 1.0083102 1.0083102
26800 0.35202544 0 0.10295075 1.0193906 1.0193906
26900 0.33382028 0 0.088148483 1.0193906 1.0193906
27000 0.33252808 0 0.078275659 1.0193906 1.0193906
27100 0.35433636 0 0.076729989 1.0304709 1.0193906
27200 0.34824881 0 0.065720375 1.0193906 1.0083102
27300 0.33525644 0 0.051611147 1.0083102 1.0193906
27400 0.34685762 0 0.045597284 1.0193906 1.0083102
27500 0.35181712 0 0.037076034 1.0083102 1.0083102
27600 0.34541685 0 0.022287411 1.0083102 1.0083102
27700 0.34559823 0 0.0056480168 1.0083102 1.0304709
27800 0.33646375 0 -0.015571541 1.0193906 1.0193906
27900 0.33681932 0 -0.031777883 1.0193906 1.0193906
28000 0.35093514 0 -0.041519343 1.0083102 1.0083102
28100 0.34345697 0 -0.057623438 1.0083102 1.0083102
28200 0.33655073 0 -0.072228985 1.0083102 1.0083102
28300 0.34428448 0 -0.080015243 1.0083102 1.0193906
28400 0.34089922 0 -0.089955339 1.0193906 1.0193906
28500 0.34522966 0 -0.096529413 1.0304709 1.0083102
28600 0.34713819 0 -0.10221712 1.0304709 1.0304709
28700 0.33692049 0 -0.10868625 1.0193906 1.0083102
28800 0.34522852 0 -0.10679446 1.0083102 1.0193906
28900 0.33956477 0 -0.1105454 1.0304709 1.0083102
29000 0.30989301 0 -0.12332622 1.0193906 1.0193906
29100 0.32373738 0 -0.11985261 1.0083102 1.0083102
29200 0.35156812 0 -0.10956099 1.0083102 1.0193906
29300 0.33938829 0 -0.11259535 1.0083102 1.0193906
29400 0.32401178 0 -0.11664978 1.0193906 1.0193906
29500 0.32320492 0 -0.11336533 1.0193906 1.0193906
29600 0.32928877 0 -0.10404547 1.0193906 1.0193906
29700 0.3436911 0 -0.089845529 1.0193906 1.0193906
29800 0.34194019 0 -0.081660797 1.0193906 1.0193906
29900 0.32909826 0 -0.07807778 1.0083102 1.0083102
30000 0.34092826 0 -0.06626489 1.0083102 1.0083102
30100 0.34763086 0 -0.055589635 1.0083102 1.0083102
30200 0.34479984 0 -0.047402672 1.0193906 1.0193906
30300 0.34783224 0 -0.036371931 1.0083102 1.0083102
30400 0.34525176 0 -0.027246663 1.0193906 1.0083102
30500 0.35266364 0 -0.016275033 1.0083102 1.0193906
30600 0.35792479 0 -0.007158119 1.0193906 1.0193906
30700 0.33607567 0 -0.0064391529 1.0083102 1.0083102
30800 0.34311607 0 0.005382948 1.0304709 1.0083102
30900 0.37218574 0 0.025004945 1.0083102 1.0083102
31000 0.35196541 0 0.027902483 1.0083102 1.0083102
31100 0.33533693 0 0.032349025 1.0083102 1.0083102
31200 0.34382193 0 0.046631454 1.0193906 1.0083102
31300 0.32886237 0 0.05405956 1.0083102 1.0083102
31400 0.32738754 0 0.066295734 1.0083102 1.0083102
31500 0.35367575 0 0.087140904 1.0083102 1.0083102
31600 0.33756811 0 0.092135887 1.0083102 1.0083102
31700 0.31701631 0 0.094576339 1.0083102 1.0083102
31800 0.34217612 0 0.11195071 1.0083102 1.0083102
31900 0.33725187 0 0.11924087 1.0193906 1.0083102
32000 0.30966055 0 0.1199329 1.0193906 1.0083102
32100 0.32771084 0 0.13627552 1.0083102 1.0083102
32200 0.3400914 0 0.14816015 1.0083102 1.0193906
32300 0.32210513 0 0.14569378 1.0193906 1.0083102
32400 0.32096229 0 0.14515284 1.0083102 1.0193906
32500 0.31781969 0 0.14124479 1.0193906 1.0193906
32600 0.3146986 0 0.13616644 1.0193906 1.0193906
32700 0.33526021 0 0.13913538 1.0083102 1.0083102
32800 0.33561156 0 0.13481353 1.0083102 1.0083102
32900 0.31418235 0 0.12161202 1.0193906 1.0193906
33000 0.31952054 0 0.11558871 1.0304709 1.0083102
33100 0.33437451 0 0.11011602 1.0193906 1.0193906
33200 0.33381704 0 0.096535424 1.0193906 1.0304709
33300 0.33786259 0 0.08382113 1.0304709 1.0304709
33400 0.34590937 0 0.073879824 1.0083102 1.0083102
33500 0.33844204 0 0.060854835 1.0193906 1.0193906
33600 0.33845544 0 0.052237152 1.0083102 1.0193906
33700 0.35419837 0 0.048922784 1.0083102 1.0083102
33800 0.3485977 0 0.036886422 1.0083102 1.0083102
33900 0.33816081 0 0.021599335 1.0083102 1.0083102
34000 0.34241389 0 0.010436074 1.0083102 1.0083102
34100 0.33934235 0 -0.002581075 1.0193906 1.0083102
34200 0.34579204 0 -0.011373729 1.0083102 1.0193906
34300 0.35778336 0 -0.018118327 1.0193906 1.0193906
34400 0.35522938 0 -0.030427967 1.0083102 1.0193906
34500 0.34820709 0 -0.042562699 1.0083102 1.0083102
34600 0.35026547 0 -0.047488326 1.0083102 1.0083102
34700 0.35221351 0 -0.050832178 1.0083102 1.0083102
34800 0.33043515 0 -0.062718859 1.0083102 1.0083102
34900 0.32750488 0 -0.068765033 1.0083102 1.0083102
35000 0.35323787 0 -0.067326627 1.0083102 1.0083102
35100 0.34732304 0 -0.080326407 1.0193906 1.0083102
35200 0.3248439 0 -0.099312427 1.0083102 1.0083102
35300 0.32854244 0 -0.10509437 1.0083102 1.0083102
35400 0.33511384 0 -0.10605662 1.0083102 1.0083102
35500 0.33532722 0 -0.10993967 1.0083102 1.0083102
35600 0.33523312 0 -0.11653983 1.0083102 1.0193906
35700 0.32405906 0 -0.12564005 1.0193906 1.0193906
35800 0.32914902 0 -0.12476137 1.0193906 1.0083102
35900 0.34093492 0 -0.11716996 1.0083102 1.0083102
36000 0.33557882 0 -0.11216382 1.0083102 1.0083102
36100 0.3342841 0 -0.10445781 1.0193906 1.0193906
36200 0.33557348 0 -0.0983036 1.0193906 1.0083102
36300 0.33052024 0 -0.097594107 1.0304709 1.0083102
36400 0.34570912 0 -0.089010349 1.0083102 1.0193906
36500 0.35735704 0 -0.078483059 1.0193906 1.0193906
36600 0.33199022 0 -0.079452064 1.0193906 1.0083102
36700 0.3191692 0 -0.074378584 1.0083102 1.0083102
36800 0.34473865 0 -0.052467819 1.0083102 1.0083102
36900 0.35012922 0 -0.034841373 1.0193906 1.0083102
37000 0.34543508 0 -0.019956141 1.0083102 1.0083102
37100 0.36637971 0 0.0034123108 1.0083102 1.0083102
37200 0.36008557 0 0.016667331 1.0304709 1.0304709
37300 0.34027931 0 0.024177377 1.0304709 1.0083102
37400 0.35097853 0 0.041160628 1.0083102 1.0083102
37500 0.35024671 0 0.052433671 1.0083102 1.0083102
37600 0.33483801 0 0.05655083 1.0193906 1.0193906
37700 0.3402098 0 0.067222448 1.0193906 1.0193906
37800 0.33859985 0 0.075720813 1.0193906 1.0193906
37900 0.32323549 0 0.079678841 1.0193906 1.0083102
38000 0.33701532 0 0.092666162 1.0193906 1.0193906
38100 0.3424632 0 0.10094611 1.0083102 1.0193906
38200 0.32167421 0 0.099350179 1.0193906 1.0193906
38300 0.32540911 0 0.10664752 1.0083102 1.0193906
38400 0.33574781 0 0.11614552 1.0193906 1.0083102
38500 0.33125908 0 0.11940265 1.0193906 1.0083102
38600 0.33885801 0 0.12616083 1.0083102 1.0083102
38700 0.33813506 0 0.1298943 1.0083102 1.0193906
38800 0.31888318 0 0.1260135 1.0083102 1.0193906
38900 0.31006429 0 0.12450345 1.0193906 1.0083102
39000 0.31407783 0 0.12693078 1.0193906 1.0193906
39100 0.33078021 0 0.13111094 1.0304709 1.0193906
39200 0.34311375 0 0.12937945 1.0083102 1.0193906
39300 0.33594172 0 0.11839992 1.0083102 1.0083102
39400 0.32763204 0 0.10898509 1.0304709 1.0193906
39500 0.33114946 0 0.10782558 1.0083102 1.0083102
39600 0.32905328 0 0.10631627 1.0083102 1.0193906
39700 0.32416114 0 0.10142386 1.0193906 1.0083102
39800 0.32709132 0 0.096046083 1.0083102 1.0193906
39900 0.32910896 0 0.087876394 1.0083102 1.0083102
40000 0.33462908 0 0.07810396 1.0193906 1.0193906
Loop time of 0.489746 on 4 procs for 40000 steps with 361 atoms
Performance: 7056721.575 tau/day, 81675.018 timesteps/s, 29.485 Matom-step/s
91.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.007919 | 0.0093951 | 0.010867 | 1.2 | 1.92
Bond | 0.070755 | 0.085453 | 0.096684 | 3.3 | 17.45
Neigh | 0.030371 | 0.030384 | 0.030393 | 0.0 | 6.20
Comm | 0.16386 | 0.17988 | 0.19412 | 2.6 | 36.73
Output | 0.0037789 | 0.0040841 | 0.0048475 | 0.7 | 0.83
Modify | 0.090035 | 0.098104 | 0.1037 | 1.8 | 20.03
Other | | 0.08244 | | | 16.83
Nlocal: 90.25 ave 92 max 88 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 60 ave 61 max 58 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 31.024931
Neighbor list builds = 800
Dangerous builds = 0
Total wall time: 0:00:00

234
examples/balance/log.3Nov23.balance.clock.dynamic.g++.2 Normal file
View File

@ -0,0 +1,234 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.001 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.559 | 4.75 | 4.941 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
Loop time of 1.71386 on 2 procs for 500 steps with 4000 atoms
Performance: 126031.028 tau/day, 291.738 timesteps/s, 1.167 Matom-step/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1357 | 1.1768 | 1.2179 | 3.8 | 68.66
Neigh | 0.40728 | 0.42812 | 0.44897 | 3.2 | 24.98
Comm | 0.075827 | 0.095749 | 0.11567 | 6.4 | 5.59
Output | 0.0002928 | 0.0003251 | 0.00035739 | 0.0 | 0.02
Modify | 0.0076492 | 0.0080146 | 0.00838 | 0.4 | 0.47
Other | | 0.004868 | | | 0.28
Nlocal: 2000 ave 2149 max 1851 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10459.5 ave 10836 max 10083 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298070 ave 307801 max 288338 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596139
Ave neighs/atom = 149.03475
Neighbor list builds = 51
Dangerous builds = 0
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.945 | 4.949 | 4.953 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
Loop time of 1.67419 on 2 procs for 500 steps with 4000 atoms
Performance: 129017.323 tau/day, 298.651 timesteps/s, 1.195 Matom-step/s
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1354 | 1.1632 | 1.191 | 2.6 | 69.48
Neigh | 0.39683 | 0.42125 | 0.44567 | 3.8 | 25.16
Comm | 0.073552 | 0.076486 | 0.07942 | 1.1 | 4.57
Output | 0.00028662 | 0.00031609 | 0.00034556 | 0.0 | 0.02
Modify | 0.0075098 | 0.0079796 | 0.0084494 | 0.5 | 0.48
Other | | 0.004917 | | | 0.29
Nlocal: 2000 ave 2127 max 1873 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10413.5 ave 10886 max 9941 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 300836 ave 314685 max 286986 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 601671
Ave neighs/atom = 150.41775
Neighbor list builds = 51
Dangerous builds = 0
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.953 | 5.144 | 5.336 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
Loop time of 2.16148 on 2 procs for 500 steps with 4000 atoms
Performance: 99931.753 tau/day, 231.324 timesteps/s, 925.294 katom-step/s
98.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.79846 | 1.1842 | 1.5699 | 35.4 | 54.79
Neigh | 0.37845 | 0.43466 | 0.49086 | 8.5 | 20.11
Comm | 0.08708 | 0.52938 | 0.97168 | 60.8 | 24.49
Output | 0.0002959 | 0.0003233 | 0.00035071 | 0.0 | 0.01
Modify | 0.0072841 | 0.0078691 | 0.0084541 | 0.7 | 0.36
Other | | 0.005076 | | | 0.23
Nlocal: 2000 ave 2298 max 1702 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10344.5 ave 11222 max 9467 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 302958 ave 343175 max 262742 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 605917
Ave neighs/atom = 151.47925
Neighbor list builds = 51
Dangerous builds = 0
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.957 | 5.337 | 5.718 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
1550 0.53713589 -6.2504069 0 -5.4449045 -1.764709 4738.2137
1600 0.54679555 -6.2646482 0 -5.44466 -1.8115779 4738.2137
1650 0.53806567 -6.2519005 0 -5.4450038 -1.7409139 4738.2137
1700 0.53479485 -6.2468959 0 -5.4449041 -1.7162328 4738.2137
1750 0.53714536 -6.2506572 0 -5.4451406 -1.7340479 4738.2137
1800 0.52749909 -6.2358678 0 -5.444817 -1.6875013 4738.2137
1850 0.54585987 -6.2629365 0 -5.4443514 -1.7758757 4738.2137
1900 0.53010207 -6.2387514 0 -5.4437971 -1.6381553 4738.2137
1950 0.54287913 -6.2582893 0 -5.4441742 -1.7367856 4738.2137
2000 0.52766186 -6.2348576 0 -5.4435627 -1.5589066 4738.2137
Loop time of 2.18418 on 2 procs for 500 steps with 4000 atoms
Performance: 98892.757 tau/day, 228.918 timesteps/s, 915.674 katom-step/s
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87818 | 1.1728 | 1.4674 | 27.2 | 53.69
Neigh | 0.38155 | 0.42626 | 0.47096 | 6.8 | 19.52
Comm | 0.23213 | 0.57157 | 0.91101 | 44.9 | 26.17
Output | 0.00030069 | 0.00032376 | 0.00034684 | 0.0 | 0.01
Modify | 0.0076232 | 0.0079287 | 0.0082342 | 0.3 | 0.36
Other | | 0.005329 | | | 0.24
Nlocal: 2000 ave 2300 max 1700 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10324 ave 11204 max 9444 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 303986 ave 345018 max 262954 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 607972
Ave neighs/atom = 151.993
Neighbor list builds = 51
Dangerous builds = 0
Total wall time: 0:00:07

234
examples/balance/log.3Nov23.balance.clock.dynamic.g++.4 Normal file
View File

@ -0,0 +1,234 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.000 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
fix p all property/atom d_WEIGHT
compute p all property/atom d_WEIGHT
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
variable maximb equal f_0[1]
variable iter equal f_0[2]
variable prev equal f_0[3]
variable final equal f_0
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
fix 1 all nve
#dump id all atom 50 dump.melt
#dump id all custom 50 dump.lammpstrj id type x y z c_p
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.692 | 4.073 | 4.455 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
Loop time of 1.25319 on 4 procs for 500 steps with 4000 atoms
Performance: 172359.605 tau/day, 398.981 timesteps/s, 1.596 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34653 | 0.64351 | 0.91663 | 28.5 | 51.35
Neigh | 0.21165 | 0.23194 | 0.25847 | 4.2 | 18.51
Comm | 0.11416 | 0.36777 | 0.63774 | 34.3 | 29.35
Output | 0.00027595 | 0.00030885 | 0.00034514 | 0.0 | 0.02
Modify | 0.0044031 | 0.005039 | 0.0057452 | 0.8 | 0.40
Other | | 0.004619 | | | 0.37
Nlocal: 1000 ave 1250 max 767 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 8594.25 ave 9068 max 8005 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 149308 ave 207861 max 76482 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 597231
Ave neighs/atom = 149.30775
Neighbor list builds = 50
Dangerous builds = 0
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.082 | 4.271 | 4.459 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
Loop time of 1.21278 on 4 procs for 500 steps with 4000 atoms
Performance: 178103.015 tau/day, 412.275 timesteps/s, 1.649 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34456 | 0.63182 | 0.88173 | 27.7 | 52.10
Neigh | 0.21634 | 0.24141 | 0.2701 | 4.5 | 19.91
Comm | 0.10554 | 0.32979 | 0.58781 | 34.4 | 27.19
Output | 0.00027303 | 0.00029988 | 0.00033111 | 0.0 | 0.02
Modify | 0.0042091 | 0.0049092 | 0.0056581 | 0.9 | 0.40
Other | | 0.004556 | | | 0.38
Nlocal: 1000 ave 1448 max 649 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8681.25 ave 9365 max 7993 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 150170 ave 187956 max 103584 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 600678
Ave neighs/atom = 150.1695
Neighbor list builds = 53
Dangerous builds = 0
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.082 | 4.271 | 4.459 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
Loop time of 1.11039 on 4 procs for 500 steps with 4000 atoms
Performance: 194526.606 tau/day, 450.293 timesteps/s, 1.801 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42944 | 0.62743 | 0.76349 | 18.0 | 56.51
Neigh | 0.1745 | 0.22812 | 0.29389 | 10.7 | 20.54
Comm | 0.15606 | 0.24538 | 0.37672 | 18.4 | 22.10
Output | 0.00028277 | 0.00030572 | 0.00033535 | 0.0 | 0.03
Modify | 0.0036942 | 0.0046797 | 0.0057281 | 1.4 | 0.42
Other | | 0.00448 | | | 0.40
Nlocal: 1000 ave 1289 max 764 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 8639.25 ave 9512 max 8090 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 150494 ave 209619 max 82578 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 601974
Ave neighs/atom = 150.4935
Neighbor list builds = 51
Dangerous builds = 0
run 500
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.082 | 4.272 | 4.459 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137
1550 0.55327014 -6.2750125 0 -5.4453148 -1.9506585 4738.2137
1600 0.54418991 -6.261262 0 -5.4451812 -1.8559426 4738.2137
1650 0.54710046 -6.266198 0 -5.4457525 -1.888284 4738.2137
1700 0.53665701 -6.2504958 0 -5.4457115 -1.8067998 4738.2137
1750 0.5486465 -6.2681117 0 -5.4453477 -1.8662621 4738.2137
1800 0.54476258 -6.2615089 0 -5.4445693 -1.8352878 4738.2137
1850 0.541431 -6.255553 0 -5.4436095 -1.8005746 4738.2137
1900 0.53992581 -6.2541254 0 -5.4444392 -1.7768566 4738.2137
1950 0.54667259 -6.264121 0 -5.4443171 -1.7947882 4738.2137
2000 0.54556851 -6.2625542 0 -5.444406 -1.8072484 4738.2137
Loop time of 1.14143 on 4 procs for 500 steps with 4000 atoms
Performance: 189237.081 tau/day, 438.049 timesteps/s, 1.752 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42201 | 0.63026 | 0.77752 | 18.6 | 55.22
Neigh | 0.18905 | 0.2462 | 0.31411 | 10.7 | 21.57
Comm | 0.15495 | 0.25528 | 0.39485 | 18.8 | 22.36
Output | 0.00027662 | 0.00030437 | 0.00033645 | 0.0 | 0.03
Modify | 0.0037058 | 0.0046791 | 0.0056663 | 1.4 | 0.41
Other | | 0.004707 | | | 0.41
Nlocal: 1000 ave 1309 max 769 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 8636.75 ave 9520 max 8192 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 151656 ave 211059 max 85091 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 606625
Ave neighs/atom = 151.65625
Neighbor list builds = 56
Dangerous builds = 0
Total wall time: 0:00:04

207
examples/balance/log.3Nov23.balance.clock.static.g++.2 Normal file
View File

@ -0,0 +1,207 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.001 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
rebalancing time: 0.001 seconds
iteration count = 1
time weight factor: 1
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.294 | 4.485 | 4.675 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162
200 0.536665 -6.2530113 0 -5.448215 -1.933468
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
Loop time of 0.952998 on 2 procs for 250 steps with 4000 atoms
Performance: 113326.532 tau/day, 262.330 timesteps/s, 1.049 Matom-step/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4745 | 0.59305 | 0.7116 | 15.4 | 62.23
Neigh | 0.19129 | 0.20528 | 0.21927 | 3.1 | 21.54
Comm | 0.016122 | 0.14873 | 0.28134 | 34.4 | 15.61
Output | 0.00015798 | 0.00017139 | 0.0001848 | 0.0 | 0.02
Modify | 0.0032698 | 0.0033573 | 0.0034449 | 0.2 | 0.35
Other | | 0.00241 | | | 0.25
Nlocal: 2000 ave 2051 max 1949 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10443 ave 10506 max 10380 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 363449 max 233215 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 24
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 3
time weight factor: 1
initial/final maximal load/proc = 1.0308705 0.92612715
initial/final imbalance factor = 1.1475395 1.0309418
x cuts: 0 0.4375 1
y cuts: 0 1
z cuts: 0 1
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.68 | 4.683 | 4.687 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
Loop time of 0.88104 on 2 procs for 250 steps with 4000 atoms
Performance: 122582.335 tau/day, 283.755 timesteps/s, 1.135 Matom-step/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.54838 | 0.58404 | 0.6197 | 4.7 | 66.29
Neigh | 0.18083 | 0.20191 | 0.22299 | 4.7 | 22.92
Comm | 0.032279 | 0.089285 | 0.14629 | 19.1 | 10.13
Output | 0.00014548 | 0.00016198 | 0.00017849 | 0.0 | 0.02
Modify | 0.0029024 | 0.0032448 | 0.0035871 | 0.6 | 0.37
Other | | 0.002397 | | | 0.27
Nlocal: 2000 ave 2284 max 1716 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10450 ave 10742 max 10158 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298063 ave 326003 max 270123 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596126
Ave neighs/atom = 149.0315
Neighbor list builds = 25
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 4
time weight factor: 1
initial/final maximal load/proc = 0.94269243 0.91089769
initial/final imbalance factor = 1.0640447 1.028157
x cuts: 0 0.47265625 1
y cuts: 0 1
z cuts: 0 1
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.68 | 4.683 | 4.687 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523
Loop time of 0.879484 on 2 procs for 250 steps with 4000 atoms
Performance: 122799.292 tau/day, 284.258 timesteps/s, 1.137 Matom-step/s
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52834 | 0.59047 | 0.6526 | 8.1 | 67.14
Neigh | 0.20544 | 0.20695 | 0.20845 | 0.3 | 23.53
Comm | 0.015738 | 0.076296 | 0.13685 | 21.9 | 8.68
Output | 0.00016028 | 0.00017427 | 0.00018825 | 0.0 | 0.02
Modify | 0.0032547 | 0.0033096 | 0.0033644 | 0.1 | 0.38
Other | | 0.002288 | | | 0.26
Nlocal: 2000 ave 2089 max 1911 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10347.5 ave 10639 max 10056 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 299628 ave 327997 max 271259 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 599256
Ave neighs/atom = 149.814
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:02

207
examples/balance/log.3Nov23.balance.clock.static.g++.4 Normal file
View File

@ -0,0 +1,207 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.000 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
rebalancing time: 0.000 seconds
iteration count = 2
time weight factor: 1
initial/final maximal load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.713 | 4.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
Loop time of 0.73733 on 4 procs for 250 steps with 4000 atoms
Performance: 146474.412 tau/day, 339.061 timesteps/s, 1.356 Matom-step/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17561 | 0.32661 | 0.58554 | 29.3 | 44.30
Neigh | 0.082409 | 0.10388 | 0.12511 | 5.7 | 14.09
Comm | 0.022216 | 0.30253 | 0.46162 | 31.8 | 41.03
Output | 0.00014228 | 0.00015708 | 0.00017991 | 0.0 | 0.02
Modify | 0.0015077 | 0.001891 | 0.0022549 | 0.7 | 0.26
Other | | 0.002266 | | | 0.31
Nlocal: 1000 ave 1263 max 712 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 8711.5 ave 9045 max 8325 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 149325 ave 275165 max 77227 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 597299
Ave neighs/atom = 149.32475
Neighbor list builds = 23
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 3
time weight factor: 1
initial/final maximal load/proc = 0.81065095 0.60308204
initial/final imbalance factor = 1.5281141 1.1368372
x cuts: 0 0.28125 0.46875 0.6171875 1
y cuts: 0 1
z cuts: 0 1
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.788 | 3.909 | 4.194 Mbytes
Step Temp E_pair E_mol TotEng Press
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995
300 0.5477618 -6.2678071 0 -5.4463698 -1.997842
350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056
400 0.53241503 -6.2453665 0 -5.4469436 -1.878594
450 0.5439158 -6.2623 0 -5.4466302 -1.9744161
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
Loop time of 0.574974 on 4 procs for 250 steps with 4000 atoms
Performance: 187834.605 tau/day, 434.802 timesteps/s, 1.739 Matom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22579 | 0.30378 | 0.43857 | 15.5 | 52.83
Neigh | 0.065619 | 0.099114 | 0.13721 | 8.3 | 17.24
Comm | 0.044004 | 0.16804 | 0.24011 | 18.1 | 29.23
Output | 0.0001362 | 0.00015185 | 0.00017014 | 0.0 | 0.03
Modify | 0.001083 | 0.0017628 | 0.0025897 | 1.4 | 0.31
Other | | 0.002125 | | | 0.37
Nlocal: 1000 ave 1467 max 599 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 8613.75 ave 9708 max 7894 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149356 ave 216864 max 107229 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 597424
Ave neighs/atom = 149.356
Neighbor list builds = 24
Dangerous builds = 0
balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 3
time weight factor: 1
initial/final maximal load/proc = 0.62725559 0.55791509
initial/final imbalance factor = 1.2472897 1.109407
x cuts: 0 0.3046875 0.4453125 0.59863281 1
y cuts: 0 1
z cuts: 0 1
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.806 | 3.927 | 4.211 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015
550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834
600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993
650 0.54526651 -6.265098 0 -5.4474027 -2.0303672
700 0.54369381 -6.263201 0 -5.4478642 -1.9921967
750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675
Loop time of 0.542284 on 4 procs for 250 steps with 4000 atoms
Performance: 199157.784 tau/day, 461.013 timesteps/s, 1.844 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27261 | 0.30921 | 0.36016 | 5.7 | 57.02
Neigh | 0.067401 | 0.10933 | 0.15726 | 11.2 | 20.16
Comm | 0.098733 | 0.11963 | 0.17136 | 8.7 | 22.06
Output | 0.00013971 | 0.00015475 | 0.00017256 | 0.0 | 0.03
Modify | 0.00098217 | 0.0017424 | 0.0025707 | 1.6 | 0.32
Other | | 0.002205 | | | 0.41
Nlocal: 1000 ave 1553 max 533 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 8745 ave 9835 max 8005 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 149124 ave 181946 max 128563 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 596497
Ave neighs/atom = 149.12425
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:01

213
examples/balance/log.3Nov23.balance.g++.2 Normal file
View File

@ -0,0 +1,213 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.061 | 3.066 | 3.071 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -29.143179 -1.2407285 2 1.0193906
100 25.842512 -29.285247 0.26525204 1.0193906 1.0027701
200 26.307268 -29.748808 1.8402984 1.0193906 1.0027701
300 26.746717 -30.187064 3.3160966 1.0193906 1.0083102
400 26.877952 -30.317954 5.3251792 1.0304709 1.0027701
500 26.266471 -29.708192 7.9166641 1.0193906 1.0027701
600 26.005495 -29.448014 9.4696736 1.0193906 1.0027701
700 26.321835 -29.763442 8.7529756 1.0304709 1.0027701
800 26.677822 -30.118375 4.840886 1.0193906 1.0027701
900 26.708823 -30.149264 2.8898542 1.0304709 1.0083102
1000 26.373337 -29.814704 1.6422658 1.0193906 1.0027701
1100 25.893585 -29.335362 0.97146057 1.0304709 1.0027701
1200 25.710916 -29.147328 0.80754847 1.0193906 1.0027701
1300 25.76291 -29.201881 0.88170364 1.0304709 1.0027701
1400 26.080337 -29.52159 1.2169926 1.0304709 1.0083102
1500 26.473221 -29.914282 2.3873969 1.0304709 1.0027701
1600 26.738055 -30.178413 4.1057361 1.0304709 1.0027701
1700 26.589182 -30.030057 6.6930875 1.0304709 1.0083102
1800 26.122828 -29.565007 8.897304 1.0304709 1.0027701
1900 26.16025 -29.602425 8.4722268 1.0304709 1.0083102
2000 26.510754 -29.951778 6.6913672 1.0304709 1.0027701
2100 26.732291 -30.172707 4.1328654 1.0193906 1.0083102
2200 26.479423 -29.92049 2.3106996 1.0193906 1.0027701
2300 26.058035 -29.500247 1.2582222 1.0193906 1.0027701
2400 25.732051 -29.175166 0.54231521 1.0304709 1.0083102
2500 25.733864 -29.176523 0.66714018 1.0193906 1.0083102
2600 25.990734 -29.433139 1.2035223 1.0304709 1.0027701
2700 26.383788 -29.82468 2.162696 1.0193906 1.0027701
2800 26.679604 -30.120134 3.6992506 1.0193906 1.0083102
2900 26.600714 -30.041505 5.7237864 1.0304709 1.0027701
3000 26.250766 -29.692594 7.9725502 1.0304709 1.0027701
3100 26.121363 -29.563584 8.9373309 1.0193906 1.0027701
3200 26.477192 -29.918373 7.1092175 1.0193906 1.0027701
3300 26.689536 -30.129977 4.5776139 1.0304709 1.0027701
3400 26.586629 -30.026764 2.7417726 1.0304709 1.0027701
3500 26.220686 -29.659572 1.6498578 1.0304709 1.0027701
3600 25.866231 -29.300814 1.1210814 1.0193906 1.0027701
3700 25.659205 -29.142497 0.88115023 1.0193906 1.0027701
3800 25.68947 -29.145676 1.4621172 1.0304709 1.0027701
3900 25.842813 -29.305171 2.6326543 1.0304709 1.0027701
4000 25.919278 -29.470226 4.5283838 1.0304709 1.0027701
4100 24.903798 -28.514051 8.027658 1.0304709 1.0027701
4200 23.423542 -27.070178 11.619766 1.0304709 1.0083102
4300 22.043492 -25.928725 13.445594 1.0304709 1.0083102
4400 22.154748 -25.970203 12.572064 1.0304709 1.0027701
4500 23.469652 -27.084691 9.6953414 1.0249307 1.0083102
4600 23.645224 -27.247805 6.5087935 1.0249307 1.0027701
4700 23.449403 -26.921826 3.8388213 1.0249307 1.0027701
4800 22.978713 -26.375077 2.2105686 1.0249307 1.0027701
4900 22.547461 -25.880668 1.6287577 1.0138504 1.0083102
5000 22.34432 -25.632296 1.3146711 1.0304709 1.0083102
5100 21.859416 -25.132381 1.4466766 1.0138504 1.0083102
5200 21.854255 -25.131546 1.6303448 1.0138504 1.0027701
5300 21.425171 -24.876722 2.6133634 1.0027701 1.0027701
5400 19.687643 -23.234478 5.4446821 1.0138504 1.0027701
5500 18.102224 -21.98985 7.8007647 1.0138504 1.0027701
5600 17.402396 -21.218157 8.8854058 1.0138504 1.0027701
5700 17.49995 -21.430274 8.8193841 1.0083102 1.0083102
5800 18.01284 -21.490424 8.2097589 1.0083102 1.0083102
5900 17.565819 -21.169657 7.3645475 1.0027701 1.0027701
6000 17.002407 -20.455432 8.0176011 1.0083102 1.0083102
6100 17.527412 -20.899213 6.0280989 1.0027701 1.0027701
6200 17.068329 -20.522823 5.4665249 1.0027701 1.0027701
6300 16.424762 -19.676043 5.1320371 1.0027701 1.0027701
6400 16.186199 -19.427212 4.3019107 1.0027701 1.0027701
6500 15.691963 -18.890331 3.8910044 1.0027701 1.0027701
6600 15.525701 -18.788954 3.5106407 1.0083102 1.0083102
6700 15.641437 -18.744896 2.9139189 1.0027701 1.0083102
6800 15.656899 -18.774587 2.1876061 1.0138504 1.0027701
6900 15.094185 -18.163325 2.3500048 1.0138504 1.0027701
7000 14.991269 -18.044483 2.5047107 1.0249307 1.0027701
7100 14.727757 -17.740443 2.0066013 1.0138504 1.0027701
7200 14.32011 -17.413392 1.5370313 1.0083102 1.0027701
7300 14.153835 -17.154266 2.2823938 1.0138504 1.0027701
7400 13.644555 -16.662895 2.1522299 1.0083102 1.0083102
7500 14.14831 -17.129791 1.5888858 1.0138504 1.0027701
7600 13.625238 -16.591406 1.4121129 1.0138504 1.0027701
7700 13.471137 -16.441146 1.3192621 1.0193906 1.0083102
7800 13.262113 -16.221083 1.516185 1.0083102 1.0027701
7900 13.146175 -16.128839 1.6154309 1.0193906 1.0027701
8000 13.030735 -15.972746 1.5756469 1.0083102 1.0027701
8100 12.742337 -15.790849 1.5660957 1.0138504 1.0027701
8200 13.111618 -16.038849 1.4662027 1.0027701 1.0083102
8300 12.847359 -15.82086 1.9249118 1.0138504 1.0027701
8400 13.136509 -16.066829 1.6715045 1.0138504 1.0027701
8500 12.929796 -15.955279 1.1388437 1.0083102 1.0027701
8600 13.000263 -15.983556 1.5854841 1.0083102 1.0027701
8700 12.524346 -15.443794 1.8406232 1.0083102 1.0027701
8800 12.718004 -15.691429 1.4077935 1.0193906 1.0027701
8900 12.98278 -15.92931 1.5950893 1.0083102 1.0027701
9000 12.444974 -15.506365 1.6085567 1.0249307 1.0027701
9100 12.5341 -15.471682 1.6458191 1.0027701 1.0027701
9200 12.411742 -15.374927 1.7423964 1.0027701 1.0027701
9300 12.613 -15.543866 1.6002664 1.0027701 1.0027701
9400 12.315079 -15.231839 1.7207652 1.0138504 1.0027701
9500 12.49493 -15.406632 1.5330057 1.0138504 1.0027701
9600 12.332602 -15.240282 1.2401605 1.0027701 1.0027701
9700 11.894396 -14.794216 1.4072165 1.0083102 1.0027701
9800 12.140847 -15.113816 1.6174151 1.0027701 1.0083102
9900 12.326936 -15.241095 1.2077951 1.0083102 1.0027701
10000 12.212835 -15.106252 1.2704949 1.0083102 1.0027701
Loop time of 0.177325 on 2 procs for 10000 steps with 361 atoms
Performance: 4872405.392 tau/day, 56393.581 timesteps/s, 20.358 Matom-step/s
96.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.082172 | 0.083041 | 0.08391 | 0.3 | 46.83
Neigh | 0.025221 | 0.025625 | 0.026029 | 0.3 | 14.45
Comm | 0.022461 | 0.026564 | 0.030666 | 2.5 | 14.98
Output | 0.00084416 | 0.00098787 | 0.0011316 | 0.0 | 0.56
Modify | 0.024707 | 0.025096 | 0.025485 | 0.2 | 14.15
Other | | 0.01601 | | | 9.03
Nlocal: 180.5 ave 181 max 180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 38 ave 44 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1018.5 ave 1032 max 1005 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2037
Ave neighs/atom = 5.6426593
Neighbor list builds = 987
Dangerous builds = 0
Total wall time: 0:00:00

213
examples/balance/log.3Nov23.balance.g++.4 Normal file
View File

@ -0,0 +1,213 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
create_atoms CPU = 0.000 seconds
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
timestep 0.001
run 10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 42 29 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.048 | 3.06 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
100 25.842512 -29.285247 0.26525204 1.0526316 1.0083102
200 26.307268 -29.748808 1.8402984 1.0526316 1.0083102
300 26.746717 -30.187064 3.3160966 1.0526316 1.0083102
400 26.877952 -30.317954 5.3251792 1.0526316 1.0083102
500 26.266471 -29.708192 7.9166641 1.0526316 1.0304709
600 26.005495 -29.448014 9.4696736 1.0526316 1.0083102
700 26.321835 -29.763442 8.7529756 1.0526316 1.0193906
800 26.677822 -30.118375 4.840886 1.0526316 1.0083102
900 26.708823 -30.149264 2.8898542 1.0526316 1.0193906
1000 26.373337 -29.814704 1.6422658 1.0526316 1.0083102
1100 25.893585 -29.335362 0.97146057 1.0526316 1.0083102
1200 25.710916 -29.147328 0.80754847 1.0526316 1.0193906
1300 25.76291 -29.201881 0.88170364 1.0858726 1.0193906
1400 26.080337 -29.52159 1.2169926 1.0526316 1.0083102
1500 26.473221 -29.914282 2.3873969 1.0969529 1.0304709
1600 26.738055 -30.178413 4.1057361 1.0526316 1.0083102
1700 26.589182 -30.030057 6.6930875 1.0526316 1.0193906
1800 26.122828 -29.565007 8.897304 1.0526316 1.0083102
1900 26.16025 -29.602425 8.4722268 1.0969529 1.0083102
2000 26.510754 -29.951778 6.6913672 1.0969529 1.0083102
2100 26.732291 -30.172707 4.1328654 1.0526316 1.0304709
2200 26.479423 -29.92049 2.3106996 1.0526316 1.0083102
2300 26.058035 -29.500247 1.2582222 1.0526316 1.0193906
2400 25.732051 -29.175166 0.54231521 1.0526316 1.0304709
2500 25.733864 -29.176523 0.66714018 1.0526316 1.0083102
2600 25.990734 -29.433139 1.2035223 1.0526316 1.0083102
2700 26.383788 -29.82468 2.162696 1.0526316 1.0083102
2800 26.679604 -30.120134 3.6992506 1.0526316 1.0304709
2900 26.600714 -30.041505 5.7237864 1.0526316 1.0083102
3000 26.250766 -29.692594 7.9725502 1.0526316 1.0083102
3100 26.121363 -29.563584 8.9373309 1.0526316 1.0083102
3200 26.477192 -29.918373 7.1092175 1.0526316 1.0083102
3300 26.689536 -30.129977 4.5776139 1.0969529 1.0304709
3400 26.586629 -30.026764 2.7417726 1.0969529 1.0083102
3500 26.220686 -29.659572 1.6498578 1.0969529 1.0083102
3600 25.866231 -29.300814 1.1210814 1.0526316 1.0304709
3700 25.659205 -29.142497 0.88115023 1.0526316 1.0083102
3800 25.68947 -29.145676 1.4621172 1.0969529 1.0304709
3900 25.842813 -29.305171 2.6326543 1.0969529 1.0083102
4000 25.919278 -29.470226 4.5283838 1.0969529 1.0083102
4100 24.903798 -28.514051 8.027658 1.0526316 1.0083102
4200 23.423542 -27.070178 11.619766 1.0858726 1.0193906
4300 22.043492 -25.928725 13.445594 1.0858726 1.0083102
4400 22.154748 -25.970203 12.572064 1.0415512 1.0083102
4500 23.469652 -27.084691 9.6953414 1.0415512 1.0193906
4600 23.645224 -27.247805 6.5087935 1.0526316 1.0083102
4700 23.449403 -26.921826 3.8388213 1.0415512 1.0193906
4800 22.978713 -26.375077 2.2105686 1.0304709 1.0193906
4900 22.547461 -25.880668 1.6287577 1.0415512 1.0193906
5000 22.34432 -25.632296 1.3146711 1.0415512 1.0083102
5100 21.859416 -25.132381 1.4466766 1.0193906 1.0304709
5200 21.854255 -25.131546 1.6303448 1.0193906 1.0083102
5300 21.425171 -24.876722 2.6133634 1.0193906 1.0193906
5400 19.687643 -23.234478 5.4446821 1.0193906 1.0193906
5500 18.102224 -21.98985 7.8007647 1.0193906 1.0083102
5600 17.402396 -21.218157 8.8854058 1.0193906 1.0083102
5700 17.49995 -21.430274 8.8193838 1.0193906 1.0083102
5800 18.012839 -21.490423 8.2097596 1.0083102 1.0083102
5900 17.565818 -21.169657 7.3645466 1.0304709 1.0083102
6000 17.00239 -20.455416 8.0176192 1.0304709 1.0193906
6100 17.527455 -20.899259 6.0280748 1.0193906 1.0083102
6200 17.068393 -20.522944 5.4664014 1.0083102 1.0083102
6300 16.424576 -19.675908 5.13206 1.0083102 1.0193906
6400 16.18682 -19.428005 4.2994462 1.0083102 1.0083102
6500 15.692498 -18.890361 3.8912337 1.0193906 1.0083102
6600 15.543565 -18.808306 3.4752832 1.0637119 1.0083102
6700 15.657432 -18.758221 2.9143187 1.0415512 1.0083102
6800 15.730059 -18.834511 2.1741976 1.0193906 1.0083102
6900 14.954711 -18.033715 2.4588698 1.0415512 1.0083102
7000 15.332203 -18.367577 2.1869698 1.0415512 1.0193906
7100 14.54279 -17.554326 2.1617263 1.0304709 1.0193906
7200 14.485747 -17.494113 1.362177 1.0193906 1.0193906
7300 14.266906 -17.269915 1.6961885 1.0193906 1.0083102
7400 13.635947 -16.654801 2.1133026 1.0193906 1.0193906
7500 14.029933 -17.022405 1.6716246 1.0193906 1.0083102
7600 14.119782 -17.107927 1.516669 1.0304709 1.0083102
7700 14.0984 -17.079131 1.6226374 1.0193906 1.0193906
7800 13.895083 -16.873848 1.6965546 1.0083102 1.0193906
7900 13.55953 -16.536866 1.9893454 1.0193906 1.0083102
8000 13.649101 -16.633977 1.4873767 1.0526316 1.0083102
8100 13.534848 -16.5239 1.5030254 1.0304709 1.0083102
8200 13.039311 -16.021896 1.9003186 1.0083102 1.0083102
8300 13.212394 -16.15257 1.6325076 1.0304709 1.0083102
8400 12.719582 -15.761108 1.7061831 1.0193906 1.0193906
8500 12.954096 -15.962673 1.2631089 1.0193906 1.0193906
8600 12.583443 -15.65611 1.3899368 1.0083102 1.0083102
8700 12.678764 -15.710348 1.0530056 1.0304709 1.0083102
8800 12.740618 -15.660427 1.5864512 1.0193906 1.0083102
8900 12.249135 -15.232792 1.624414 1.0304709 1.0193906
9000 12.500318 -15.426035 1.1440223 1.0193906 1.0083102
9100 12.322373 -15.221333 1.5141173 1.0193906 1.0083102
9200 12.259837 -15.16384 1.4848297 1.0193906 1.0083102
9300 11.928997 -14.955513 1.3933259 1.0193906 1.0083102
9400 12.08076 -14.972026 1.6436388 1.0415512 1.0083102
9500 12.059618 -14.952921 1.6617096 1.0083102 1.0304709
9600 11.840796 -14.759488 1.6735572 1.0304709 1.0083102
9700 11.781829 -14.678411 1.6633417 1.0083102 1.0083102
9800 11.947375 -14.931443 1.6695696 1.0083102 1.0193906
9900 12.031986 -14.904841 0.97065132 1.0193906 1.0083102
10000 11.564772 -14.48025 1.627038 1.0304709 1.0083102
Loop time of 0.161375 on 4 procs for 10000 steps with 361 atoms
Performance: 5353997.284 tau/day, 61967.561 timesteps/s, 22.370 Matom-step/s
86.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.04238 | 0.045072 | 0.04897 | 1.3 | 27.93
Neigh | 0.01265 | 0.013679 | 0.014709 | 0.6 | 8.48
Comm | 0.043614 | 0.054438 | 0.062719 | 3.0 | 33.73
Output | 0.00097457 | 0.0010711 | 0.0012879 | 0.4 | 0.66
Modify | 0.022286 | 0.022773 | 0.023314 | 0.3 | 14.11
Other | | 0.02434 | | | 15.08
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 42.75 ave 70 max 26 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 492.5 ave 588 max 427 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 1970
Ave neighs/atom = 5.4570637
Neighbor list builds = 1087
Dangerous builds = 0
Total wall time: 0:00:00

116
examples/balance/log.3Nov23.balance.group.dynamic.g++.2 Normal file
View File

@ -0,0 +1,116 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.001 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
rebalancing time: 0.001 seconds
iteration count = 1
group weights: fast=1 slow=1
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor}
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.434 | 4.625 | 4.816 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
Loop time of 0.925475 on 2 procs for 250 steps with 4000 atoms
Performance: 116696.804 tau/day, 270.131 timesteps/s, 1.081 Matom-step/s
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.49759 | 0.59065 | 0.68371 | 12.1 | 63.82
Neigh | 0.20391 | 0.21106 | 0.21821 | 1.6 | 22.81
Comm | 0.016226 | 0.11642 | 0.21661 | 29.4 | 12.58
Output | 0.00014767 | 0.00016136 | 0.00017504 | 0.0 | 0.02
Modify | 0.0049562 | 0.0049875 | 0.0050188 | 0.0 | 0.54
Other | | 0.002194 | | | 0.24
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 10441 ave 10457 max 10425 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 349156 max 247508 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:00

116
examples/balance/log.3Nov23.balance.group.dynamic.g++.4 Normal file
View File

@ -0,0 +1,116 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.000 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
rebalancing time: 0.000 seconds
iteration count = 2
group weights: fast=1 slow=1
initial/final maximal load/proc = 1200 1200
initial/final imbalance factor = 1.2 1.2
x cuts: 0 0.25 0.5 0.6875 1
y cuts: 0 1
z cuts: 0 1
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor}
fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.567 | 3.949 | 4.33 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
Loop time of 0.805708 on 4 procs for 250 steps with 4000 atoms
Performance: 134043.547 tau/day, 310.286 timesteps/s, 1.241 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14028 | 0.36957 | 0.61955 | 31.5 | 45.87
Neigh | 0.11839 | 0.13333 | 0.14552 | 3.2 | 16.55
Comm | 0.034173 | 0.29629 | 0.5404 | 37.3 | 36.77
Output | 0.00016223 | 0.00017113 | 0.00019287 | 0.0 | 0.02
Modify | 0.0041243 | 0.0042239 | 0.0043322 | 0.1 | 0.52
Other | | 0.002124 | | | 0.26
Nlocal: 1000 ave 1001 max 999 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 8727 ave 8761 max 8674 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 149349 ave 260848 max 51191 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 597396
Ave neighs/atom = 149.349
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:00

160
examples/balance/log.3Nov23.balance.group.static.g++.2 Normal file
View File

@ -0,0 +1,160 @@
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
processors * 1 1
variable factor index 1.0
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 3 box
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
2 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
create_atoms CPU = 0.001 seconds
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
Setting atom values ...
1400 settings made for type
velocity all create 1.0 87287
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_coeff * 2 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
balance 1.0 shift x 5 1.1 # out unweighted.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 2 steps, delay = 4 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
rebalancing time: 0.001 seconds
iteration count = 1
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 0
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
variable weight atom (type==1)*1.0+(type==2)*v_factor
balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 1
weight variable: weight
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
balance 1.0 x uniform
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 0
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
group fast type 1
2600 atoms in group fast
group slow type 2
1400 atoms in group slow
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0
Balancing ...
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
rebalancing time: 0.000 seconds
iteration count = 1
group weights: fast=1 slow=1
initial/final maximal load/proc = 2000 2000
initial/final imbalance factor = 1 1
x cuts: 0 0.5 1
y cuts: 0 1
z cuts: 0 1
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.294 | 4.485 | 4.675 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -6.9453205 0 -5.4456955 -5.6812358
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162
200 0.536665 -6.2530113 0 -5.448215 -1.933468
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847
Loop time of 1.07049 on 2 procs for 250 steps with 4000 atoms
Performance: 100888.200 tau/day, 233.537 timesteps/s, 934.150 katom-step/s
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.55726 | 0.68002 | 0.80278 | 14.9 | 63.52
Neigh | 0.21838 | 0.23004 | 0.2417 | 2.4 | 21.49
Comm | 0.01941 | 0.15387 | 0.28832 | 34.3 | 14.37
Output | 0.00017519 | 0.00021161 | 0.00024802 | 0.0 | 0.02
Modify | 0.0036966 | 0.0037375 | 0.0037784 | 0.1 | 0.35
Other | | 0.002623 | | | 0.25
Nlocal: 2000 ave 2051 max 1949 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 10443 ave 10506 max 10380 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 298332 ave 363449 max 233215 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 596664
Ave neighs/atom = 149.166
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:01

Some files were not shown because too many files have changed in this diff Show More