forked from lijiext/lammps
Merge branch 'master' into gran_mods
This commit is contained in:
Axel Kohlmeyer
commit
2fa6e913ef
|
|
@ -381,19 +381,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
|
|||
endif()
|
||||
|
||||
if(PKG_PYTHON)
|
||||
find_package(PythonInterp REQUIRED)
|
||||
find_package(PythonLibs REQUIRED)
|
||||
add_definitions(-DLMP_PYTHON)
|
||||
include_directories(${PYTHON_INCLUDE_DIR})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
|
||||
if(BUILD_LIB AND BUILD_SHARED_LIBS)
|
||||
if(NOT PYTHON_INSTDIR)
|
||||
execute_process(COMMAND ${PYTHON_EXECUTABLE}
|
||||
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
|
||||
OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
find_package(JPEG QUIET)
|
||||
|
|
@ -613,8 +604,9 @@ if(PKG_USER-PLUMED)
|
|||
endif()
|
||||
|
||||
if(PKG_USER-MOLFILE)
|
||||
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
|
||||
add_library(molfile INTERFACE)
|
||||
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
|
||||
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
|
||||
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
|
||||
list(APPEND LAMMPS_LINK_LIBS molfile)
|
||||
endif()
|
||||
|
|
@ -626,7 +618,6 @@ if(PKG_USER-NETCDF)
|
|||
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
|
||||
endif()
|
||||
|
||||
|
||||
if(PKG_USER-SMD)
|
||||
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
|
||||
if(DOWNLOAD_EIGEN3)
|
||||
|
|
@ -670,6 +661,12 @@ if(PKG_USER-VTK)
|
|||
endif()
|
||||
|
||||
if(PKG_KIM)
|
||||
find_package(CURL)
|
||||
if(CURL_FOUND)
|
||||
include_directories(${CURL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
|
||||
add_definitions(-DLMP_KIM_CURL)
|
||||
endif()
|
||||
option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
|
||||
if(DOWNLOAD_KIM)
|
||||
message(STATUS "KIM-API v2 download requested - we will build our own")
|
||||
|
|
@ -1331,36 +1328,14 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
|
|||
######################################
|
||||
# Generate lmpgitversion.h
|
||||
######################################
|
||||
set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
|
||||
set(temp_git_commit "(unknown)")
|
||||
set(temp_git_branch "(unknown)")
|
||||
set(temp_git_describe "(unknown)")
|
||||
set(temp_git_info "false")
|
||||
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
|
||||
set(temp_git_info "true")
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
|
||||
OUTPUT_VARIABLE temp_git_commit
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
|
||||
OUTPUT_VARIABLE temp_git_branch
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
|
||||
OUTPUT_VARIABLE temp_git_describe
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
|
||||
set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
|
||||
set(temp "${temp}#endif\n\n")
|
||||
|
||||
message(STATUS "Generating lmpgitversion.h...")
|
||||
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
|
||||
add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
|
||||
-DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
|
||||
-DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
|
||||
-DGIT_FOUND="${GIT_FOUND}"
|
||||
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
|
||||
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
|
||||
set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
|
||||
list(APPEND LAMMPS_DEPS gitversion)
|
||||
|
||||
###########################################
|
||||
# Actually add executable and lib to build
|
||||
|
|
@ -1483,6 +1458,49 @@ install(
|
|||
DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
|
||||
)
|
||||
|
||||
###############################################################################
|
||||
# Install LAMMPS lib and python module into site-packages folder with
|
||||
# "install-python" target. Behaves exactly like "make install-python" for
|
||||
# conventional build. Only available, if a shared library is built.
|
||||
# This is primarily for people that only want to use the Python wrapper.
|
||||
###############################################################################
|
||||
if(BUILD_LIB AND BUILD_SHARED_LIBS)
|
||||
find_package(PythonInterp)
|
||||
if (PYTHONINTERP_FOUND)
|
||||
add_custom_target(
|
||||
install-python
|
||||
${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
|
||||
-m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
|
||||
-l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../python
|
||||
COMMENT "Installing LAMMPS Python module")
|
||||
else()
|
||||
add_custom_target(
|
||||
install-python
|
||||
${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
|
||||
endif()
|
||||
else()
|
||||
add_custom_target(
|
||||
install-python
|
||||
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
|
||||
endif()
|
||||
|
||||
###############################################################################
|
||||
# Add LAMMPS python module to "install" target. This is taylored for building
|
||||
# LAMMPS for package managers and with different prefix settings.
|
||||
# This requires either a shared library or that the PYTHON package is included.
|
||||
###############################################################################
|
||||
if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
|
||||
find_package(PythonInterp)
|
||||
if (PYTHONINTERP_FOUND)
|
||||
execute_process(COMMAND ${PYTHON_EXECUTABLE}
|
||||
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
|
||||
OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
|
||||
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
###############################################################################
|
||||
# Testing
|
||||
#
|
||||
|
|
|
|||
|
|
@ -0,0 +1,30 @@
|
|||
set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
|
||||
set(temp_git_commit "(unknown)")
|
||||
set(temp_git_branch "(unknown)")
|
||||
set(temp_git_describe "(unknown)")
|
||||
set(temp_git_info "false")
|
||||
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
|
||||
set(temp_git_info "true")
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
|
||||
OUTPUT_VARIABLE temp_git_commit
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
|
||||
OUTPUT_VARIABLE temp_git_branch
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
|
||||
OUTPUT_VARIABLE temp_git_describe
|
||||
ERROR_QUIET
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
|
||||
set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
|
||||
set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
|
||||
set(temp "${temp}#endif\n\n")
|
||||
|
||||
message(STATUS "Generating lmpgitversion.h...")
|
||||
file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
|
||||
16
doc/Makefile
16
doc/Makefile
|
|
@ -116,6 +116,13 @@ mobi: epub
|
|||
@echo "Conversion finished. The MOBI manual file is created."
|
||||
|
||||
pdf: $(OBJECTS) $(ANCHORCHECK)
|
||||
@(\
|
||||
cd src/Developer; \
|
||||
pdflatex developer; \
|
||||
pdflatex developer; \
|
||||
mv developer.pdf ../../Developer.pdf; \
|
||||
cd ../../; \
|
||||
)
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
cp -r src/* $(RSTDIR)/ ;\
|
||||
|
|
@ -135,14 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
|
|||
make && \
|
||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
@(\
|
||||
cd src/Developer; \
|
||||
pdflatex developer; \
|
||||
pdflatex developer; \
|
||||
mv developer.pdf ../../Developer.pdf; \
|
||||
cd ../../; \
|
||||
)
|
||||
cd ../;
|
||||
@rm -rf latex/_sources
|
||||
@rm -rf latex/PDF
|
||||
@rm -rf latex/USER
|
||||
|
|
|
|||
|
|
@ -169,16 +169,18 @@ used to build the GPU library.
|
|||
|
||||
KIM package :h4,link(kim)
|
||||
|
||||
To build with this package, the KIM library must be downloaded and
|
||||
built on your system. It must include the KIM models that you want to
|
||||
use with LAMMPS.
|
||||
To build with this package, the KIM library with API v2 must be downloaded
|
||||
and built on your system. It must include the KIM models that you want to
|
||||
use with LAMMPS. If you want to use the "kim_query"_kim_query.html
|
||||
command, you also need to have libcurl installed with the matching
|
||||
development headers and the curl-config tool.
|
||||
|
||||
Note that in LAMMPS lingo, a KIM model driver is a pair style
|
||||
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
|
||||
element or alloy and set of parameters, e.g. EAM for Cu with a
|
||||
specific EAM potential file. Also note that installing the KIM API
|
||||
library with all its models, may take around 30 min to build. Of
|
||||
course you only need to do that once.
|
||||
specific EAM potential file. Also note that downloading and installing
|
||||
the KIM API library with all its models, may take a long time (10s of
|
||||
minutes to hours) to build. Of course you only need to do that once.
|
||||
|
||||
See the list of KIM model drivers here:
|
||||
https://openkim.org/browse/model-drivers/alphabetical
|
||||
|
|
@ -893,7 +895,17 @@ USER-MOLFILE package :h4,link(user-molfile)
|
|||
|
||||
[CMake build]:
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
|
||||
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
|
||||
-D PKG_USER-MOLFILE=yes :pre
|
||||
|
||||
|
||||
Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
|
||||
"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
|
||||
the molfile plugin header files. These should match the ABI of the
|
||||
plugin files used, and thus one typically sets them to include
|
||||
folder of the local VMD installation in use. LAMMPS ships with a
|
||||
couple of default header files that correspond to a popular VMD
|
||||
version, usually the latest release.
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
|
|
@ -902,7 +914,11 @@ loading library libdl.a that is typically present on all systems. It
|
|||
is required for LAMMPS to link with this package. If the setting is
|
||||
not valid for your system, you will need to edit the Makefile.lammps
|
||||
file. See lib/molfile/README and lib/molfile/Makefile.lammps for
|
||||
details.
|
||||
details. It is also possible to configure a different folder with
|
||||
the VMD molfile plugin header files. LAMMPS ships with a couple of
|
||||
default headers, but these are not compatible with all VMD versions,
|
||||
so it is often best to change this setting to the location of the
|
||||
same include files of the local VMD installation in use.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
|
|||
"improper_style"_improper_style.html,
|
||||
"include"_include.html,
|
||||
"jump"_jump.html,
|
||||
"kim_query"_kim_query.html,
|
||||
"kspace_modify"_kspace_modify.html,
|
||||
"kspace_style"_kspace_style.html,
|
||||
"label"_label.html,
|
||||
|
|
@ -78,6 +79,7 @@ An alphabetic list of all general LAMMPS commands.
|
|||
"minimize"_minimize.html,
|
||||
"min_modify"_min_modify.html,
|
||||
"min_style"_min_style.html,
|
||||
"min_style spin"_min_spin.html,
|
||||
"molecule"_molecule.html,
|
||||
"ndx2group"_group2ndx.html,
|
||||
"neb"_neb.html,
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 6.9 KiB |
|
|
@ -0,0 +1,13 @@
|
|||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 5.8 KiB |
|
|
@ -0,0 +1,14 @@
|
|||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
{\Delta t}_{\rm max} = \frac{2\pi}{\kappa
|
||||
\left|\vec{\omega}_{\rm max} \right|}
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
|
|
@ -57,6 +57,17 @@ library is then loaded by the Python interface. In this example we enable the
|
|||
MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
|
||||
output support enabled.
|
||||
|
||||
Step 1a: For the CMake based build system, the steps are:
|
||||
|
||||
mkdir $LAMMPS_DIR/build-shared
|
||||
cd $LAMMPS_DIR/build-shared :pre
|
||||
|
||||
# MPI, PNG, Jpeg, FFMPEG are auto-detected
|
||||
cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
|
||||
make :pre
|
||||
|
||||
Step 1b: For the legacy, make based build system, the steps are:
|
||||
|
||||
cd $LAMMPS_DIR/src :pre
|
||||
|
||||
# add packages if necessary
|
||||
|
|
@ -68,10 +79,9 @@ make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS
|
|||
Step 2: Installing the LAMMPS Python package :h6
|
||||
|
||||
PyLammps is part of the lammps Python package. To install it simply install
|
||||
that package into your current Python installation.
|
||||
that package into your current Python installation with:
|
||||
|
||||
cd $LAMMPS_DIR/python
|
||||
python install.py :pre
|
||||
make install-python :pre
|
||||
|
||||
NOTE: Recompiling the shared library requires re-installing the Python package
|
||||
|
||||
|
|
@ -94,14 +104,21 @@ apt-get install python-virtualenv :pre
|
|||
|
||||
Creating a virtualenv with lammps installed :h6
|
||||
|
||||
# create virtualenv name 'testing' :pre
|
||||
# create virtualenv named 'testing'
|
||||
virtualenv $HOME/python/testing :pre
|
||||
|
||||
# activate 'testing' environment
|
||||
source testing/bin/activate :pre
|
||||
source $HOME/python/testing/bin/activate :pre
|
||||
|
||||
Now configure and compile the LAMMPS shared library as outlined above.
|
||||
When using CMake and the shared library has already been build, you
|
||||
need to re-run CMake to update the location of the python executable
|
||||
to the location in the virtual environment with:
|
||||
|
||||
cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
|
||||
|
||||
# install LAMMPS package in virtualenv
|
||||
(testing) cd $LAMMPS_DIR/python
|
||||
(testing) python install.py :pre
|
||||
(testing) make install-python :pre
|
||||
|
||||
# install other useful packages
|
||||
(testing) pip install matplotlib jupyter mpi4py :pre
|
||||
|
|
|
|||
|
|
@ -341,6 +341,8 @@ KIM package :link(PKG-KIM),h4
|
|||
A "pair_style kim"_pair_kim.html command which is a wrapper on the
|
||||
Knowledge Base for Interatomic Models (KIM) repository of interatomic
|
||||
potentials, enabling any of them to be used in LAMMPS simulations.
|
||||
Also a "kim_query"_kim_query.html command, which allows to query
|
||||
the OpenKIM database for stored properties.
|
||||
|
||||
To use this package you must have the KIM library available on your
|
||||
system.
|
||||
|
|
|
|||
|
|
@ -12,16 +12,23 @@ Installing LAMMPS in Python :h3
|
|||
For Python to invoke LAMMPS, there are 2 files it needs to know about:
|
||||
|
||||
python/lammps.py
|
||||
src/liblammps.so :ul
|
||||
liblammps.so or liblammps.dylib :ul
|
||||
|
||||
Lammps.py is the Python wrapper on the LAMMPS library interface.
|
||||
Liblammps.so is the shared LAMMPS library that Python loads, as
|
||||
described above.
|
||||
The python source code in lammps.py is the Python wrapper on the
|
||||
LAMMPS library interface. The liblammps.so or liblammps.dylib file
|
||||
is the shared LAMMPS library that Python loads dynamically.
|
||||
|
||||
You can insure Python can find these files in one of two ways:
|
||||
You can achieve that Python can find these files in one of two ways:
|
||||
|
||||
set two environment variables
|
||||
run the python/install.py script :ul
|
||||
set two environment variables pointing to the location in the source tree
|
||||
run "make install-python" or run the python/install.py script explicitly :ul
|
||||
|
||||
When calling "make install-python" LAMMPS will try to install the
|
||||
python module and the shared library into the python site-packages folders;
|
||||
either the system-wide ones, or the local users ones (in case of insufficient
|
||||
permissions for the global install). Python will then find the module
|
||||
and shared library file automatically. The exact location of these folders
|
||||
depends on your python version and your operating system.
|
||||
|
||||
If you set the paths to these files as environment variables, you only
|
||||
have to do it once. For the csh or tcsh shells, add something like
|
||||
|
|
@ -30,42 +37,28 @@ this to your ~/.cshrc file, one line for each of the two files:
|
|||
setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
|
||||
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
If you use the python/install.py script, you need to invoke it every
|
||||
time you rebuild LAMMPS (as a shared library) or make changes to the
|
||||
python/lammps.py file.
|
||||
On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.
|
||||
For Bourne/Korn shells accordingly into the corresponding files using
|
||||
the "export" shell builtin.
|
||||
|
||||
You can invoke install.py from the python directory as
|
||||
If you use "make install-python" or the python/install.py script, you need
|
||||
to invoke it every time you rebuild LAMMPS (as a shared library) or
|
||||
make changes to the python/lammps.py file, so that the site-packages
|
||||
files are updated with the new version.
|
||||
|
||||
% python install.py \[libdir\] \[pydir\] :pre
|
||||
If the default settings of "make install-python" are not what you want,
|
||||
you can invoke install.py from the python directory manually as
|
||||
|
||||
The optional libdir is where to copy the LAMMPS shared library to; the
|
||||
default is /usr/local/lib. The optional pydir is where to copy the
|
||||
lammps.py file to; the default is the site-packages directory of the
|
||||
version of Python that is running the install script.
|
||||
% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre
|
||||
|
||||
Note that libdir must be a location that is in your default
|
||||
LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a
|
||||
location that Python looks in by default for imported modules, like
|
||||
its site-packages dir. If you want to copy these files to
|
||||
non-standard locations, such as within your own user space, you will
|
||||
need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
|
||||
accordingly, as above.
|
||||
The -m flag points to the lammps.py python module file to be installed,
|
||||
the -l flag points to the LAMMPS shared library file to be installed,
|
||||
the -v flag points to the version.h file in the LAMMPS source
|
||||
and the optional -d flag to a custom (legacy) installation folder :ul
|
||||
|
||||
If the install.py script does not allow you to copy files into system
|
||||
directories, prefix the python command with "sudo". If you do this,
|
||||
make sure that the Python that root runs is the same as the Python you
|
||||
run. E.g. you may need to do something like
|
||||
|
||||
% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
|
||||
|
||||
You can also invoke install.py from the make command in the src
|
||||
directory as
|
||||
|
||||
% make install-python :pre
|
||||
|
||||
In this mode you cannot append optional arguments. Again, you may
|
||||
need to prefix this with "sudo". In this mode you cannot control
|
||||
which Python is invoked by root.
|
||||
If you use a legacy installation folder, you will need to set your
|
||||
PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment
|
||||
variables accordingly, as described above.
|
||||
|
||||
Note that if you want Python to be able to load different versions of
|
||||
the LAMMPS shared library (see "this section"_Python_shlib.html), you will
|
||||
|
|
|
|||
|
|
@ -13,11 +13,11 @@ Overview of Python and LAMMPS :h3
|
|||
LAMMPS can work together with Python in three ways. First, Python can
|
||||
wrap LAMMPS through the its "library interface"_Howto_library.html, so
|
||||
that a Python script can create one or more instances of LAMMPS and
|
||||
launch one or more simulations. In Python lingo, this is "extending"
|
||||
Python with LAMMPS.
|
||||
launch one or more simulations. In Python lingo, this is called
|
||||
"extending" Python with a LAMMPS module.
|
||||
|
||||
Second, a lower-level Python interface can be used indirectly through
|
||||
provided PyLammps and IPyLammps wrapper classes, written in Python.
|
||||
the provided PyLammps and IPyLammps wrapper classes, written in Python.
|
||||
These wrappers try to simplify the usage of LAMMPS in Python by
|
||||
providing an object-based interface to common LAMMPS functionality.
|
||||
They also reduces the amount of code necessary to parameterize LAMMPS
|
||||
|
|
@ -25,11 +25,12 @@ scripts through Python and make variables and computes directly
|
|||
accessible.
|
||||
|
||||
Third, LAMMPS can use the Python interpreter, so that a LAMMPS
|
||||
input script can invoke Python code directly, and pass information
|
||||
back-and-forth between the input script and Python functions you
|
||||
write. This Python code can also callback to LAMMPS to query or change
|
||||
its attributes. In Python lingo, this is "embedding" Python in
|
||||
LAMMPS. When used in this mode, Python can perform operations that
|
||||
the simple LAMMPS input script syntax cannot.
|
||||
input script or styles can invoke Python code directly, and pass
|
||||
information back-and-forth between the input script and Python
|
||||
functions you write. This Python code can also callback to LAMMPS
|
||||
to query or change its attributes through the LAMMPS Python module
|
||||
mentioned above. In Python lingo, this is "embedding" Python in
|
||||
LAMMPS. When used in this mode, Python can perform script operations
|
||||
that the simple LAMMPS input script syntax can not.
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -53,6 +53,7 @@ Commands :h1
|
|||
include
|
||||
info
|
||||
jump
|
||||
kim_query
|
||||
kspace_modify
|
||||
kspace_style
|
||||
label
|
||||
|
|
@ -61,6 +62,7 @@ Commands :h1
|
|||
mass
|
||||
message
|
||||
min_modify
|
||||
min_spin
|
||||
min_style
|
||||
minimize
|
||||
molecule
|
||||
|
|
|
|||
|
|
@ -54,9 +54,10 @@ local quantities have the word "local" in their style,
|
|||
e.g. {bond/local}. Styles with neither "atom" or "local" in their
|
||||
style produce global quantities.
|
||||
|
||||
Note that a single compute produces either global or per-atom or local
|
||||
quantities, but never more than one of these (with only a few
|
||||
exceptions, as documented by individual compute commands).
|
||||
Note that a single compute can produce either global or per-atom or
|
||||
local quantities, but not both global and per-atom. It can produce
|
||||
local quantities in tandem with global or per-atom quantities. The
|
||||
compute doc page will explain.
|
||||
|
||||
Global, per-atom, and local quantities each come in three kinds: a
|
||||
single scalar value, a vector of values, or a 2d array of values. The
|
||||
|
|
|
|||
|
|
@ -83,8 +83,10 @@ not in the specified fix group. Local quantities are calculated by
|
|||
each processor based on the atoms it owns, but there may be zero or
|
||||
more per atoms.
|
||||
|
||||
Note that a single fix may produces either global or per-atom or local
|
||||
quantities (or none at all), but never more than one of these.
|
||||
Note that a single fix can produce either global or per-atom or local
|
||||
quantities (or none at all), but not both global and per-atom. It can
|
||||
produce local quantities in tandem with global or per-atom quantities.
|
||||
The fix doc page will explain.
|
||||
|
||||
Global, per-atom, and local quantities each come in three kinds: a
|
||||
single scalar value, a vector of values, or a 2d array of values. The
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
|
|||
{mode} arg = {scalar} or {vector}
|
||||
scalar = all input values are scalars
|
||||
vector = all input values are vectors
|
||||
{kind} arg = {global} or {peratom} or {local}
|
||||
{file} arg = filename
|
||||
filename = name of file to output histogram(s) to
|
||||
{ave} args = {one} or {running} or {window}
|
||||
|
|
@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities. Inputs of
|
|||
different kinds (e.g. global and per-atom) cannot be mixed. Atom
|
||||
attributes are per-atom vector values. See the doc page for
|
||||
individual "compute" and "fix" commands to see what kinds of
|
||||
quantities they generate.
|
||||
quantities they generate. See the optional {kind} keyword below for
|
||||
how to force the fix ave/histo command to disambiguate if necessary.
|
||||
|
||||
Note that the output of this command is a single histogram for all
|
||||
input values combined together, not one histogram per input value.
|
||||
|
|
@ -231,6 +233,14 @@ 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 set if a compute or fix produces
|
||||
more than one kind of output (global, per-atom, local). If this is
|
||||
not the case, then LAMMPS will determine what kind of input is
|
||||
provided and whether all the input arguments are consistent. If a
|
||||
compute or fix produces more than one kind of output, the {kind}
|
||||
keyword should be used to specify which output will be used. The
|
||||
remaining input arguments must still be consistent.
|
||||
|
||||
The {beyond} keyword determines how input values that fall outside the
|
||||
{lo} to {hi} bounds are treated. Values such that {lo} <= value <=
|
||||
{hi} are assigned to one bin. Values on a bin boundary are assigned
|
||||
|
|
@ -240,7 +250,7 @@ If {beyond} is set to {end} then values < {lo} are counted in the
|
|||
first bin and values > {hi} are counted in the last bin. If {beyond}
|
||||
is set to {extend} then two extra bins are created, so that there are
|
||||
Nbins+2 total bins. Values < {lo} are counted in the first bin and
|
||||
values > {hi} are counted in the last bin (Nbins+1). Values between
|
||||
values > {hi} are counted in the last bin (Nbins+2). Values between
|
||||
{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1. The
|
||||
"coordinate" stored and printed for these two extra bins is {lo} and
|
||||
{hi}.
|
||||
|
|
@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
|
|||
|
||||
[Default:] none
|
||||
|
||||
The option defaults are mode = scalar, ave = one, start = 0, no file
|
||||
output, beyond = ignore, and title 1,2,3 = strings as described above.
|
||||
The option defaults are mode = scalar, kind = figured out from input
|
||||
arguments, ave = one, start = 0, no file output, beyond = ignore, and
|
||||
title 1,2,3 = strings as described above.
|
||||
|
|
|
|||
|
|
@ -102,7 +102,7 @@ Bi = exp(beta * Vij(max)) :pre
|
|||
where beta = 1/kTequil, and {Tequil} is the temperature of the system
|
||||
and an argument to this fix. Note that Bi >= 1 at every step.
|
||||
|
||||
NOTE: To run GHD, the input script must also use the "fix
|
||||
NOTE: To run a GHD simulation, the input script must also use the "fix
|
||||
langevin"_fix_langevin.html command to thermostat the atoms at the
|
||||
same {Tequil} as specified by this fix, so that the system is running
|
||||
constant-temperature (NVT) dynamics. LAMMPS does not check that this
|
||||
|
|
@ -166,9 +166,9 @@ correctly. There will just be fewer events because the hyper time
|
|||
|
||||
NOTE: If you have no physical intuition as to the smallest barrier
|
||||
height in your system, a reasonable strategy to determine the largest
|
||||
{Vmax} you can use for an LHD model, is to run a sequence of
|
||||
{Vmax} you can use for a GHD model, is to run a sequence of
|
||||
simulations with smaller and smaller {Vmax} values, until the event
|
||||
rate does not change.
|
||||
rate does not change (as a function of hyper time).
|
||||
|
||||
The {Tequil} argument is the temperature at which the system is
|
||||
simulated; see the comment above about the "fix
|
||||
|
|
@ -177,7 +177,8 @@ beta term in the exponential factor that determines how much boost is
|
|||
achieved as a function of the bias potential.
|
||||
|
||||
In general, the lower the value of {Tequil} and the higher the value
|
||||
of {Vmax}, the more boost will be achievable by the GHD algorithm.
|
||||
of {Vmax}, the more time boost will be achievable by the GHD
|
||||
algorithm.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -190,41 +191,43 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
|
|||
fix to add the energy of the bias potential to the the system's
|
||||
potential energy as part of "thermodynamic output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar and global vector of length 11, which
|
||||
This fix computes a global scalar and global vector of length 12, which
|
||||
can be accessed by various "output commands"_Howto_output.html. The
|
||||
scalar is the magnitude of the bias potential (energy units) applied on
|
||||
the current timestep. The vector stores the following quantities:
|
||||
|
||||
1 = boost factor on this step (unitless)
|
||||
2 = max strain Eij of any bond on this step (unitless)
|
||||
2 = max strain Eij of any bond on this step (absolute value, unitless)
|
||||
3 = ID of first atom in the max-strain bond
|
||||
4 = ID of second atom in the max-strain bond
|
||||
5 = average # of bonds/atom on this step :ul
|
||||
|
||||
6 = fraction of timesteps with bias = 0.0 during this run
|
||||
7 = max drift distance of any atom during this run (distance units)
|
||||
8 = max bond length during this run (distance units) :ul
|
||||
6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
|
||||
7 = fraction of timesteps where the biased bond has negative strain during this run
|
||||
8 = max drift distance of any atom during this run (distance units)
|
||||
9 = max bond length during this run (distance units) :ul
|
||||
|
||||
9 = cumulative hyper time since fix was defined (time units)
|
||||
10 = cumulative count of event timesteps since fix was defined
|
||||
11 = cumulative count of atoms in events since fix was defined :ul
|
||||
10 = cumulative hyper time since fix was defined (time units)
|
||||
11 = cumulative count of event timesteps since fix was defined
|
||||
12 = cumulative count of atoms in events since fix was defined :ul
|
||||
|
||||
The first 5 quantities are for the current timestep. Quantities 6-8
|
||||
are for the current hyper run. Quantities 9-11 are cumulative across
|
||||
multiple runs (since the fix was defined in the input script).
|
||||
The first 5 quantities are for the current timestep. Quantities 6-9
|
||||
are for the current hyper run. They are reset each time a new hyper
|
||||
run is performed. Quantities 19-12 are cumulative across multiple
|
||||
runs (since the point in the input script the fix was defined).
|
||||
|
||||
For value 7, drift is the distance an atom moves between timesteps
|
||||
when the bond list is reset, i.e. between events. Atoms involved in
|
||||
an event will typically move the greatest distance since others are
|
||||
typically oscillating around their lattice site.
|
||||
For value 8, drift is the distance an atom moves between two quenched
|
||||
states when the second quench determines an event has occurred. Atoms
|
||||
involved in an event will typically move the greatest distance since
|
||||
others typically remain near their original quenched position.
|
||||
|
||||
For value 10, events are checked for by the "hyper"_hyper.html command
|
||||
For value 11, events are checked for by the "hyper"_hyper.html command
|
||||
once every {Nevent} timesteps. This value is the count of those
|
||||
timesteps on which one (or more) events was detected. It is NOT the
|
||||
number of distinct events, since more than one event may occur in the
|
||||
same {Nevent} time window.
|
||||
|
||||
For value 11, each time the "hyper"_hyper.html command checks for an
|
||||
For value 12, each time the "hyper"_hyper.html command checks for an
|
||||
event, it invokes a compute to flag zero or more atoms as
|
||||
participating in one or more events. E.g. atoms that have displaced
|
||||
more than some distance from the previous quench state. Value 11 is
|
||||
|
|
|
|||
|
|
@ -22,10 +22,9 @@ Dcut = minimum distance between boosted bonds (distance units) :l
|
|||
alpha = boostostat relaxation time (time units) :l
|
||||
Btarget = desired time boost factor (unitless) :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {lost} or {check/bias} or {check/coeff}
|
||||
{lostbond} value = error/warn/ignore
|
||||
{check/bias} values = Nevery error/warn/ignore
|
||||
{check/coeff} values = Nevery error/warn/ignore :pre
|
||||
keyword = {check/ghost} or {check/bias} :l
|
||||
{check/ghost} values = none
|
||||
{check/bias} values = Nevery error/warn/ignore :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -65,8 +64,8 @@ To understand this description, you should first read the description
|
|||
of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
|
||||
doc page. This description of LHD builds on the GHD description.
|
||||
|
||||
The definition of bonds, Eij, and Emax are the same for GHD and LHD.
|
||||
The formulas for Vij(max) and Fij(max) are also the same except for a
|
||||
The definition of bonds and Eij are the same for GHD and LHD. The
|
||||
formulas for Vij(max) and Fij(max) are also the same except for a
|
||||
pre-factor Cij, explained below.
|
||||
|
||||
The bias energy Vij applied to a bond IJ with maximum strain is
|
||||
|
|
@ -117,11 +116,11 @@ where Vkl(max) is the bias energy of the maxstrain bond KL within bond
|
|||
IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
|
||||
of the system and an argument to this fix.
|
||||
|
||||
NOTE: To run LHD, the input script must also use the "fix
|
||||
langevin"_fix_langevin.html command to thermostat the atoms at the
|
||||
same {Tequil} as specified by this fix, so that the system is running
|
||||
constant-temperature (NVT) dynamics. LAMMPS does not check that this
|
||||
is done.
|
||||
NOTE: To run an LHD simulation, the input script must also use the
|
||||
"fix langevin"_fix_langevin.html command to thermostat the atoms at
|
||||
the same {Tequil} as specified by this fix, so that the system is
|
||||
running constant-temperature (NVT) dynamics. LAMMPS does not check
|
||||
that this is done.
|
||||
|
||||
Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
|
||||
otherwise it is not. But regardless, the boost factor Bij can be
|
||||
|
|
@ -216,20 +215,20 @@ each pair. E.g. something like 2x the cutoff of the interatomic
|
|||
potential. In practice a {Dcut} value of ~10 Angstroms seems to work
|
||||
well for many solid-state systems.
|
||||
|
||||
NOTE: You must also insure that ghost atom communication is performed
|
||||
for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
|
||||
distance one or more atoms move (between quenched states) to be
|
||||
considered an "event". It is an argument to the "compute
|
||||
event/displace" command used to detect events. By default the ghost
|
||||
communication distance is set by the pair_style cutoff, which will
|
||||
typically be < {Dcut}. The "comm_modify cutoff"_comm_modify.html
|
||||
command can be used to set the ghost cutoff explicitly, e.g.
|
||||
NOTE: You should insure that ghost atom communication is performed for
|
||||
a distance of at least {Dcut} + {cutevent} = the distance one or more
|
||||
atoms move (between quenched states) to be considered an "event". It
|
||||
is an argument to the "compute event/displace" command used to detect
|
||||
events. By default the ghost communication distance is set by the
|
||||
pair_style cutoff, which will typically be < {Dcut}. The "comm_modify
|
||||
cutoff"_comm_modify.html command should be used to override the ghost
|
||||
cutoff explicitly, e.g.
|
||||
|
||||
comm_modify cutoff 12.0 :pre
|
||||
|
||||
This fix does not know the {cutevent} parameter, but uses half the
|
||||
bond length as an estimate to warn if the ghost cutoff is not long
|
||||
enough.
|
||||
Note that this fix does not know the {cutevent} parameter, but uses
|
||||
half the {cutbond} parameter as an estimate to warn if the ghost
|
||||
cutoff is not long enough.
|
||||
|
||||
As described above the {alpha} argument is a pre-factor in the
|
||||
boostostat update equation for each bond's Cij prefactor. {Alpha} is
|
||||
|
|
@ -269,7 +268,30 @@ NOTE: If you have no physical intuition as to the smallest barrier
|
|||
height in your system, a reasonable strategy to determine the largest
|
||||
{Btarget} you can use for an LHD model, is to run a sequence of
|
||||
simulations with smaller and smaller {Btarget} values, until the event
|
||||
rate does not change.
|
||||
rate does not change (as a function of hyper time).
|
||||
|
||||
:line
|
||||
|
||||
Here is additional information on the optional keywords for this fix.
|
||||
|
||||
The {check/ghost} keyword turns on extra computation each timestep to
|
||||
compute statistics about ghost atoms used to determine which bonds to
|
||||
bias. The output of these stats are the vector values 14 and 15,
|
||||
described below. If this keyword is not enabled, the output
|
||||
of the stats will be zero.
|
||||
|
||||
The {check/bias} keyword turns on extra computation and communication
|
||||
to check if any biased bonds are closer than {Dcut} to each other,
|
||||
which should not be the case if LHD is operating correctly. Thus it
|
||||
is a debugging check. The {Nevery} setting determines how often the
|
||||
check is made. The {error}, {warn}, or {ignore} setting determines
|
||||
what is done if the count of too-close bonds is not zero. Either the
|
||||
code will exit, or issue a warning, or silently tally the count. The
|
||||
count can be output as vector value 17, as described below. If this
|
||||
keyword is not enabled, the output of that statistic will be 0.
|
||||
|
||||
Note that both of these computations are costly, hence they are only
|
||||
enabled by these keywords.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -282,95 +304,120 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
|
|||
fix to add the energy of the bias potential to the the system's
|
||||
potential energy as part of "thermodynamic output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar and global vector of length 23,
|
||||
which can be accessed by various "output
|
||||
commands"_Howto_output.html. The scalar is the magnitude of
|
||||
the bias potential (energy units) applied on the current timestep,
|
||||
summed over all biased bonds. The vector stores the following
|
||||
quantities:
|
||||
This fix computes a global scalar and global vector of length 21,
|
||||
which can be accessed by various "output commands"_Howto_output.html.
|
||||
The scalar is the magnitude of the bias potential (energy units)
|
||||
applied on the current timestep, summed over all biased bonds. The
|
||||
vector stores the following quantities:
|
||||
|
||||
1 = # of biased bonds on this step
|
||||
2 = max strain Eij of any bond on this step (unitless)
|
||||
3 = average bias potential for all biased bonds on this step (energy units)
|
||||
2 = max strain Eij of any bond on this step (absolute value, unitless)
|
||||
3 = average bias coeff for all bonds on this step (unitless)
|
||||
4 = average # of bonds/atom on this step
|
||||
5 = average neighbor bonds/bond on this step within {Dcut} :ul
|
||||
|
||||
6 = fraction of steps and bonds with no bias during this run
|
||||
7 = max drift distance of any atom during this run (distance units)
|
||||
8 = max bond length during this run (distance units)
|
||||
9 = average # of biased bonds/step during this run
|
||||
10 = average bias potential for all biased bonds during this run (energy units)
|
||||
11 = max bias potential for any biased bond during this run (energy units)
|
||||
12 = min bias potential for any biased bond during this run (energy units)
|
||||
13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
|
||||
14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
|
||||
15 = count of ghost neighbor atoms not found on reneighbor steps during this run
|
||||
16 = count of lost bond partners during this run
|
||||
17 = average bias coeff for lost bond partners during this run
|
||||
18 = count of bias overlaps found during this run
|
||||
19 = count of non-matching bias coefficients found during this run :ul
|
||||
6 = max bond length during this run (distance units)
|
||||
7 = average # of biased bonds/step during this run
|
||||
8 = fraction of biased bonds with no bias during this run
|
||||
9 = fraction of biased bonds with negative strain during this run
|
||||
10 = average bias coeff for all bonds during this run (unitless)
|
||||
11 = min bias coeff for any bond during this run (unitless)
|
||||
12 = max bias coeff for any bond during this run (unitless)
|
||||
|
||||
20 = cumulative hyper time since fix created (time units)
|
||||
21 = cumulative count of event timesteps since fix created
|
||||
22 = cumulative count of atoms in events since fix created
|
||||
23 = cumulative # of new bonds since fix created :ul
|
||||
13 = max drift distance of any bond atom during this run (distance units)
|
||||
14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
|
||||
15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
|
||||
16 = count of ghost atoms that could not be found on reneighbor steps during this run
|
||||
17 = count of bias overlaps (< Dcut) found during this run
|
||||
|
||||
18 = cumulative hyper time since fix created (time units)
|
||||
19 = cumulative count of event timesteps since fix created
|
||||
20 = cumulative count of atoms in events since fix created
|
||||
21 = cumulative # of new bonds formed since fix created :ul
|
||||
|
||||
The first quantities (1-5) are for the current timestep. Quantities
|
||||
6-19 are for the current hyper run. They are reset each time a new
|
||||
hyper run is performed. Quantities 20-23 are cumulative across
|
||||
multiple runs (since the fix was defined in the input script).
|
||||
6-17 are for the current hyper run. They are reset each time a new
|
||||
hyper run is performed. Quantities 18-21 are cumulative across
|
||||
multiple runs (since the point in the input script the fix was
|
||||
defined).
|
||||
|
||||
For value 6, the numerator is a count of all biased bonds on every
|
||||
For value 8, the numerator is a count of all biased bonds on each
|
||||
timestep whose bias energy = 0.0 due to Eij >= {qfactor}. The
|
||||
denominator is the count of all biased bonds on all timesteps.
|
||||
|
||||
For value 7, drift is the distance an atom moves between timesteps
|
||||
when the bond list is reset, i.e. between events. Atoms involved in
|
||||
an event will typically move the greatest distance since others are
|
||||
typically oscillating around their lattice site.
|
||||
For value 9, the numerator is a count of all biased bonds on each
|
||||
timestep with negative strain. The denominator is the count of all
|
||||
biased bonds on all timesteps.
|
||||
|
||||
For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
|
||||
of any bond it is part of, and it is checked for ghost atoms within
|
||||
the bond neighbor cutoff.
|
||||
Values 13-17 are mostly useful for debugging and diagnostic purposes.
|
||||
|
||||
Values 15-19 are mostly useful for debugging and diagnostic purposes.
|
||||
For value 13, drift is the distance an atom moves between two quenched
|
||||
states when the second quench determines an event has occurred. Atoms
|
||||
involved in an event will typically move the greatest distance since
|
||||
others typically remain near their original quenched position.
|
||||
|
||||
For values 15-17, it is possible that a ghost atom owned by another
|
||||
processor will move far enough (e.g. as part of an event-in-progress)
|
||||
that it will no longer be within the communication cutoff distance for
|
||||
acquiring ghost atoms. Likewise it may be a ghost atom bond partner
|
||||
that cannot be found because it has moved too far. These values count
|
||||
those occurrences. Because they typically involve atoms that are part
|
||||
of events, they do not usually indicate bad dynamics. Value 16 is the
|
||||
average bias coefficient for bonds where a partner atom was lost.
|
||||
For values 14-16, neighbor atoms in the full neighbor list with cutoff
|
||||
{Dcut} may be ghost atoms outside a processor's sub-box. Before the
|
||||
next event occurs they may move further than {Dcut} away from the
|
||||
sub-box boundary. Value 14 is the furthest (from the sub-box) any
|
||||
ghost atom in the neighbor list with maxstrain < {qfactor} was
|
||||
accessed during the run. Value 15 is the same except that the ghost
|
||||
atom's maxstrain may be >= {qfactor}, which may mean it is about to
|
||||
participate in an event. Value 16 is a count of how many ghost atoms
|
||||
could not be found on reneighbor steps, presumably because they moved
|
||||
too far away due to their participation in an event (which will likely
|
||||
be detected at the next quench).
|
||||
|
||||
For value 18, no two bonds should be biased if they are within a
|
||||
Typical values for 14 and 15 should be slightly larger than {Dcut},
|
||||
which accounts for ghost atoms initially at a {Dcut} distance moving
|
||||
thermally before the next event takes place.
|
||||
|
||||
Note that for values 14 and 15 to be computed, the optional keyword
|
||||
{check/ghost} must be specified. Otherwise these values will be zero.
|
||||
This is because computing them incurs overhead, so the values are only
|
||||
computed if requested.
|
||||
|
||||
Value 16 should be zero or small. As explained above a small count
|
||||
likely means some ghost atoms were participating in their own events
|
||||
and moved a longer distance. If the value is large, it likely means
|
||||
the communication cutoff for ghosts is too close to {Dcut} leading to
|
||||
many not-found ghost atoms before the next event. This may lead to a
|
||||
reduced number of bonds being selected for biasing, since the code
|
||||
assumes those atoms are part of highly strained bonds. As explained
|
||||
above, the "comm_modify cutoff"_comm_modify.html command can be used
|
||||
to set a longer cutoff.
|
||||
|
||||
For value 17, no two bonds should be biased if they are within a
|
||||
{Dcut} distance of each other. This value should be zero, indicating
|
||||
that no pair of bonds "overlap", meaning they are closer than {Dcut}
|
||||
from each other.
|
||||
that no pair of biased bonds are closer than {Dcut} from each other.
|
||||
|
||||
For value 19, the same bias coefficient is stored by both atoms in an
|
||||
IJ bond. This value should be zero, indicating that for all bonds,
|
||||
each atom in the bond stores the a bias coefficient with the same
|
||||
value.
|
||||
Note that for values 17 to be computed, the optional keyword
|
||||
{check/bias} must be specified and it determines how often this check
|
||||
is performed. This is because performing the check incurs overhead,
|
||||
so if only computed as often as requested.
|
||||
|
||||
Value 20 is simply the specified {boost} factor times the number of
|
||||
timestep times the timestep size.
|
||||
The result at the end of the run is the cumulative total from every
|
||||
timestep the check was made. Note that the value is a count of atoms
|
||||
in bonds which found other atoms in bonds too close, so it is almost
|
||||
always an over-count of the number of too-close bonds.
|
||||
|
||||
For value 21, events are checked for by the "hyper"_hyper.html command
|
||||
Value 18 is simply the specified {boost} factor times the number of
|
||||
timesteps times the timestep size.
|
||||
|
||||
For value 19, events are checked for by the "hyper"_hyper.html command
|
||||
once every {Nevent} timesteps. This value is the count of those
|
||||
timesteps on which one (or more) events was detected. It is NOT the
|
||||
number of distinct events, since more than one event may occur in the
|
||||
same {Nevent} time window.
|
||||
|
||||
For value 22, each time the "hyper"_hyper.html command checks for an
|
||||
For value 20, each time the "hyper"_hyper.html command checks for an
|
||||
event, it invokes a compute to flag zero or more atoms as
|
||||
participating in one or more events. E.g. atoms that have displaced
|
||||
more than some distance from the previous quench state. Value 22 is
|
||||
more than some distance from the previous quench state. Value 20 is
|
||||
the cumulative count of the number of atoms participating in any of
|
||||
the events that were found.
|
||||
|
||||
Value 23 tallies the number of new bonds created by the bond reset
|
||||
Value 21 tallies the number of new bonds created by the bond reset
|
||||
operation. Bonds between a specific I,J pair of atoms may persist for
|
||||
the entire hyperdynamics simulation if neither I or J are involved in
|
||||
an event.
|
||||
|
|
@ -378,6 +425,16 @@ an event.
|
|||
The scalar and vector values calculated by this fix are all
|
||||
"intensive".
|
||||
|
||||
This fix also computes a local vector of length the number of bonds
|
||||
currently in the system. The value for each bond is its Cij prefactor
|
||||
(bias coefficient). These values can be can be accessed by various
|
||||
"output commands"_Howto_output.html. A particularly useful one is the
|
||||
"fix ave/histo"_fix_ave_histo.html command which can be used to
|
||||
histogram the Cij values to see if they are distributed reasonably
|
||||
close to 1.0, which indicates a good choice of {Vmax}.
|
||||
|
||||
The local values calculated by this fix are unitless.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
|
@ -392,7 +449,9 @@ doc page for more info.
|
|||
|
||||
"hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
|
||||
|
||||
[Default:] None
|
||||
[Default:]
|
||||
|
||||
The check/ghost and check/bias keywords are not enabled by default.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,45 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
kim_query command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
kim_query variable query_function web_query_flags :pre
|
||||
|
||||
variable = name of a (string style) variable where the result of the query is stored
|
||||
query_function = name of the OpenKIM web API query function to be used
|
||||
web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
|
||||
prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The kim_query command allows to retrieve properties from the OpenKIM
|
||||
through a web query. The result is stored in a string style
|
||||
"variable"_variable.html, the name of which must be given as the first
|
||||
argument of the kim_query command. The second required argument is the
|
||||
name of the actual query function (e.g. {get_test_result}). All following
|
||||
arguments are parameters handed over to the web query in the format
|
||||
{keyword=value}. This list of supported keywords and the type of how
|
||||
the value has to be encoded depends on the query function used.
|
||||
For more details on this, please refer to the OpenKIM homepage.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the KIM package. It is only enabled if
|
||||
LAMMPS was built with that package. Furthermore, its correct
|
||||
functioning depends on compiling LAMMPS with libcurl support.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style kim"_pair_kim.html, "variable"_variable.html
|
||||
|
|
@ -167,6 +167,7 @@ if.html
|
|||
include.html
|
||||
info.html
|
||||
jump.html
|
||||
kim_query.html
|
||||
label.html
|
||||
lattice.html
|
||||
log.html
|
||||
|
|
@ -174,6 +175,7 @@ mass.html
|
|||
message.html
|
||||
min_modify.html
|
||||
min_style.html
|
||||
min_spin.html
|
||||
minimize.html
|
||||
molecule.html
|
||||
neb.html
|
||||
|
|
|
|||
|
|
@ -13,11 +13,15 @@ min_modify command :h3
|
|||
min_modify keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be listed :ulb,l
|
||||
keyword = {dmax} or {line}
|
||||
keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
|
||||
{dmax} value = max
|
||||
max = maximum distance for line search to move (distance units)
|
||||
{line} value = {backtrack} or {quadratic} or {forcezero}
|
||||
backtrack,quadratic,forcezero = style of linesearch to use :pre
|
||||
backtrack,quadratic,forcezero = style of linesearch to use
|
||||
{alpha_damp} value = damping
|
||||
damping = fictitious Gilbert damping for spin minimization (adim)
|
||||
{discrete_factor} value = factor
|
||||
factor = discretization factor for adaptive spin timestep (adim) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -65,6 +69,17 @@ difference of two large values (energy before and energy after) and
|
|||
that difference may be smaller than machine epsilon even if atoms
|
||||
could move in the gradient direction to reduce forces further.
|
||||
|
||||
Keywords {alpha_damp} and {discrete_factor} only make sense when
|
||||
a "min_spin"_min_spin.html command is declared.
|
||||
Keyword {alpha_damp} defines an analog of a magnetic Gilbert
|
||||
damping. It defines a relaxation rate toward an equilibrium for
|
||||
a given magnetic system.
|
||||
Keyword {discrete_factor} defines a discretization factor for the
|
||||
adaptive timestep used in the {spin} minimization.
|
||||
See "min_spin"_min_spin.html for more information about those
|
||||
quantities.
|
||||
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -0,0 +1,65 @@
|
|||
"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
:line
|
||||
|
||||
min_style spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
min_style spin :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
min_style spin :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a minimization algorithm to use when a "minimize"_minimize.html
|
||||
command is performed.
|
||||
|
||||
Style {spin} defines a damped spin dynamics with an adaptive
|
||||
timestep, according to:
|
||||
|
||||
:c,image(Eqs/min_spin_damping.jpg)
|
||||
|
||||
with lambda a damping coefficient (similar to a Gilbert
|
||||
damping).
|
||||
Lambda can be defined by setting the {alpha_damp} keyword with the
|
||||
"min_modify"_min_modify.html command.
|
||||
|
||||
The minimization procedure solves this equation using an
|
||||
adaptive timestep. The value of this timestep is defined
|
||||
by the largest precession frequency that has to be solved in the
|
||||
system:
|
||||
|
||||
:c,image(Eqs/min_spin_timestep.jpg)
|
||||
|
||||
with {|omega|_{max}} the norm of the largest precession frequency
|
||||
in the system (across all processes, and across all replicas if a
|
||||
spin/neb calculation is performed).
|
||||
|
||||
Kappa defines a discretization factor {discrete_factor} for the
|
||||
definition of this timestep.
|
||||
{discrete_factor} can be defined with the "min_modify"_min_modify.html
|
||||
command.
|
||||
|
||||
NOTE: The {spin} style replaces the force tolerance by a torque
|
||||
tolerance. See "minimize"_minimize.html for more explanation.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This minimization procedure is only applied to spin degrees of
|
||||
freedom for a frozen lattice configuration.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"min_style"_min_style.html, "minimize"_minimize.html,
|
||||
"min_modify"_min_modify.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
|
||||
10.0.
|
||||
|
|
@ -11,11 +11,12 @@ min_style command :h3
|
|||
|
||||
min_style style :pre
|
||||
|
||||
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
|
||||
style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
min_style cg
|
||||
min_style spin
|
||||
min_style fire :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -61,6 +62,10 @@ the velocity non-parallel to the current force vector. The velocity
|
|||
of each atom is initialized to 0.0 by this style, at the beginning of
|
||||
a minimization.
|
||||
|
||||
Style {spin} is a damped spin dynamics with an adaptive
|
||||
timestep.
|
||||
See the "min/spin"_min_spin.html doc page for more information.
|
||||
|
||||
Either the {quickmin} and {fire} styles are useful in the context of
|
||||
nudged elastic band (NEB) calculations via the "neb"_neb.html command.
|
||||
|
||||
|
|
|
|||
|
|
@ -103,6 +103,13 @@ the line search fails because the step distance backtracks to 0.0
|
|||
the number of outer iterations or timesteps exceeds {maxiter}
|
||||
the number of total force evaluations exceeds {maxeval} :ul
|
||||
|
||||
NOTE: the "minimization style"_min_style.html {spin} replaces
|
||||
the force tolerance {ftol} by a torque tolerance.
|
||||
The minimization procedure stops if the 2-norm (length) of the
|
||||
global torque vector (defined as the cross product between the
|
||||
spins and their precession vectors omega) is less than {ftol},
|
||||
or if any of the other criteria are met.
|
||||
|
||||
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
|
||||
a general criterion for exiting a minimization, that is a calculation
|
||||
performed on the state of the current system, as defined by an
|
||||
|
|
|
|||
|
|
@ -42,12 +42,9 @@ section of the "Packages details"_Packages_details.html doc page has
|
|||
instructions on how to do this with a simple make command, when
|
||||
building LAMMPS.
|
||||
|
||||
See the examples/kim dir for an input script that uses a KIM model (potential)
|
||||
for Lennard-Jones. Note, for this example input script, the example models
|
||||
shipped with with kim-api package must be installed. See the "Build
|
||||
package"_Build_package.html section and the ./lib/kim/README for details
|
||||
on how to build LAMMSPS with the kim-api and how to install the example models.
|
||||
|
||||
See the examples/kim dir for an input script that uses a KIM model
|
||||
(potential) for Lennard-Jones.
|
||||
|
||||
:line
|
||||
|
||||
The argument {model} is the name of the KIM model for a specific
|
||||
|
|
|
|||
|
|
@ -252,6 +252,7 @@ Boresch
|
|||
Botero
|
||||
Botu
|
||||
Bouguet
|
||||
Bourne
|
||||
boxcolor
|
||||
bp
|
||||
bpls
|
||||
|
|
@ -634,6 +635,7 @@ dVx
|
|||
dW
|
||||
dx
|
||||
dy
|
||||
dylib
|
||||
dyn
|
||||
dyne
|
||||
dynes
|
||||
|
|
@ -1308,6 +1310,7 @@ Kondor
|
|||
konglt
|
||||
Koning
|
||||
Kooser
|
||||
Korn
|
||||
Koskinen
|
||||
Koster
|
||||
Kosztin
|
||||
|
|
@ -1392,6 +1395,7 @@ libAtoms
|
|||
libawpmd
|
||||
libch
|
||||
libcolvars
|
||||
libcurl
|
||||
libdir
|
||||
libdl
|
||||
libfftw
|
||||
|
|
|
|||
|
|
@ -0,0 +1,55 @@
|
|||
# bfo in a 3d periodic box
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice sc 3.96
|
||||
region box block 0.0 34.0 0.0 34.0 0.0 1.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 1.0
|
||||
set group all spin/random 11 2.50
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
|
||||
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
|
||||
#pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
|
||||
pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
|
||||
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
|
||||
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 10.0
|
||||
minimize 1.0e-10 0.0 1000 100
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
# bcc iron in a 3d periodic box
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
region box block 0.0 4.0 0.0 4.0 0.0 4.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
set group all spin/random 31 2.2
|
||||
#set group all spin 2.2 1.0 1.0 -1.0
|
||||
|
||||
pair_style spin/exchange 3.5
|
||||
pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
|
||||
fix 1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 10.0
|
||||
minimize 1.0e-10 1.0e-10 100000 1000
|
||||
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|
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|
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|
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|
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|
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|
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|
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|
Before Width: | Height: | Size: 69 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 70 KiB |
|
|
@ -12,6 +12,8 @@ variable cutevent index 1.1
|
|||
variable steps index 100000
|
||||
variable nevent index 1000
|
||||
variable zoom index 1.8
|
||||
variable seed index 826626413
|
||||
variable tol index 1.0e-15
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
|
@ -45,7 +47,7 @@ neighbor 0.5 bin
|
|||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 mobile nve
|
||||
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 858872873 zero yes
|
||||
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
|
||||
|
||||
timestep 0.005
|
||||
|
||||
|
|
@ -92,4 +94,4 @@ dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
|
|||
|
||||
# run
|
||||
|
||||
hyper ${steps} ${nevent} HG event min 1.0e-6 1.0e-6 100 100 dump 1
|
||||
hyper ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1
|
||||
|
|
|
|||
|
|
@ -107,6 +107,12 @@ dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
|
|||
zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
|
||||
dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
|
||||
|
||||
# test of histogramming and dump output of bias coeffs
|
||||
|
||||
#fix histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL &
|
||||
# mode vector kind local file tmp.histo
|
||||
#dump 2 all local 1000 tmp.local f_HL
|
||||
|
||||
# run
|
||||
|
||||
hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
|
||||
|
|
|
|||
|
Before Width: | Height: | Size: 482 KiB After Width: | Height: | Size: 482 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 479 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 479 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 477 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 479 KiB |
File diff suppressed because it is too large
Load Diff
|
|
@ -1,993 +0,0 @@
|
|||
LAMMPS (10 Oct 2018)
|
||||
# 3d EAM surface for local HD
|
||||
|
||||
# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
|
||||
# hop event on (100) surface is same distance
|
||||
# exchange event is 2 atoms moving same distance
|
||||
|
||||
variable Tequil index 400.0
|
||||
variable Vmax index 0.4
|
||||
variable qfactor index 0.3
|
||||
variable cutbond index 3.2
|
||||
variable Dcut index 10.0
|
||||
variable cutevent index 1.1
|
||||
variable alpha index 200.0
|
||||
variable boost index 4000.0
|
||||
variable ghostcut index 12.0
|
||||
variable steps index 1500
|
||||
variable nevent index 100
|
||||
variable nx index 8
|
||||
variable ny index 8
|
||||
variable zoom index 1.8
|
||||
variable seed index 826626413
|
||||
variable tol index 1.0e-15
|
||||
variable add index 37K
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
comm_modify cutoff ${ghostcut}
|
||||
comm_modify cutoff 12.0
|
||||
|
||||
lattice fcc 3.92
|
||||
Lattice spacing in x,y,z = 3.92 3.92 3.92
|
||||
region box block 0 6 0 6 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (23.52 23.52 15.68)
|
||||
2 by 4 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 576 atoms
|
||||
Time spent = 0.00108504 secs
|
||||
|
||||
mass * 1.0
|
||||
|
||||
change_box all z final -0.1 5.0 boundary p p f
|
||||
orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6)
|
||||
|
||||
# replicate in xy
|
||||
|
||||
replicate ${nx} ${ny} 1
|
||||
replicate 8 ${ny} 1
|
||||
replicate 8 8 1
|
||||
orthogonal box = (0 0 -0.392) to (188.16 188.16 19.6)
|
||||
4 by 4 by 1 MPI processor grid
|
||||
36864 atoms
|
||||
Time spent = 0.0028758 secs
|
||||
|
||||
# add adatoms
|
||||
|
||||
include adatoms.list.${add}
|
||||
include adatoms.list.37K
|
||||
create_atoms 1 single 27.5 9.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000183105 secs
|
||||
create_atoms 1 single 16 9 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000178099 secs
|
||||
create_atoms 1 single 10 12 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000179768 secs
|
||||
create_atoms 1 single 31 44 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000184059 secs
|
||||
create_atoms 1 single 13 17 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000173807 secs
|
||||
create_atoms 1 single 8.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000167847 secs
|
||||
create_atoms 1 single 23 26 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000179052 secs
|
||||
create_atoms 1 single 38 27 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000169992 secs
|
||||
create_atoms 1 single 37.5 4.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166178 secs
|
||||
create_atoms 1 single 41.5 47.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000172138 secs
|
||||
create_atoms 1 single 20.5 37.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 5 8 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00018096 secs
|
||||
create_atoms 1 single 2.5 16.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 38.5 45.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 9 0 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000168085 secs
|
||||
create_atoms 1 single 39 32 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000170946 secs
|
||||
create_atoms 1 single 45.5 11.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00018096 secs
|
||||
create_atoms 1 single 40 0 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000168085 secs
|
||||
create_atoms 1 single 44.5 2.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 4.5 44.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000168085 secs
|
||||
create_atoms 1 single 24.5 13.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 47.5 23.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00018096 secs
|
||||
create_atoms 1 single 1 20 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166893 secs
|
||||
create_atoms 1 single 38.5 31.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000168085 secs
|
||||
create_atoms 1 single 12.5 12.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000169992 secs
|
||||
create_atoms 1 single 2 27 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000188828 secs
|
||||
create_atoms 1 single 21 5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000174999 secs
|
||||
create_atoms 1 single 47 12 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 32.5 46.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 9.5 40.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166893 secs
|
||||
create_atoms 1 single 8.5 2.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 41.5 22.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000174046 secs
|
||||
create_atoms 1 single 29 11 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166893 secs
|
||||
create_atoms 1 single 3.5 3.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165224 secs
|
||||
create_atoms 1 single 5 21 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 46.5 31.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166178 secs
|
||||
create_atoms 1 single 35 46 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000183105 secs
|
||||
create_atoms 1 single 40.5 41.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 10 22 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 43.5 14.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000169992 secs
|
||||
create_atoms 1 single 42 42 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 4 26 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000174999 secs
|
||||
create_atoms 1 single 19 34 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000163078 secs
|
||||
create_atoms 1 single 33 9 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 0.5 45.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000163078 secs
|
||||
create_atoms 1 single 30.5 32.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 25.5 5.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000178099 secs
|
||||
create_atoms 1 single 47.5 39.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000165939 secs
|
||||
create_atoms 1 single 15 13 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 21 21 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 14 28 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 9 34 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000174999 secs
|
||||
create_atoms 1 single 7 38 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000175953 secs
|
||||
create_atoms 1 single 11 35 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 20.5 45.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 30.5 31.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000159979 secs
|
||||
create_atoms 1 single 32.5 2.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000166178 secs
|
||||
create_atoms 1 single 21.5 3.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000157833 secs
|
||||
create_atoms 1 single 23 12 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 4.5 33.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 46 43 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 42.5 45.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 4.5 10.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000158072 secs
|
||||
create_atoms 1 single 33.5 15.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000157833 secs
|
||||
create_atoms 1 single 24 5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 13 16 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000158072 secs
|
||||
create_atoms 1 single 16.5 23.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156164 secs
|
||||
create_atoms 1 single 45.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000247002 secs
|
||||
create_atoms 1 single 44.5 5.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156164 secs
|
||||
create_atoms 1 single 27.5 46.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 44.5 12.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000157833 secs
|
||||
create_atoms 1 single 12 41 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 6 4 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.0001688 secs
|
||||
create_atoms 1 single 31.5 10.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00015521 secs
|
||||
create_atoms 1 single 1 44 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 31 4 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 21 33 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000156879 secs
|
||||
create_atoms 1 single 3 33 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164032 secs
|
||||
create_atoms 1 single 15 10 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.0001719 secs
|
||||
create_atoms 1 single 28.5 22.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000153065 secs
|
||||
create_atoms 1 single 43 1 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 3.5 0.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 41 37 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000153065 secs
|
||||
create_atoms 1 single 18.5 43.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000213146 secs
|
||||
create_atoms 1 single 17 27 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000159979 secs
|
||||
create_atoms 1 single 3 5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000153065 secs
|
||||
create_atoms 1 single 18.5 23.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 31.5 14.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 41 31 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 22 3 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00015521 secs
|
||||
create_atoms 1 single 14.5 40.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 9 38 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 36 42 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 33 22 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000163078 secs
|
||||
create_atoms 1 single 15.5 47.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 3 0 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 25.5 27.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000176907 secs
|
||||
create_atoms 1 single 2.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 29.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000162125 secs
|
||||
create_atoms 1 single 44.5 18.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000152826 secs
|
||||
create_atoms 1 single 26 40 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 41 27 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000158072 secs
|
||||
create_atoms 1 single 39.5 5.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000155926 secs
|
||||
create_atoms 1 single 3 38 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000152826 secs
|
||||
create_atoms 1 single 35 29 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 11 19 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164986 secs
|
||||
create_atoms 1 single 18 1 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146866 secs
|
||||
create_atoms 1 single 39.5 40.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146866 secs
|
||||
create_atoms 1 single 46 17 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 1.5 23.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 28.5 23.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 10 28 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000159979 secs
|
||||
create_atoms 1 single 19 47 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000148058 secs
|
||||
create_atoms 1 single 10.5 16.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000147104 secs
|
||||
create_atoms 1 single 38 45 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 42.5 41.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000161886 secs
|
||||
create_atoms 1 single 47.5 42.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000147104 secs
|
||||
create_atoms 1 single 38 7 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 10 44 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 29.5 27.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 45 30 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 3 9 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 8.5 35.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 24 44 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 47 4 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 7.5 8.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 32.5 41.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000157833 secs
|
||||
create_atoms 1 single 0.5 34.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 11 8 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000147104 secs
|
||||
create_atoms 1 single 2 40 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 25 24 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 47.5 6.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000147104 secs
|
||||
create_atoms 1 single 39.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 17 21 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000164032 secs
|
||||
create_atoms 1 single 32 43 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 16.5 29.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 34 34 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 11.5 3.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154018 secs
|
||||
create_atoms 1 single 39 22 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 24.5 36.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 33 31 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 35.5 35.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 14.5 34.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146866 secs
|
||||
create_atoms 1 single 34 28 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000153065 secs
|
||||
create_atoms 1 single 37 41 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 33 46 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 27.5 28.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145197 secs
|
||||
create_atoms 1 single 40.5 22.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000150919 secs
|
||||
create_atoms 1 single 27.5 1.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 12 2 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000151873 secs
|
||||
create_atoms 1 single 36 43 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144005 secs
|
||||
create_atoms 1 single 28.5 9.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 20.5 25.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 3 3 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144005 secs
|
||||
create_atoms 1 single 38 33 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 3 20 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000154972 secs
|
||||
create_atoms 1 single 35 11 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000145912 secs
|
||||
create_atoms 1 single 5 25 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144005 secs
|
||||
create_atoms 1 single 36.5 6.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144005 secs
|
||||
create_atoms 1 single 19.5 24.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000236988 secs
|
||||
create_atoms 1 single 27 41 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000169992 secs
|
||||
create_atoms 1 single 39.5 11.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138998 secs
|
||||
create_atoms 1 single 21.5 2.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000136852 secs
|
||||
create_atoms 1 single 46.5 15.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138998 secs
|
||||
create_atoms 1 single 13 24 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000137091 secs
|
||||
create_atoms 1 single 11 37 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144005 secs
|
||||
create_atoms 1 single 11.5 31.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000144958 secs
|
||||
create_atoms 1 single 47 0 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 25.5 17.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.00014019 secs
|
||||
create_atoms 1 single 32 11 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 8 17 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 27.5 12.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000137806 secs
|
||||
create_atoms 1 single 25 7 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000146151 secs
|
||||
create_atoms 1 single 25.5 37.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000139952 secs
|
||||
create_atoms 1 single 12 15 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 1 7 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138998 secs
|
||||
create_atoms 1 single 18.5 47.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 5 38 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000136852 secs
|
||||
create_atoms 1 single 42 19 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000149012 secs
|
||||
create_atoms 1 single 30.5 7.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138044 secs
|
||||
create_atoms 1 single 42.5 7.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000138998 secs
|
||||
create_atoms 1 single 26.5 18.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000153065 secs
|
||||
create_atoms 1 single 18.5 1.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000137091 secs
|
||||
create_atoms 1 single 41.5 10.5 4
|
||||
Created 1 atoms
|
||||
Time spent = 0.000140905 secs
|
||||
|
||||
# define frozen substrate and mobile atoms
|
||||
|
||||
region base block INF INF INF INF 0 1.8
|
||||
set region base type 2
|
||||
18432 settings made for type
|
||||
group base type 2
|
||||
18432 atoms in group base
|
||||
group mobile type 1
|
||||
18616 atoms in group mobile
|
||||
|
||||
# pair style
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ptvoterlammps.eam Pt Pt
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 mobile nve
|
||||
fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
|
||||
fix 2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
|
||||
fix 2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
|
||||
fix 2 mobile langevin 400.0 400.0 1.0 826626413 zero yes
|
||||
|
||||
timestep 0.005
|
||||
|
||||
compute tmobile mobile temp
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp tmobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
|
||||
|
||||
# thermal equilibration
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.07583
|
||||
ghost atom cutoff = 12
|
||||
binsize = 3.03792, bins = 62 62 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eam/alloy, 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) = 3.359 | 3.359 | 3.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -206220.22 0 -206220.22 -52155.664
|
||||
100 188.18127 -206044.43 0 -205591.63 -25068.83
|
||||
200 274.34464 -205860.78 0 -205200.66 -40191.797
|
||||
300 325.66286 -205750.01 0 -204966.4 -31510.222
|
||||
400 352.48242 -205675.42 0 -204827.28 -35058.064
|
||||
500 370.88571 -205619.66 0 -204727.25 -32735.022
|
||||
600 388.62129 -205592.87 0 -204657.78 -33904.556
|
||||
700 389.54874 -205579.73 0 -204642.4 -32769.852
|
||||
800 395.56074 -205576.82 0 -204625.03 -33755.948
|
||||
900 398.03458 -205564.48 0 -204606.74 -32777.103
|
||||
1000 401.24089 -205562.85 0 -204597.4 -33785.341
|
||||
Loop time of 4.3687 on 16 procs for 1000 steps with 37048 atoms
|
||||
|
||||
Performance: 98.885 ns/day, 0.243 hours/ns, 228.901 timesteps/s
|
||||
98.4% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.2988 | 3.3828 | 3.4667 | 2.3 | 77.43
|
||||
Neigh | 0.20856 | 0.23127 | 0.24382 | 1.9 | 5.29
|
||||
Comm | 0.33313 | 0.45075 | 0.55485 | 9.2 | 10.32
|
||||
Output | 0.00042987 | 0.00044042 | 0.00049591 | 0.0 | 0.01
|
||||
Modify | 0.18811 | 0.28363 | 0.36798 | 9.7 | 6.49
|
||||
Other | | 0.01983 | | | 0.45
|
||||
|
||||
Nlocal: 2315.5 ave 2332 max 2297 min
|
||||
Histogram: 2 0 0 3 4 0 2 1 2 2
|
||||
Nghost: 3186.31 ave 3205 max 3170 min
|
||||
Histogram: 2 1 3 0 2 3 2 1 0 2
|
||||
Neighs: 55590.9 ave 56174 max 55103 min
|
||||
Histogram: 2 2 1 1 4 1 3 0 0 2
|
||||
|
||||
Total # of neighbors = 889454
|
||||
Ave neighs/atom = 24.0082
|
||||
Neighbor list builds = 105
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# pin base so will not move during quenches
|
||||
|
||||
fix freeze base setforce 0.0 0.0 0.0
|
||||
|
||||
# event detection
|
||||
|
||||
compute event all event/displace ${cutevent}
|
||||
compute event all event/displace 1.1
|
||||
|
||||
# hyper/local
|
||||
|
||||
fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 0.4 ${Tequil} ${Dcut} ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 ${Dcut} ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 ${alpha} ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 ${boost}
|
||||
fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 4000.0
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp pe f_HL f_HL[*]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
|
||||
|
||||
thermo_modify lost ignore
|
||||
thermo_modify temp tmobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
|
||||
|
||||
thermo ${nevent}
|
||||
thermo 100
|
||||
|
||||
# dump
|
||||
|
||||
region substrate block INF INF INF INF 1.8 3.8
|
||||
region adatoms block INF INF INF INF 3.8 INF
|
||||
variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
|
||||
|
||||
dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
|
||||
dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
|
||||
dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green
|
||||
|
||||
# run
|
||||
|
||||
hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
|
||||
hyper 1500 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
|
||||
hyper 1500 100 HL event min ${tol} ${tol} 1000 1000 dump 1
|
||||
hyper 1500 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
|
||||
hyper 1500 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
|
||||
WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.07583
|
||||
ghost atom cutoff = 12
|
||||
binsize = 3.03792, bins = 62 62 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair eam/alloy, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix hyper/local, occasional
|
||||
attributes: full, newton on, cut 10
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.566 | 7.567 | 7.567 Mbytes
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
0 401.24089 -205562.85 0 0 0 1 0 0 0 0 0 0 0 0 4e+19 0 0 0 0 0 0 0 0 0 0 0
|
||||
77 401.24089 -206534.96 0 0 0 1 0 0 0 0 0 0 0 0 4e+19 0 0 0 0 0 0 0 1540 0 0 0
|
||||
Loop time of 0.540347 on 16 procs for 77 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
0 401.24089 -205562.85 23.271302 74 0.18753621 1 6.0138739 703.62325 0 0.55802338 3.5350432 0 0 0 4e+19 10.115141 10.115141 0 0 0 0 0 0 0 0 0
|
||||
100 399.15639 -205546.21 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
|
||||
Loop time of 0.579085 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
100 399.15639 -205546.21 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
|
||||
184 399.15639 -206534.96 22.904368 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 49.934783 0.21714886 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 3680 0 0 0
|
||||
Loop time of 0.556056 on 16 procs for 84 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
100 399.15639 -205546.21 22.903938 90 0.32935524 0.39929142 6.0138739 703.62325 0.026229865 0.91517139 3.9968927 91.88 0.3995539 0.4009724 0.39695676 10.262823 10.262823 0 0 0 0 0 2000 0 0 0
|
||||
200 403.01717 -205543.17 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
|
||||
Loop time of 0.581214 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
200 403.01717 -205543.17 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
|
||||
275 403.01717 -206534.96 20.844359 90 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 66.145455 0.29040418 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 5500 0 0 0
|
||||
Loop time of 0.481812 on 16 procs for 75 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
200 403.01717 -205543.17 21.115577 91 0.3291605 0.39888693 6.0138739 703.62325 0.039527213 0.94418421 4.0368484 90.95 0.39930574 0.4019706 0.39554353 10.262823 10.262823 0 0 0 0 0 4000 0 0 0
|
||||
300 399.01963 -205541.46 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
|
||||
Loop time of 0.5757 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
300 399.01963 -205541.46 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
|
||||
377 399.01963 -206534.96 19.137336 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 73.225464 0.31760598 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 7540 0 0 0
|
||||
Loop time of 0.514907 on 16 procs for 77 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
300 399.01963 -205541.46 19.137003 85 0.32442182 0.39862755 6.0138739 703.62325 0.046873868 0.94776891 4.0368484 92.02 0.39912484 0.40296919 0.39497622 10.288936 10.288936 0 0 0 0 0 6000 0 0 0
|
||||
400 398.15351 -205544.87 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
|
||||
Loop time of 0.577371 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
400 398.15351 -205544.87 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
|
||||
471 398.15351 -206534.96 20.470844 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 78.163482 0.33881076 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 9420 0 0 0
|
||||
Loop time of 0.465473 on 16 procs for 71 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
400 398.15351 -205544.87 20.470689 93 0.34589451 0.39828754 6.0138739 703.62325 0.049952465 0.94776891 4.0779385 92.0375 0.39894967 0.40395328 0.3932824 10.307052 10.307052 0 0 0 0 0 8000 0 0 0
|
||||
500 400.29399 -205544.98 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0907861 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
|
||||
Loop time of 0.579188 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
500 400.29399 -205544.98 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0907861 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
|
||||
577 400.29399 -206534.96 17.051242 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0910651 4.0779385 79.710572 0.3455768 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 11540 0 0 0
|
||||
Loop time of 0.502193 on 16 procs for 77 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
500 400.29399 -205544.98 17.051107 83 0.42140172 0.39805251 6.0138739 703.62325 0.056986933 1.0910651 4.0779385 91.986 0.39879563 0.40493836 0.39165573 10.307052 10.307052 0 0 0 0 0 10000 0 0 0
|
||||
600 400.96099 -205544.56 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
|
||||
Loop time of 0.694955 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
600 400.96099 -205544.56 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
|
||||
680 400.96099 -206534.96 20.904479 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 81.188235 0.35174818 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 13600 0 0 0
|
||||
Loop time of 0.529041 on 16 procs for 80 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
600 400.96099 -205544.56 20.904088 91 0.41219484 0.39780769 6.0138739 703.62325 0.061331691 1.1358732 4.0779385 92.013333 0.39864794 0.40593806 0.39067432 10.307052 10.307052 0 0 0 0 0 12000 0 0 0
|
||||
700 397.78618 -205534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 1.1853748 4.1995704 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 0 0 0
|
||||
Loop time of 0.590093 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
700 397.78618 -205534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 1.2139704 4.1995704 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 0 0 0
|
||||
790 397.78618 -206534.96 20.361513 95 0.54466603 0.39757442 6.0138739 703.62325 0.061146951 2.2107138 4.1995704 81.625316 0.35310868 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 15800 0 0 0
|
||||
Loop time of 0.594281 on 16 procs for 90 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
700 397.78618 -205534.96 20.236364 94 0.51088027 0.39757442 6.0138739 703.62325 0.061146951 2.2107138 4.205089 92.12 0.39850836 0.40693553 0.38981834 10.307052 10.307052 0 0 0 0 0 14000 1 2 6
|
||||
800 399.66919 -205547.44 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.2107138 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 1 2 6
|
||||
Loop time of 0.583824 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
800 399.66919 -205547.44 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.2107138 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 1 2 6
|
||||
872 399.66919 -206535.54 21.285461 94 0.56079766 0.39739855 6.0138739 703.62325 0.06556778 2.3177682 4.3041291 84.739679 0.36548679 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 17440 1 2 6
|
||||
Loop time of 0.46886 on 16 procs for 72 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
800 399.66919 -205547.44 21.2852 94 0.44964213 0.39739855 6.0138739 703.62325 0.06556778 2.3177682 4.3041291 92.36625 0.3983806 0.40793368 0.38875 10.307052 10.385797 0 0 0 0 0 16000 2 4 13
|
||||
900 401.5853 -205544.22 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
|
||||
Loop time of 0.585137 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
900 401.5853 -205544.22 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
|
||||
975 401.5853 -206535.54 19.308189 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 84.939487 0.36762438 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 19500 2 4 13
|
||||
Loop time of 0.502012 on 16 procs for 75 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
900 401.5853 -205544.22 19.307938 94 0.47610389 0.39719191 6.0138739 703.62325 0.066991886 2.3177682 4.3041291 92.017778 0.39825974 0.40893337 0.3878576 10.307052 10.385797 0 0 0 0 0 18000 2 4 13
|
||||
1000 395.06218 -205526.35 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
|
||||
Loop time of 0.588597 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1000 395.06218 -205526.35 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
|
||||
1083 395.06218 -206535.54 17.514295 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 85.421053 0.36763584 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 21660 2 4 13
|
||||
Loop time of 0.543222 on 16 procs for 83 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1000 395.06218 -205526.35 17.514191 91 0.42044925 0.39716259 6.0138739 703.62325 0.067937867 2.3177682 4.3041291 92.511 0.39814962 0.40993184 0.3867545 10.307052 10.385797 0 0 0 0 0 20000 2 4 13
|
||||
1100 400.04484 -205545.92 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 2 4 13
|
||||
Loop time of 0.590075 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1100 400.04484 -205545.92 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 2 4 13
|
||||
1177 400.04484 -206535.53 19.52012 89 0.58919981 0.39704631 6.0138739 703.62325 0.069136967 2.3177682 4.4265979 86.464741 0.37201529 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 23540 2 4 13
|
||||
Loop time of 0.500839 on 16 procs for 77 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1100 400.04484 -205545.92 19.518413 89 0.429675 0.39705701 6.0137119 703.6043 0.069136967 2.3177682 4.4265979 92.517273 0.39805636 0.41093134 0.38574293 10.307052 10.385797 0 0 0 0 0 22000 3 6 19
|
||||
1200 400.7462 -205543.2 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
|
||||
Loop time of 0.583971 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1200 400.7462 -205543.2 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
|
||||
1277 400.7462 -206535.53 21.169548 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 86.806578 0.37396584 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 25540 3 6 19
|
||||
Loop time of 0.509118 on 16 procs for 77 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1200 400.7462 -205543.2 21.169281 91 0.32511134 0.39679665 6.0137119 703.6043 0.06750442 2.3177682 4.4265979 92.376667 0.39796198 0.41191655 0.3846039 10.307052 10.385797 0 0 0 0 0 24000 3 6 19
|
||||
1300 398.53702 -205539.33 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
|
||||
Loop time of 0.587306 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1300 398.53702 -205539.33 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
|
||||
1375 398.53702 -206535.53 21.35815 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 87.455273 0.37616341 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 27500 3 6 19
|
||||
Loop time of 0.483781 on 16 procs for 75 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1300 398.53702 -205539.33 21.35787 94 0.38773898 0.39659935 6.0137119 703.6043 0.067808168 2.3177682 4.4265979 92.500769 0.39786514 0.41289519 0.3846039 10.307052 10.385797 0 0 0 0 0 26000 3 6 19
|
||||
1400 402.80537 -205549.3 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
|
||||
Loop time of 0.586411 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1400 402.80537 -205549.3 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
|
||||
1471 402.80537 -206535.53 19.481887 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 88.193746 0.37856948 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 29420 3 6 19
|
||||
Loop time of 0.473799 on 16 procs for 71 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1400 402.80537 -205549.3 19.481632 95 0.32554201 0.39648737 6.0137119 703.6043 0.069550538 2.3177682 4.4265979 92.666429 0.39776836 0.41389491 0.38420043 10.307052 10.385797 0 0 0 0 0 28000 3 6 19
|
||||
1500 402.0803 -205537.7 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 92.857333 0.39767858 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 30000 3 6 19
|
||||
Loop time of 0.587342 on 16 procs for 100 steps with 37048 atoms
|
||||
|
||||
Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23]
|
||||
1500 402.0803 -205537.7 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 92.857333 0.39767858 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 30000 3 6 19
|
||||
1574 402.0803 -206535.53 20.903964 99 0.3340498 0.39635609 6.0137119 703.6043 0.070409086 2.3177682 4.4265979 88.491741 0.37898213 0.41489448 0.38372784 10.333041 10.385797 0 0 0 0 0 31480 3 6 19
|
||||
Loop time of 0.493982 on 16 procs for 74 steps with 37048 atoms
|
||||
|
||||
Final hyper stats ...
|
||||
|
||||
Cummulative quantities for fix hyper:
|
||||
hyper time = 30000
|
||||
event timesteps = 3
|
||||
# of atoms in events = 6
|
||||
Quantities for this hyper run:
|
||||
event timesteps = 3
|
||||
# of atoms in events = 6
|
||||
max length of any bond = 4.4266
|
||||
max drift distance of any atom = 2.31777
|
||||
fraction of steps & bonds with zero bias = 0.0704091
|
||||
Current quantities:
|
||||
ave bonds/atom = 6.01371
|
||||
Cummulative quantities specific tofix hyper/local:
|
||||
# of new bonds formed = 19
|
||||
max bonds/atom = 13
|
||||
Quantities for this hyper run specific to fix hyper/local:
|
||||
ave boosted bonds/step = 92.8573
|
||||
ave boost coeff of all bonds = 0.397679
|
||||
max boost coeff of any bond = 0.414894
|
||||
min boost coeff of any bond = 0.383728
|
||||
max dist from my box of any non-maxstrain bond ghost atom = 10.333
|
||||
max dist from my box of any bond ghost atom = 10.3858
|
||||
count of ghost bond neighbors not found on reneighbor steps = 0
|
||||
lost bond partners = 0
|
||||
ave bias coeff for lost bond partners = 0
|
||||
bias overlaps = 0
|
||||
non-matching bias coeffs = 0
|
||||
CPU time for bond builds = 0.044807
|
||||
Current quantities specific to fix hyper/local:
|
||||
neighbor bonds/bond = 703.604
|
||||
ave boost coeff for all bonds = 0.396356
|
||||
|
||||
Loop time of 17.9972 on 16 procs for 1500 steps with 37048 atoms
|
||||
|
||||
Performance: 36.006 ns/day, 0.667 hours/ns, 83.346 timesteps/s
|
||||
120.7% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
Hyper stats:
|
||||
Dynamics time (%) = 8.87027 (49.2869)
|
||||
Quench time (%) = 8.15972 (45.3388)
|
||||
Other time (%) = 1.2212 (6.78552)
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.6 | 11.848 | 12.043 | 3.9 | 65.83
|
||||
Neigh | 0.50025 | 0.52638 | 0.55163 | 2.1 | 2.92
|
||||
Comm | 0.34528 | 0.49905 | 0.66742 | 13.3 | 2.77
|
||||
Output | 0.0021305 | 0.0021461 | 0.0022686 | 0.1 | 0.01
|
||||
Modify | 3.7498 | 3.9009 | 3.9786 | 2.8 | 21.67
|
||||
Other | | 1.221 | | | 6.79
|
||||
|
||||
Nlocal: 2315.5 ave 2361 max 2267 min
|
||||
Histogram: 1 1 0 4 2 1 3 3 0 1
|
||||
Nghost: 3187.88 ave 3236 max 3141 min
|
||||
Histogram: 1 0 3 2 2 1 4 1 1 1
|
||||
Neighs: 53950.6 ave 54989 max 53049 min
|
||||
Histogram: 2 0 3 2 1 2 4 1 0 1
|
||||
FullNghs: 542951 ave 554654 max 533224 min
|
||||
Histogram: 1 2 3 1 2 2 2 2 0 1
|
||||
|
||||
Total # of neighbors = 8687214
|
||||
Ave neighs/atom = 234.485
|
||||
Neighbor list builds = 165
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:22
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,11 @@
|
|||
|
||||
# example for performing a query to the OpenKIM test database to retrieve
|
||||
# a parameter to be used in the input. here it requests the aluminium
|
||||
# lattice constant for a specific test used for a specific model and then
|
||||
# assigns it to the variable 'latconst'
|
||||
|
||||
units metal
|
||||
info variables out log
|
||||
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
|
||||
info variables out log
|
||||
lattice fcc ${latconst}
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
LAMMPS (28 Feb 2019)
|
||||
|
||||
# example for performing a query to the OpenKIM test database to retrieve
|
||||
# a parameter to be used in the input. here it requests the aluminium
|
||||
# lattice constant for a specific test used for a specific model and then
|
||||
# assigns it to the variable 'latconst'
|
||||
|
||||
units metal
|
||||
info variables out log
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
Printed on Fri Mar 22 20:00:56 2019
|
||||
|
||||
|
||||
Variable information:
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
|
||||
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
|
||||
info variables out log
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
Printed on Fri Mar 22 20:00:57 2019
|
||||
|
||||
|
||||
Variable information:
|
||||
Variable[ 0]: latconst , style = string , def = 4.03208274841
|
||||
|
||||
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
|
||||
|
||||
lattice fcc ${latconst}
|
||||
lattice fcc 4.03208274841
|
||||
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -49,7 +49,7 @@
|
|||
22 0 1 25.100 0.000 0.000
|
||||
23 0 1 26.295 0.000 0.000
|
||||
24 110 2 27.490 0.000 0.000
|
||||
25 128 2 28.685 0.000 0.000
|
||||
25 128 2 28.685 35.85686 0.000
|
||||
26 0 1 29.881 0.000 0.000
|
||||
27 0 1 31.076 0.000 0.000
|
||||
28 0 1 32.271 0.000 0.000
|
||||
|
|
@ -175,7 +175,7 @@
|
|||
148 0 1 32.271 4.781 0.000
|
||||
149 0 1 33.466 4.781 0.000
|
||||
150 0 1 34.662 4.781 0.000
|
||||
151 53 2 0.000 5.976 0.000
|
||||
151 53 2 35.85686 5.976 0.000
|
||||
152 0 1 1.195 5.976 0.000
|
||||
153 0 1 2.390 5.976 0.000
|
||||
154 0 1 3.586 5.976 0.000
|
||||
|
|
@ -655,7 +655,7 @@
|
|||
628 0 1 32.271 23.905 0.000
|
||||
629 0 1 33.466 23.905 0.000
|
||||
630 0 1 34.662 23.905 0.000
|
||||
631 148 2 0.000 25.100 0.000
|
||||
631 148 2 35.85686 25.100 0.000
|
||||
632 0 1 1.195 25.100 0.000
|
||||
633 0 1 2.390 25.100 0.000
|
||||
634 0 1 3.586 25.100 0.000
|
||||
|
|
@ -976,7 +976,7 @@
|
|||
949 25 3 0.677 33.143 0.000
|
||||
950 25 4 1.353 32.819 0.000
|
||||
951 26 3 35.071 18.557 0.000
|
||||
952 26 4 35.480 19.186 0.000
|
||||
952 26 4 35.48000 19.186 0.000
|
||||
953 27 3 29.131 15.504 0.000
|
||||
954 27 4 28.382 15.470 0.000
|
||||
955 28 3 23.456 33.395 0.000
|
||||
|
|
@ -1096,7 +1096,7 @@
|
|||
1069 85 3 33.021 33.461 0.000
|
||||
1070 85 4 33.771 33.455 0.000
|
||||
1071 86 3 0.552 18.315 0.000
|
||||
1072 86 4 35.766 18.701 0.000
|
||||
1072 86 4 -0.09086 18.701 0.000
|
||||
1073 87 3 28.026 32.796 0.000
|
||||
1074 87 4 28.562 33.321 0.000
|
||||
1075 88 3 24.351 29.925 0.000
|
||||
|
|
@ -1112,7 +1112,7 @@
|
|||
1085 93 3 26.170 16.278 0.000
|
||||
1086 93 4 26.046 17.017 0.000
|
||||
1087 94 3 10.380 0.547 0.000
|
||||
1088 94 4 10.003 35.755 0.000
|
||||
1088 94 4 10.003 -0.10186 0.000
|
||||
1089 95 3 0.419 29.308 0.000
|
||||
1090 95 4 0.837 29.930 0.000
|
||||
1091 96 3 13.712 28.191 0.000
|
||||
|
|
|
|||
|
|
@ -0,0 +1,86 @@
|
|||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
special_bonds fene
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
group solute subtract all solvent
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
unfix 5
|
||||
unfix 4
|
||||
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
|
|
@ -1,255 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 2582728.958 tau/day, 5978.539 timesteps/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 | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
|
||||
Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
|
||||
Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
|
||||
Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
|
||||
Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
|
||||
Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
|
||||
Other | | 0.006227 | | | 3.72
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 4.024 | 4.024 | 4.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298
|
||||
2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
|
||||
3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
|
||||
4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
|
||||
5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
|
||||
6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
|
||||
7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
|
||||
8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
|
||||
9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
|
||||
10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
|
||||
11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
|
||||
12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
|
||||
13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
|
||||
14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
|
||||
15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
|
||||
16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
|
||||
17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
|
||||
18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
|
||||
19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
|
||||
20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
|
||||
21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
|
||||
22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
|
||||
23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
|
||||
24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
|
||||
25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
|
||||
26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
|
||||
27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
|
||||
28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
|
||||
29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
|
||||
30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
|
||||
31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
|
||||
32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
|
||||
33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
|
||||
34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
|
||||
35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
|
||||
36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
|
||||
37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
|
||||
38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
|
||||
39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
|
||||
40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
|
||||
41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
|
||||
42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
|
||||
43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
|
||||
44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
|
||||
45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
|
||||
46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
|
||||
47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
|
||||
48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
|
||||
49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
|
||||
50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
|
||||
51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
|
||||
52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
|
||||
53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
|
||||
54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
|
||||
55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
|
||||
56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
|
||||
57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
|
||||
58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
|
||||
59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
|
||||
60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
|
||||
Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 1859917.639 tau/day, 4305.365 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
|
||||
Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
|
||||
Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
|
||||
Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
|
||||
Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
|
||||
Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
|
||||
Other | | 0.3493 | | | 2.51
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 405 ave 405 max 405 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9565 ave 9565 max 9565 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9565
|
||||
Ave neighs/atom = 7.97083
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4876
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:14
|
||||
|
|
@ -1,255 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 6729792.131 tau/day, 15578.223 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 | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
|
||||
Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
|
||||
Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
|
||||
Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
|
||||
Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
|
||||
Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
|
||||
Other | | 0.003891 | | | 6.06
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 4.001 | 4.032 | 4.124 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402
|
||||
2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
|
||||
3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
|
||||
4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
|
||||
5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
|
||||
6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
|
||||
7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
|
||||
8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
|
||||
9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
|
||||
10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
|
||||
11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
|
||||
12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
|
||||
13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
|
||||
14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
|
||||
15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
|
||||
16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
|
||||
17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
|
||||
18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
|
||||
19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
|
||||
20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
|
||||
21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
|
||||
22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
|
||||
23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
|
||||
24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
|
||||
25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
|
||||
26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
|
||||
27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
|
||||
28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
|
||||
29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
|
||||
30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
|
||||
31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
|
||||
32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
|
||||
33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
|
||||
34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
|
||||
35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
|
||||
36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
|
||||
37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
|
||||
38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
|
||||
39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
|
||||
40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
|
||||
41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
|
||||
42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
|
||||
43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
|
||||
44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
|
||||
45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
|
||||
46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
|
||||
47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
|
||||
48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
|
||||
49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
|
||||
50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
|
||||
51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
|
||||
52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
|
||||
53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
|
||||
54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
|
||||
55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
|
||||
56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
|
||||
57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
|
||||
58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
|
||||
59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
|
||||
60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
|
||||
Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 5681397.232 tau/day, 13151.382 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
|
||||
Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
|
||||
Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
|
||||
Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
|
||||
Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
|
||||
Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
|
||||
Other | | 0.2346 | | | 5.14
|
||||
|
||||
Nlocal: 300 ave 306 max 289 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 227.25 ave 250 max 216 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Neighs: 2373.25 ave 2489 max 2283 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9493
|
||||
Ave neighs/atom = 7.91083
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4888
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
|
|
@ -0,0 +1,259 @@
|
|||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000394821 secs
|
||||
read_data CPU = 0.00212336 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.00018549 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 3792167.464 tau/day, 8778.165 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44
|
||||
Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67
|
||||
Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98
|
||||
Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67
|
||||
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15
|
||||
Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85
|
||||
Other | | 0.002551 | | | 2.24
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 4.024 | 4.024 | 4.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326
|
||||
2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269
|
||||
3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618
|
||||
4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016
|
||||
5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164
|
||||
6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891
|
||||
7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333
|
||||
8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396
|
||||
9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554
|
||||
10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213
|
||||
11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469
|
||||
12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225
|
||||
13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283
|
||||
14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427
|
||||
15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836
|
||||
16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323
|
||||
17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919
|
||||
18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638
|
||||
19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341
|
||||
20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768
|
||||
21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935
|
||||
22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734
|
||||
23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013
|
||||
24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789
|
||||
25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875
|
||||
26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118
|
||||
27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415
|
||||
28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526
|
||||
29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376
|
||||
30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113
|
||||
31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708
|
||||
32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106
|
||||
33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458
|
||||
34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584
|
||||
35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396
|
||||
36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939
|
||||
37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603
|
||||
38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359
|
||||
39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385
|
||||
40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955
|
||||
41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756
|
||||
42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561
|
||||
43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063
|
||||
44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473
|
||||
45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054
|
||||
46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974
|
||||
47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182
|
||||
48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142
|
||||
49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467
|
||||
50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865
|
||||
51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859
|
||||
52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593
|
||||
53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158
|
||||
54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814
|
||||
55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307
|
||||
56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892
|
||||
57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988
|
||||
58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146
|
||||
59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911
|
||||
60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471
|
||||
Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 3233199.903 tau/day, 7484.259 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39
|
||||
Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94
|
||||
Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95
|
||||
Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80
|
||||
Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01
|
||||
Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03
|
||||
Other | | 0.1508 | | | 1.88
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 395 ave 395 max 395 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9652 ave 9652 max 9652 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9652
|
||||
Ave neighs/atom = 8.04333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4886
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -0,0 +1,259 @@
|
|||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000130415 secs
|
||||
read_data CPU = 0.00132132 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 4.76837e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0377742 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 11436375.633 tau/day, 26473.092 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80
|
||||
Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81
|
||||
Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86
|
||||
Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52
|
||||
Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75
|
||||
Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55
|
||||
Other | | 0.002912 | | | 7.71
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 4.001 | 4.032 | 4.124 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727652 0.058608073 -1.4645321 1.9982444
|
||||
2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263
|
||||
3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772
|
||||
4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276
|
||||
5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351
|
||||
6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586
|
||||
7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035
|
||||
8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914
|
||||
9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868
|
||||
10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581
|
||||
11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435
|
||||
12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059
|
||||
13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813
|
||||
14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778
|
||||
15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821
|
||||
16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235
|
||||
17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504
|
||||
18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232
|
||||
19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496
|
||||
20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973
|
||||
21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522
|
||||
22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529
|
||||
23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844
|
||||
24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138
|
||||
25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438
|
||||
26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386
|
||||
27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759
|
||||
28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249
|
||||
29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527
|
||||
30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894
|
||||
31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973
|
||||
32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153
|
||||
33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104
|
||||
34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425
|
||||
35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751
|
||||
36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487
|
||||
37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821
|
||||
38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923
|
||||
39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695
|
||||
40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322
|
||||
41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684
|
||||
42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362
|
||||
43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741
|
||||
44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946
|
||||
45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542
|
||||
46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494
|
||||
47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899
|
||||
48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556
|
||||
49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984
|
||||
50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037
|
||||
51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462
|
||||
52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227
|
||||
53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365
|
||||
54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429
|
||||
55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299
|
||||
56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556
|
||||
57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633
|
||||
58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658
|
||||
59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272
|
||||
60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511
|
||||
Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 9821248.084 tau/day, 22734.371 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 | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43
|
||||
Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49
|
||||
Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78
|
||||
Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19
|
||||
Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07
|
||||
Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77
|
||||
Other | | 0.1131 | | | 4.28
|
||||
|
||||
Nlocal: 300 ave 309 max 281 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Nghost: 232.75 ave 234 max 231 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 2450.25 ave 2576 max 2179 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 9801
|
||||
Ave neighs/atom = 8.1675
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4887
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,290 @@
|
|||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000271559 secs
|
||||
read_data CPU = 0.00115585 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 8.39233e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 4029800.456 tau/day, 9328.242 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20
|
||||
Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72
|
||||
Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00
|
||||
Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71
|
||||
Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15
|
||||
Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95
|
||||
Other | | 0.002429 | | | 2.27
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 5.274 | 5.274 | 5.274 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
|
||||
1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
|
||||
2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
|
||||
3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
|
||||
4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
|
||||
5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
|
||||
6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
|
||||
7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
|
||||
8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
|
||||
9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
|
||||
10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
|
||||
11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
|
||||
12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
|
||||
13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
|
||||
14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
|
||||
15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
|
||||
16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
|
||||
17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
|
||||
18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
|
||||
19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
|
||||
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
|
||||
Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 2347175.802 tau/day, 5433.277 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13
|
||||
Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16
|
||||
Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33
|
||||
Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33
|
||||
Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01
|
||||
Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58
|
||||
Other | | 0.05369 | | | 1.46
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 395 ave 395 max 395 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8915 ave 8915 max 8915 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8915
|
||||
Ave neighs/atom = 7.42917
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1580
|
||||
Dangerous builds = 0
|
||||
unfix 5
|
||||
unfix 4
|
||||
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
|
||||
create bodies CPU = 0.00012517 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
1.04536 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
|
||||
21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
|
||||
22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
|
||||
23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
|
||||
24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
|
||||
25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
|
||||
26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
|
||||
27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
|
||||
28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
|
||||
29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
|
||||
30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
|
||||
31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
|
||||
32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
|
||||
33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
|
||||
34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
|
||||
35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
|
||||
36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
|
||||
37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
|
||||
38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
|
||||
39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
|
||||
40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
|
||||
Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 2341388.948 tau/day, 5419.882 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59
|
||||
Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15
|
||||
Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30
|
||||
Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31
|
||||
Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01
|
||||
Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19
|
||||
Other | | 0.05386 | | | 1.46
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 393 ave 393 max 393 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9091 ave 9091 max 9091 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9091
|
||||
Ave neighs/atom = 7.57583
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1582
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
|
|
@ -0,0 +1,290 @@
|
|||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000175714 secs
|
||||
read_data CPU = 0.00145626 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 7.22408e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, 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) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 11101855.138 tau/day, 25698.739 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 | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73
|
||||
Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08
|
||||
Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59
|
||||
Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12
|
||||
Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71
|
||||
Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34
|
||||
Other | | 0.002501 | | | 6.43
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair 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) = 5.251 | 5.282 | 5.374 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
|
||||
1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869
|
||||
2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671
|
||||
3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553
|
||||
4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215
|
||||
5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897
|
||||
6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512
|
||||
7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309
|
||||
8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852
|
||||
9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071
|
||||
10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464
|
||||
11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699
|
||||
12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823
|
||||
13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171
|
||||
14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645
|
||||
15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206
|
||||
16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281
|
||||
17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975
|
||||
18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943
|
||||
19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417
|
||||
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952
|
||||
Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 5025468.853 tau/day, 11633.030 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77
|
||||
Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27
|
||||
Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16
|
||||
Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92
|
||||
Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03
|
||||
Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76
|
||||
Other | | 0.05327 | | | 3.10
|
||||
|
||||
Nlocal: 300 ave 303 max 298 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 218.5 ave 226 max 215 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 2258.75 ave 2283 max 2216 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 9035
|
||||
Ave neighs/atom = 7.52917
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1580
|
||||
Dangerous builds = 0
|
||||
unfix 5
|
||||
unfix 4
|
||||
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
|
||||
create bodies CPU = 5.43594e-05 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
0.916597 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643
|
||||
21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285
|
||||
22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965
|
||||
23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871
|
||||
24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675
|
||||
25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122
|
||||
26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501
|
||||
27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661
|
||||
28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448
|
||||
29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989
|
||||
30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951
|
||||
31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891
|
||||
32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966
|
||||
33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641
|
||||
34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091
|
||||
35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508
|
||||
36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696
|
||||
37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854
|
||||
38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763
|
||||
39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345
|
||||
40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727
|
||||
Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 6885775.862 tau/day, 15939.296 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30
|
||||
Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72
|
||||
Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51
|
||||
Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27
|
||||
Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04
|
||||
Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52
|
||||
Other | | 0.03321 | | | 2.65
|
||||
|
||||
Nlocal: 300 ave 304 max 293 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 215.25 ave 217 max 213 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 2340 ave 2378 max 2290 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 9360
|
||||
Ave neighs/atom = 7.8
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1579
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -237,7 +237,7 @@ int DeviceT::set_ocl_params(char *ocl_vendor) {
|
|||
" -DBLOCK_CELL_ID="+params[11]+
|
||||
" -DMAX_BIO_SHARED_TYPES="+params[12];
|
||||
}
|
||||
_ocl_compile_string="-cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
|
||||
_ocl_compile_string="-cl-std=CL1.2 -cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
|
||||
std::string(OCL_PRECISION_COMPILE)+" "+_ocl_vendor_string;
|
||||
#endif
|
||||
return 0;
|
||||
|
|
|
|||
|
|
@ -17,13 +17,18 @@
|
|||
ifeq ($(strip $(shell pkg-config --version)),)
|
||||
$(error 'pkg-config' not found, but is required to configure the KIM API)
|
||||
endif
|
||||
|
||||
kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
|
||||
kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
|
||||
kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))
|
||||
|
||||
# there is no usable libcurl installation
|
||||
ifeq ($(shell curl-config --version 2> /dev/null),)
|
||||
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
|
||||
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null)
|
||||
else
|
||||
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL
|
||||
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null) $(shell curl-config --libs)
|
||||
endif
|
||||
|
||||
ifeq ($(strip $(kim_SYSINC)),)
|
||||
$(error 'pkg-config' could not find an installed KIM API library.)
|
||||
|
|
|
|||
|
|
@ -13,6 +13,12 @@ do the same thing by typing "python Install.py" from within this
|
|||
directory, or you can do it manually by following the instructions
|
||||
below.
|
||||
|
||||
As of KIM API version 2, the KIM package also provides a LAMMPS command
|
||||
to perform queries through the OpenKIM web API. This feature requires
|
||||
that the CURL library (libcurl) development package and its configuration
|
||||
query tool, curl-config, are installed. The provided Makefile.lammps
|
||||
is set up to automatically detect this.
|
||||
|
||||
-----------------
|
||||
|
||||
Instructions:
|
||||
|
|
|
|||
|
|
@ -9,12 +9,12 @@ doc/Section_python.html and in doc/Section_start.html#start_5.
|
|||
Basically you need to follow these steps in the src directory:
|
||||
|
||||
% make g++ mode=shlib # build for whatever machine target you wish
|
||||
% make install-python # may need to do this via sudo
|
||||
% make install-python # install into site-packages folder
|
||||
|
||||
You can replace the last step by a one-time setting of environment
|
||||
variables in your shell script. Or you can run the python/install.py
|
||||
script directly to give you more control over where the two relevant
|
||||
files are installed. See doc/Section_python.html for details.
|
||||
files are installed. See doc/Python_install.html for details.
|
||||
|
||||
You should then be able to launch Python and instantiate an instance
|
||||
of LAMMPS:
|
||||
|
|
|
|||
|
|
@ -1,56 +1,96 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# copy LAMMPS src/liblammps.so and lammps.py to system dirs
|
||||
|
||||
from __future__ import print_function
|
||||
|
||||
instructions = """
|
||||
Syntax: python install.py [-h] [pydir]
|
||||
pydir = target dir for lammps.py and liblammps.so
|
||||
default = Python site-packages dir
|
||||
"""
|
||||
Installer script to install the LAMMPS python module and the corresponding
|
||||
shared library into either the system-wide site-packages tree, or - failing
|
||||
that - into the corresponding user tree. Called from the 'install-python'
|
||||
build target in the conventional and CMake based build systems
|
||||
"""
|
||||
|
||||
# copy LAMMPS shared library and lammps.py to system dirs
|
||||
|
||||
from __future__ import print_function
|
||||
import sys,os,shutil
|
||||
from argparse import ArgumentParser
|
||||
|
||||
if (len(sys.argv) > 1 and sys.argv[1] == "-h") or len(sys.argv) > 2:
|
||||
print(instructions)
|
||||
sys.exit()
|
||||
parser = ArgumentParser(prog='install.py',
|
||||
description='LAMMPS python module installer script')
|
||||
|
||||
if len(sys.argv) == 2: pydir = sys.argv[1]
|
||||
else: pydir = ""
|
||||
parser.add_argument("-m", "--module", required=True,
|
||||
help="path to the source of the LAMMPS Python module")
|
||||
parser.add_argument("-l", "--lib", required=True,
|
||||
help="path to the compiled LAMMPS shared library")
|
||||
parser.add_argument("-v", "--version", required=True,
|
||||
help="path to the LAMMPS version.h header file")
|
||||
|
||||
# copy lammps.py to pydir if it exists
|
||||
# if pydir not specified, install in site-packages via distutils setup()
|
||||
parser.add_argument("-d","--dir",
|
||||
help="Legacy custom installation folder selection for module and library")
|
||||
|
||||
if pydir:
|
||||
if not os.path.isdir(pydir):
|
||||
print( "ERROR: pydir %s does not exist" % pydir)
|
||||
sys.exit()
|
||||
str = "cp ../python/lammps.py %s" % pydir
|
||||
print(str)
|
||||
args = parser.parse_args()
|
||||
|
||||
# validate arguments and make paths absolute
|
||||
|
||||
if args.module:
|
||||
if not os.path.exists(args.module):
|
||||
print( "ERROR: LAMMPS module file %s does not exist" % args.module)
|
||||
parser.print_help()
|
||||
sys.exit(1)
|
||||
else:
|
||||
args.module = os.path.abspath(args.module)
|
||||
|
||||
if args.lib:
|
||||
if not os.path.exists(args.lib):
|
||||
print( "ERROR: LAMMPS shared library %s does not exist" % args.lib)
|
||||
parser.print_help()
|
||||
sys.exit(1)
|
||||
else:
|
||||
args.lib = os.path.abspath(args.lib)
|
||||
|
||||
if args.version:
|
||||
if not os.path.exists(args.version):
|
||||
print( "ERROR: LAMMPS version header file %s does not exist" % args.version)
|
||||
parser.print_help()
|
||||
sys.exit(1)
|
||||
else:
|
||||
args.version = os.path.abspath(args.version)
|
||||
|
||||
if args.dir:
|
||||
if not os.path.isdir(args.dir):
|
||||
print( "ERROR: Installation folder %s does not exist" % args.dir)
|
||||
parser.print_help()
|
||||
sys.exit(1)
|
||||
else:
|
||||
args.dir = os.path.abspath(args.dir)
|
||||
|
||||
# if a custom directory is given, we copy the files directly
|
||||
# without any special processing or additional steps to that folder
|
||||
|
||||
if args.dir:
|
||||
print("Copying LAMMPS Python module to custom folder %s" % args.dir)
|
||||
try:
|
||||
shutil.copyfile("../python/lammps.py", os.path.join(pydir,'lammps.py') )
|
||||
shutil.copyfile(args.module, os.path.join(args.dir,'lammps.py'))
|
||||
except shutil.Error:
|
||||
pass # source and destination are identical
|
||||
pass # fail silently
|
||||
|
||||
str = "cp ../src/liblammps.so %s" % pydir
|
||||
print(str)
|
||||
print("Copying LAMMPS shared library to custom folder %s" % args.dir)
|
||||
try:
|
||||
shutil.copyfile("../src/liblammps.so", os.path.join(pydir,"liblammps.so") )
|
||||
shutil.copyfile(args.lib, os.path.join(args.dir,os.path.basename(args.lib)))
|
||||
except shutil.Error:
|
||||
pass # source and destination are identical
|
||||
sys.exit()
|
||||
|
||||
print("installing lammps.py in Python site-packages dir")
|
||||
pass # fail silently
|
||||
|
||||
os.chdir('../python') # in case invoked via make in src dir
|
||||
sys.exit()
|
||||
|
||||
# extract version string from header
|
||||
fp = open('../src/version.h','r')
|
||||
fp = open(args.version,'r')
|
||||
txt=fp.read().split('"')[1].split()
|
||||
verstr=txt[0]+txt[1]+txt[2]
|
||||
fp.close()
|
||||
|
||||
print("Installing LAMMPS Python module version %s into site-packages folder" % verstr)
|
||||
|
||||
# we need to switch to the folder of the python module
|
||||
os.chdir(os.path.dirname(args.module))
|
||||
|
||||
from distutils.core import setup
|
||||
from distutils.sysconfig import get_python_lib
|
||||
import site
|
||||
|
|
@ -62,28 +102,26 @@ try:
|
|||
version = verstr,
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = "LAMMPS molecular dynamics library",
|
||||
url = "https://lammps.sandia.gov",
|
||||
description = "LAMMPS Molecular Dynamics Python module",
|
||||
license = "GPL",
|
||||
py_modules = ["lammps"],
|
||||
data_files = [(get_python_lib(), ["../src/liblammps.so"])])
|
||||
data_files = [(get_python_lib(), [args.lib])])
|
||||
except:
|
||||
tryuser=True
|
||||
print ("Installation into global site-packages dir failed.\nTrying user site dir %s now." % site.USER_SITE)
|
||||
|
||||
print ("Installation into global site-packages folder failed.\nTrying user folder %s now." % site.USER_SITE)
|
||||
|
||||
if tryuser:
|
||||
try:
|
||||
sys.argv = ["setup.py","install","--user"] # as if had run "python setup.py install --user"
|
||||
setup(name = "lammps",
|
||||
version = verstr,
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = "LAMMPS molecular dynamics library",
|
||||
py_modules = ["lammps"],
|
||||
data_files = [(site.USER_SITE, ["../src/liblammps.so"])])
|
||||
except:
|
||||
print("Installation into user site package dir failed.\nGo to ../python and install manually.")
|
||||
|
||||
|
||||
|
||||
version = verstr,
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "https://lammps.sandia.gov",
|
||||
description = "LAMMPS Molecular Dynamics Python module",
|
||||
license = "GPL",
|
||||
py_modules = ["lammps"],
|
||||
data_files = [(site.USER_SITE, [args.lib])])
|
||||
except:
|
||||
print("Installation into user site package folder failed.")
|
||||
|
|
|
|||
|
|
@ -26,6 +26,11 @@
|
|||
/*_ssa.h
|
||||
/*_ssa.cpp
|
||||
|
||||
/kim_query.cpp
|
||||
/kim_query.h
|
||||
/pair_kim.cpp
|
||||
/pair_kim.h
|
||||
|
||||
/kokkos.cpp
|
||||
/kokkos.h
|
||||
/kokkos_type.h
|
||||
|
|
@ -818,8 +823,6 @@
|
|||
/pair_hbond_dreiding_morse.h
|
||||
/pair_ilp_graphene_hbn.cpp
|
||||
/pair_ilp_graphene_hbn.h
|
||||
/pair_kim.cpp
|
||||
/pair_kim.h
|
||||
/pair_kolmogorov_crespi_full.cpp
|
||||
/pair_kolmogorov_crespi_full.h
|
||||
/pair_kolmogorov_crespi_z.cpp
|
||||
|
|
|
|||
|
|
@ -94,8 +94,7 @@ void PairGayBerne::compute(int eflag, int vflag)
|
|||
double *iquat,*jquat;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
|
|
|||
|
|
@ -77,8 +77,7 @@ void PairLineLJ::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -85,8 +85,7 @@ void PairRESquared::compute(int eflag, int vflag)
|
|||
RE2Vars wi,wj;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -77,8 +77,7 @@ void PairTriLJ::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
AtomVecTri::Bonus *bonus = avec->bonus;
|
||||
double **x = atom->x;
|
||||
|
|
|
|||
|
|
@ -77,8 +77,7 @@ void PairBodyNparticle::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -111,8 +111,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
|
|
|
|||
|
|
@ -127,8 +127,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
|
|
|
|||
|
|
@ -78,8 +78,7 @@ void AngleClass2::compute(int eflag, int vflag)
|
|||
double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
|
||||
|
||||
eangle = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -56,8 +56,7 @@ void BondClass2::compute(int eflag, int vflag)
|
|||
double rsq,r,dr,dr2,dr3,dr4,de_bond;
|
||||
|
||||
ebond = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -118,8 +118,7 @@ void DihedralClass2::compute(int eflag, int vflag)
|
|||
double fabcd[4][3];
|
||||
|
||||
edihedral = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -90,8 +90,7 @@ void ImproperClass2::compute(int eflag, int vflag)
|
|||
double fabcd[4][3];
|
||||
|
||||
eimproper = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
for (i = 0; i < 3; i++)
|
||||
for (j = 0; j < 4; j++)
|
||||
|
|
|
|||
|
|
@ -38,20 +38,20 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
PairLJClass2::~PairLJClass2()
|
||||
{
|
||||
if (!copymode) {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
if (copymode) return;
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -65,8 +65,7 @@ void PairLJClass2::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -39,23 +39,23 @@ PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
PairLJClass2CoulCut::~PairLJClass2CoulCut()
|
||||
{
|
||||
if (!copymode) {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
if (copymode) return;
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(cut_coul);
|
||||
memory->destroy(cut_coulsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(cut_coul);
|
||||
memory->destroy(cut_coulsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -70,8 +70,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -50,21 +50,21 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
PairLJClass2CoulLong::~PairLJClass2CoulLong()
|
||||
{
|
||||
if (!copymode) {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
if (copymode) return;
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
if (ftable) free_tables();
|
||||
}
|
||||
|
|
@ -82,8 +82,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -80,8 +80,7 @@ void PairBrownian::compute(int eflag, int vflag)
|
|||
double rsq,r,h_sep,radi;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -66,8 +66,7 @@ void PairBrownianPoly::compute(int eflag, int vflag)
|
|||
double rsq,r,h_sep,beta0,beta1,radi,radj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -78,8 +78,7 @@ void PairColloid::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -88,8 +88,7 @@ void PairLubricate::compute(int eflag, int vflag)
|
|||
|
||||
double vxmu2f = force->vxmu2f;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
|
|
|
|||
|
|
@ -116,8 +116,7 @@ void PairLubricateU::compute(int eflag, int vflag)
|
|||
int nghost = atom->nghost;
|
||||
int nall = nlocal + nghost;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// skip compute() if called from integrate::setup()
|
||||
// this is b/c do not want compute() to update velocities twice on a restart
|
||||
|
|
|
|||
|
|
@ -78,8 +78,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag)
|
|||
double **f = atom->f;
|
||||
double **torque = atom->torque;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// grow per-atom arrays if necessary
|
||||
// need to be atom->nmax in length
|
||||
|
|
|
|||
|
|
@ -72,8 +72,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
|
|||
|
||||
double vxmu2f = force->vxmu2f;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
|
|
|
|||
|
|
@ -46,8 +46,7 @@ void PairYukawaColloid::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -57,8 +57,7 @@ void PairBornCoulDSFCS::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -68,8 +68,7 @@ void PairBornCoulLongCS::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -53,8 +53,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag)
|
|||
double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -68,8 +68,7 @@ void PairBuckCoulLongCS::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -69,8 +69,7 @@ void PairCoulLongCS::compute(int eflag, int vflag)
|
|||
double rsq;
|
||||
|
||||
ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -53,8 +53,7 @@ void PairCoulWolfCS::compute(int eflag, int vflag)
|
|||
double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
|
||||
|
||||
ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -74,8 +74,7 @@ void PairLJCutCoulLongCS::compute(int eflag, int vflag)
|
|||
double rsq;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -399,8 +398,7 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
|
|||
double rsq;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -69,8 +69,7 @@ void PairLJCutDipoleCut::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -90,8 +90,7 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
|
|||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
|
|||
|
|
@ -405,8 +405,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
|
|||
double evdwl,ecoul,fpair;
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x, *x0 = x[0];
|
||||
double **mu = atom->mu, *mu0 = mu[0], *imu, *jmu;
|
||||
|
|
|
|||
|
|
@ -84,8 +84,7 @@ PairBeckGPU::~PairBeckGPU()
|
|||
|
||||
void PairBeckGPU::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
int inum, host_start;
|
||||
|
|
|
|||
|
|
@ -106,8 +106,7 @@ PairBornCoulLongCSGPU::~PairBornCoulLongCSGPU()
|
|||
|
||||
void PairBornCoulLongCSGPU::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
int inum, host_start;
|
||||
|
|
|
|||
|
|
@ -101,8 +101,7 @@ PairBornCoulLongGPU::~PairBornCoulLongGPU()
|
|||
|
||||
void PairBornCoulLongGPU::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
int inum, host_start;
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue