Merge branch 'master' into mpi_tests
This commit is contained in:
Axel Kohlmeyer
2
.github/CONTRIBUTING.md
vendored
2
.github/CONTRIBUTING.md
vendored
@ -108,7 +108,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
|
||||
|
||||
For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
|
||||
Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
|
||||
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
|
||||
Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit).
|
||||
You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
|
||||
The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
|
||||
If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.
|
||||
|
||||
@ -1,108 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,108 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,108 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,50 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
CUDA_HOME = /home/projects/cuda/6.0.37
|
||||
NVCC = nvcc
|
||||
|
||||
# Kepler CUDA
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
# Tesla CUDA
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
# newer CUDA
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
# older CUDA
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_DOUBLE_DOUBLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,50 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
CUDA_HOME = /home/projects/cuda/6.0.37
|
||||
NVCC = nvcc
|
||||
|
||||
# Kepler CUDA
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
# Tesla CUDA
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
# newer CUDA
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
# older CUDA
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_DOUBLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,50 +0,0 @@
|
||||
# /* ----------------------------------------------------------------------
|
||||
# Generic Linux Makefile for CUDA
|
||||
# - Change CUDA_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.standard
|
||||
|
||||
CUDA_HOME = /home/projects/cuda/6.0.37
|
||||
NVCC = nvcc
|
||||
|
||||
# Kepler CUDA
|
||||
CUDA_ARCH = -arch=sm_35
|
||||
# Tesla CUDA
|
||||
#CUDA_ARCH = -arch=sm_21
|
||||
# newer CUDA
|
||||
#CUDA_ARCH = -arch=sm_13
|
||||
# older CUDA
|
||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
# precision for GPU calculations
|
||||
# -D_SINGLE_SINGLE # Single precision for all calculations
|
||||
# -D_DOUBLE_DOUBLE # Double precision for all calculations
|
||||
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
|
||||
|
||||
CUDA_PRECISION = -D_SINGLE_SINGLE
|
||||
|
||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||
CUDA_LIB = -L$(CUDA_HOME)/lib64
|
||||
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
|
||||
|
||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||
|
||||
BIN_DIR = ./
|
||||
OBJ_DIR = ./
|
||||
LIB_DIR = ./
|
||||
AR = ar
|
||||
BSH = /bin/sh
|
||||
|
||||
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
|
||||
|
||||
include Nvidia.makefile
|
||||
|
||||
@ -1,109 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O3 -openmp -DLAMMPS_MEMALIGN=64 -no-offload \
|
||||
-xHost -fno-alias -ansi-alias -restrict -override-limits
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O -openmp
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,113 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = nvcc
|
||||
CCFLAGS = -O3 -arch=sm_35
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
OMP = yes
|
||||
CUDA = yes
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
%.o:%.cu
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,110 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
OMP = yes
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,108 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O3 -openmp -restrict -ansi-alias
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O -openmp
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,108 +0,0 @@
|
||||
# linux = Shannon Linux box, Intel icc, OpenMPI, KISS FFTW
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# compiler/linker settings
|
||||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
# specify settings for LAMMPS features you will use
|
||||
# if you change any -D setting, do full re-compile after "make clean"
|
||||
|
||||
# LAMMPS ifdef settings, OPTIONAL
|
||||
# see possible settings in doc/Section_start.html#2_2 (step 4)
|
||||
|
||||
LMP_INC =
|
||||
|
||||
# MPI library, REQUIRED
|
||||
# see discussion in doc/Section_start.html#2_2 (step 5)
|
||||
# can point to dummy MPI library in src/STUBS as in Makefile.serial
|
||||
# INC = path for mpi.h, MPI compiler settings
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/include/
|
||||
MPI_PATH = -L/home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37/lib
|
||||
MPI_LIB = -lmpi
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
# can be left blank to use provided KISS FFT library
|
||||
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB =
|
||||
|
||||
# JPEG and/or PNG library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 7)
|
||||
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
|
||||
# INC = path(s) for jpeglib.h and/or png.h
|
||||
# PATH = path(s) for JPEG library and/or PNG library
|
||||
# LIB = name(s) of JPEG library and/or PNG library
|
||||
|
||||
JPG_INC =
|
||||
JPG_PATH =
|
||||
JPG_LIB = -ljpeg
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# build rules and dependencies
|
||||
# no need to edit this section
|
||||
|
||||
include Makefile.package.settings
|
||||
include Makefile.package
|
||||
|
||||
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
|
||||
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
|
||||
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
|
||||
|
||||
# Path to src files
|
||||
|
||||
vpath %.cpp ..
|
||||
vpath %.h ..
|
||||
|
||||
# Link target
|
||||
|
||||
$(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
sinclude $(DEPENDS)
|
||||
@ -1,68 +0,0 @@
|
||||
These are build and input and run scripts used to run the LJ benchmark
|
||||
in the top-level bench directory using all the various accelerator
|
||||
packages currently available in LAMMPS. The results of running these
|
||||
benchmarks on a GPU cluster with Kepler GPUs are shown on the "GPU
|
||||
(Kepler)" section of the Benchmark page of the LAMMPS WWW site:
|
||||
lammps.sandia.gov/bench.
|
||||
|
||||
The specifics of the benchmark machine are as follows:
|
||||
|
||||
It is a small GPU cluster at Sandia National Labs called "shannon". It
|
||||
has 32 nodes, each with two 8-core Sandy Bridge Xeon CPUs (E5-2670,
|
||||
2.6GHz, HT deactivated), for a total of 512 cores. Twenty-four of the
|
||||
nodes have two NVIDIA Kepler GPUs (K20x, 2688 732 MHz cores). LAMMPS
|
||||
was compiled with the Intel icc compiler, using module
|
||||
openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37.
|
||||
|
||||
------------------------------------------------------------------------
|
||||
|
||||
You can, of course, build LAMMPS yourself with any of the accelerator
|
||||
packages installed for your platform.
|
||||
|
||||
The build.py script will build LAMMPS for the various accelerlator
|
||||
packages using the Makefile.* files in this dir, which you can edit if
|
||||
necessary for your platform. You must set the "lmpdir" variable at
|
||||
the top of build.py to the home directory of LAMMPS as installed on
|
||||
your system. Note that the build.py script hardcodes the arch setting
|
||||
for the USER-CUDA package, which should be matched to the GPUs on your
|
||||
system, e.g. sm_35 for Kepler GPUs. For the GPU package, this setting
|
||||
is in the Makefile.gpu.* files, as is the CUDA_HOME variable which
|
||||
should point to where NVIDIA Cuda software is installed on your
|
||||
system.
|
||||
|
||||
Once the Makefiles are in place, then typing, for example,
|
||||
|
||||
python build.py cpu gpu
|
||||
|
||||
will build executables for the CPU (no accelerators), and 3 variants
|
||||
(double, mixed, single precision) of the GPU package. See the list of
|
||||
possible targets at the top of the build.py script.
|
||||
|
||||
Note that the build.py script will un-install all packages in your
|
||||
LAMMPS directory, then only install the ones needed for the benchmark.
|
||||
The Makefile.* files in this dir are copied into lammps/src/MAKE, as a
|
||||
dummy Makefile.foo, so they will not conflict with makefiles that may
|
||||
already be there. The build.py script also builds the auxiliary GPU
|
||||
and USER-CUDA library as needed.
|
||||
|
||||
LAMMPS executables that are generated by build.py are copied into this
|
||||
directory when the script finishes each build.
|
||||
|
||||
------------------------------------------------------------------------
|
||||
|
||||
The in.* files can be run with any of the accelerator packages,
|
||||
if you specify the appropriate command-line switches. These
|
||||
include switches to set the problem size and number of timesteps
|
||||
to run.
|
||||
|
||||
The run*.sh scripts have sample mpirun commands for running the input
|
||||
scripts on a single node or on multiple nodes for the strong and weak
|
||||
scaling results shown on the benchmark web page. These scripts are
|
||||
provided for illustration purposes, to show what command-line
|
||||
arguments are used with each accelerator package.
|
||||
|
||||
Note that we generate these run scripts, either for interactive or
|
||||
batch submission, via Python scripts which often produces a long list
|
||||
of runs to exercise a combination of options. To perform a quick
|
||||
benchmark calculation on your platform, you will typically only want
|
||||
to run a few commands out of any of the run*.sh scripts.
|
||||
@ -1,187 +0,0 @@
|
||||
#!/usr/local/bin/python
|
||||
|
||||
# Syntax: build.py target1 target2 ...
|
||||
# targets:
|
||||
# cpu, opt, omp,
|
||||
# gpu/double, gpu/mixed, gpu/single,
|
||||
# cuda/double, cuda/mixed, cuda/single,
|
||||
# intel/cpu, intel/phi,
|
||||
# kokkos/omp, kokkos/phi, kokkos/cuda
|
||||
# gpu = gpu/double + gpu/mixed + gpu/single
|
||||
# cuda = cuda/double + cuda/mixed + cuda/single
|
||||
# intel = intel/cpu + intel/phi
|
||||
# kokkos = kokkos/omp + kokkos/phi + kokkos/cuda
|
||||
# all = cpu + opt + omp + gpu + cuda + intel + kokkos
|
||||
|
||||
# create exectuables for different packages
|
||||
# MUST set lmpdir to path of LAMMPS home directory
|
||||
|
||||
import sys,commands,os
|
||||
|
||||
lmpdir = "~/lammps"
|
||||
|
||||
# build LAMMPS
|
||||
# copy makefile into src/MAKE as Makefile.foo, then remove it
|
||||
|
||||
def build_lammps(makefile,pkg):
|
||||
print "Building LAMMPS with %s and %s packages ..." % (makefile,pkg)
|
||||
commands.getoutput("cp %s %s/src/MAKE/Makefile.foo" % (makefile,lmpdir))
|
||||
cwd = os.getcwd()
|
||||
os.chdir(os.path.expanduser(lmpdir + "/src"))
|
||||
str = "make clean-foo"
|
||||
txt = commands.getoutput(str)
|
||||
str = "make no-all"
|
||||
txt = commands.getoutput(str)
|
||||
for package in pkg:
|
||||
str = "make yes-%s" % package
|
||||
txt = commands.getoutput(str)
|
||||
print txt
|
||||
str = "make -j 16 foo"
|
||||
txt = commands.getoutput(str)
|
||||
os.remove("MAKE/Makefile.foo")
|
||||
os.chdir(cwd)
|
||||
|
||||
# build GPU library in LAMMPS
|
||||
# copy makefile into lib/gpu as Makefile.foo, then remove it
|
||||
|
||||
def build_gpu(makefile):
|
||||
print "Building GPU lib with %s ..." % makefile
|
||||
commands.getoutput("cp %s %s/lib/gpu/Makefile.foo" % (makefile,lmpdir))
|
||||
cwd = os.getcwd()
|
||||
os.chdir(os.path.expanduser(lmpdir + "/lib/gpu"))
|
||||
str = "make -f Makefile.foo clean"
|
||||
txt = commands.getoutput(str)
|
||||
str = "make -j 16 -f Makefile.foo"
|
||||
txt = commands.getoutput(str)
|
||||
os.remove("Makefile.foo")
|
||||
os.chdir(cwd)
|
||||
|
||||
# build CUDA library in LAMMPS
|
||||
# set precision and arch explicitly as options to make in lib/cuda
|
||||
|
||||
def build_cuda(precision,arch):
|
||||
print "Building USER-CUDA lib with %s and arch sm_%d ..." % (precision,arch)
|
||||
cwd = os.getcwd()
|
||||
os.chdir(os.path.expanduser(lmpdir + "/lib/cuda"))
|
||||
str = "make clean"
|
||||
txt = commands.getoutput(str)
|
||||
if precision == "double": pflag = 2
|
||||
elif precision == "mixed": pflag = 4
|
||||
elif precision == "single": pflag = 1
|
||||
str = "make -j 16 precision=%d arch=%s" % (pflag,arch)
|
||||
txt = commands.getoutput(str)
|
||||
|
||||
os.chdir(cwd)
|
||||
|
||||
# main program
|
||||
# convert target keywords into target flags
|
||||
|
||||
cpu = opt = omp = 0
|
||||
gpu = gpu_double = gpu_mixed = gpu_single = 0
|
||||
cuda = cuda_double = cuda_mixed = cuda_single = 0
|
||||
intel = intel_cpu = intel_phi = 0
|
||||
kokkos = kokkos_omp = kokkos_phi = kokkos_cuda = 0
|
||||
|
||||
targets = sys.argv[1:]
|
||||
for target in targets:
|
||||
if target == "cpu": cpu = 1
|
||||
elif target == "opt": opt = 1
|
||||
elif target == "omp": omp = 1
|
||||
elif target == "gpu/double": gpu_double = 1
|
||||
elif target == "gpu/mixed": gpu_mixed = 1
|
||||
elif target == "gpu/single": gpu_single = 1
|
||||
elif target == "gpu": gpu = 1
|
||||
elif target == "cuda/double": cuda_double = 1
|
||||
elif target == "cuda/mixed": cuda_mixed = 1
|
||||
elif target == "cuda/single": cuda_single = 1
|
||||
elif target == "cuda": cuda = 1
|
||||
elif target == "intel/cpu": intel_cpu = 1
|
||||
elif target == "intel/phi": intel_phi = 1
|
||||
elif target == "intel": intel = 1
|
||||
elif target == "kokkos/omp": kokkos_omp = 1
|
||||
elif target == "kokkos/phi": kokkos_phi = 1
|
||||
elif target == "kokkos/cuda": kokkos_cuda = 1
|
||||
elif target == "kokkos": kokkos = 1
|
||||
elif target == "all": cpu = omp = gpu = cuda = intel = kokkos = 1
|
||||
else: print "Target",target,"is unknown"
|
||||
|
||||
if gpu: gpu_double = gpu_mixed = gpu_single = 1
|
||||
if cuda: cuda_double = cuda_mixed = cuda_single = 1
|
||||
if intel: intel_cpu = intel_phi = 1
|
||||
if kokkos: kokkos_omp = kokkos_phi = kokkos_cuda = 1
|
||||
|
||||
# CPU
|
||||
|
||||
if cpu:
|
||||
build_lammps(makefile = "Makefile.cpu", pkg = [])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cpu" % lmpdir)
|
||||
|
||||
# OPT
|
||||
|
||||
if opt:
|
||||
build_lammps(makefile = "Makefile.opt", pkg = ["opt"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_opt" % lmpdir)
|
||||
|
||||
# OMP
|
||||
|
||||
if omp:
|
||||
build_lammps(makefile = "Makefile.omp", pkg = ["user-omp"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_omp" % lmpdir)
|
||||
|
||||
# GPU, 3 precisions
|
||||
|
||||
if gpu_double:
|
||||
build_gpu(makefile = "Makefile.gpu.double")
|
||||
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_double" % lmpdir)
|
||||
|
||||
if gpu_mixed:
|
||||
build_gpu(makefile = "Makefile.gpu.mixed")
|
||||
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_mixed" % lmpdir)
|
||||
|
||||
if gpu_single:
|
||||
build_gpu(makefile = "Makefile.gpu.single")
|
||||
build_lammps(makefile = "Makefile.gpu", pkg = ["gpu"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_gpu_single" % lmpdir)
|
||||
|
||||
# CUDA, 3 precisions
|
||||
|
||||
if cuda_double:
|
||||
build_cuda(precision = "double", arch = 35)
|
||||
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_double" % lmpdir)
|
||||
|
||||
if cuda_mixed:
|
||||
build_cuda(precision = "mixed", arch = 35)
|
||||
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_mixed" % lmpdir)
|
||||
|
||||
if cuda_single:
|
||||
build_cuda(precision = "single", arch = 35)
|
||||
build_lammps(makefile = "Makefile.cuda", pkg = ["kspace","user-cuda"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_cuda_single" % lmpdir)
|
||||
|
||||
# INTEL, CPU and Phi
|
||||
|
||||
if intel_cpu:
|
||||
build_lammps(makefile = "Makefile.intel.cpu", pkg = ["user-intel"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_cpu" % lmpdir)
|
||||
|
||||
if intel_phi:
|
||||
build_lammps(makefile = "Makefile.intel.phi", pkg = ["user-intel","user-omp"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_intel_phi" % lmpdir)
|
||||
|
||||
# KOKKOS, all variants
|
||||
|
||||
if kokkos_omp:
|
||||
build_lammps(makefile = "Makefile.kokkos.omp", pkg = ["kokkos"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_omp" % lmpdir)
|
||||
|
||||
if kokkos_phi:
|
||||
build_lammps(makefile = "Makefile.kokkos.phi", pkg = ["kokkos"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_phi" % lmpdir)
|
||||
|
||||
if kokkos_cuda:
|
||||
build_lammps(makefile = "Makefile.kokkos.cuda", pkg = ["kokkos"])
|
||||
print commands.getoutput("mv %s/src/lmp_foo ./lmp_kokkos_cuda" % lmpdir)
|
||||
@ -1,22 +0,0 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run $t
|
||||
@ -1,29 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.1
|
||||
|
||||
mpirun -np 2 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.2
|
||||
|
||||
mpirun -np 4 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.4
|
||||
|
||||
mpirun -np 6 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.6
|
||||
|
||||
mpirun -np 8 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.8
|
||||
|
||||
mpirun -np 10 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.10
|
||||
|
||||
mpirun -np 12 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.12
|
||||
|
||||
mpirun -np 14 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.14
|
||||
|
||||
mpirun -np 16 lmp_cpu -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cpu.128K.16
|
||||
@ -1,20 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -N 1 lmp_cuda_double -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.double.128K.1
|
||||
|
||||
mpirun -N 2 lmp_cuda_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.double.128K.2
|
||||
|
||||
mpirun -N 1 lmp_cuda_mixed -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.mixed.128K.1
|
||||
|
||||
mpirun -N 2 lmp_cuda_mixed -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.mixed.128K.2
|
||||
|
||||
mpirun -N 1 lmp_cuda_single -c on -sf cuda -pk cuda 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.single.128K.1
|
||||
|
||||
mpirun -N 2 lmp_cuda_single -c on -sf cuda -pk cuda 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.cuda.single.128K.2
|
||||
@ -1,155 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.1.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.2.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.2.2
|
||||
|
||||
mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.4.1
|
||||
|
||||
mpirun -np 4 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.4.2
|
||||
|
||||
mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.6.1
|
||||
|
||||
mpirun -np 6 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.6.2
|
||||
|
||||
mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.8.1
|
||||
|
||||
mpirun -np 8 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.8.2
|
||||
|
||||
mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.10.1
|
||||
|
||||
mpirun -np 10 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.10.2
|
||||
|
||||
mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.12.1
|
||||
|
||||
mpirun -np 12 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.12.2
|
||||
|
||||
mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.14.1
|
||||
|
||||
mpirun -np 14 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.14.2
|
||||
|
||||
mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.16.1
|
||||
|
||||
mpirun -np 16 lmp_gpu_single -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.single.128K.16.2
|
||||
|
||||
mpirun -np 1 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.1.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.2.2
|
||||
|
||||
mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.1
|
||||
|
||||
mpirun -np 4 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.4.2
|
||||
|
||||
mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.1
|
||||
|
||||
mpirun -np 6 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.6.2
|
||||
|
||||
mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.1
|
||||
|
||||
mpirun -np 8 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.8.2
|
||||
|
||||
mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.1
|
||||
|
||||
mpirun -np 10 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.10.2
|
||||
|
||||
mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.1
|
||||
|
||||
mpirun -np 12 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.12.2
|
||||
|
||||
mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.1
|
||||
|
||||
mpirun -np 14 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.14.2
|
||||
|
||||
mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.1
|
||||
|
||||
mpirun -np 16 lmp_gpu_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.mixed.128K.16.2
|
||||
|
||||
mpirun -np 1 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.1.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.2.1
|
||||
|
||||
mpirun -np 2 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.2.2
|
||||
|
||||
mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.4.1
|
||||
|
||||
mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.4.2
|
||||
|
||||
mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.6.1
|
||||
|
||||
mpirun -np 6 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.6.2
|
||||
|
||||
mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.8.1
|
||||
|
||||
mpirun -np 8 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.8.2
|
||||
|
||||
mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.10.1
|
||||
|
||||
mpirun -np 10 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.10.2
|
||||
|
||||
mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.12.1
|
||||
|
||||
mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.12.2
|
||||
|
||||
mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.14.1
|
||||
|
||||
mpirun -np 14 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.14.2
|
||||
|
||||
mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.16.1
|
||||
|
||||
mpirun -np 16 lmp_gpu_double -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.gpu.double.128K.16.2
|
||||
@ -1,83 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.1
|
||||
|
||||
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.2
|
||||
|
||||
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.4
|
||||
|
||||
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.6
|
||||
|
||||
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.8
|
||||
|
||||
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.10
|
||||
|
||||
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.12
|
||||
|
||||
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.14
|
||||
|
||||
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec single -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.single.128K.16
|
||||
|
||||
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.1
|
||||
|
||||
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.2
|
||||
|
||||
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.4
|
||||
|
||||
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.6
|
||||
|
||||
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.8
|
||||
|
||||
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.10
|
||||
|
||||
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.12
|
||||
|
||||
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.14
|
||||
|
||||
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec mixed -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.mixed.128K.16
|
||||
|
||||
mpirun -np 1 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.1
|
||||
|
||||
mpirun -np 2 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.2
|
||||
|
||||
mpirun -np 4 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.4
|
||||
|
||||
mpirun -np 6 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.6
|
||||
|
||||
mpirun -np 8 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.8
|
||||
|
||||
mpirun -np 10 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.10
|
||||
|
||||
mpirun -np 12 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.12
|
||||
|
||||
mpirun -np 14 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.14
|
||||
|
||||
mpirun -np 16 lmp_intel_cpu -sf intel -pk intel 1 prec double -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.intel.cpu.double.128K.16
|
||||
@ -1,74 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.1
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.2
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.3
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.4
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.5
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.6
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.7
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.8
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 9 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.9
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 10 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.10
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 11 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.11
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 12 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.12
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 13 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.13
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 14 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.14
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 15 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.15
|
||||
|
||||
mpirun -np 1 lmp_kokkos_cuda -k on g 1 t 16 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.1.16
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.1
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 2 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.2
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 3 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.3
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 4 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.4
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 5 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.5
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 6 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.6
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 7 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.7
|
||||
|
||||
mpirun -np 2 lmp_kokkos_cuda -k on g 2 t 8 -sf kk -pk kokkos binsize 2.8 comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.cuda.128K.2.8
|
||||
@ -1,17 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 16 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.1.16
|
||||
|
||||
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 8 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.2.8
|
||||
|
||||
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 4 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.4.4
|
||||
|
||||
mpirun -np full -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 2 -sf kk -pk kokkos neigh full newton off comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.8.2
|
||||
|
||||
mpirun -np half -bind-to socket -map-by socket -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half newton on comm device -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.kokkos.omp.128K.16.1
|
||||
@ -1,17 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_omp -sf omp -pk omp 16 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.omp.128K.1.16
|
||||
|
||||
mpirun -np 2 lmp_omp -sf omp -pk omp 8 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.omp.128K.2.8
|
||||
|
||||
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.omp.128K.4.4
|
||||
|
||||
mpirun -np 8 lmp_omp -sf omp -pk omp 2 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.omp.128K.8.2
|
||||
|
||||
mpirun -np 16 lmp_omp -sf omp -pk omp 1 -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.omp.128K.16.1
|
||||
@ -1,29 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 1 --time=12:00:00
|
||||
|
||||
mpirun -np 1 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.1
|
||||
|
||||
mpirun -np 2 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.2
|
||||
|
||||
mpirun -np 4 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.4
|
||||
|
||||
mpirun -np 6 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.6
|
||||
|
||||
mpirun -np 8 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.8
|
||||
|
||||
mpirun -np 10 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.10
|
||||
|
||||
mpirun -np 12 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.12
|
||||
|
||||
mpirun -np 14 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.14
|
||||
|
||||
mpirun -np 16 lmp_opt -sf opt -v x 32 -v y 32 -v z 32 -v t 100 < in.lj
|
||||
mv log.lammps log.10Sep14.lj.opt.128K.16
|
||||
@ -1,20 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 16 --time=12:00:00
|
||||
|
||||
mpirun -npernode 16 lmp_cpu -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.cpu.2048K.16.16
|
||||
|
||||
mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.omp.2048K.16.1.16
|
||||
|
||||
mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.cuda.2048K.2.16
|
||||
|
||||
mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.gpu.2048K.2.14.16
|
||||
|
||||
mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.kokkos.cuda.2048K.2.1.16
|
||||
|
||||
mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 64 -v y 64 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.kokkos.omp.2048K.16.1.16
|
||||
@ -1,20 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH -N 16 --time=12:00:00
|
||||
|
||||
mpirun -npernode 16 lmp_cpu -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.cpu.512K.16.16
|
||||
|
||||
mpirun -npernode 16 lmp_omp -sf omp -pk omp 1 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.omp.512K.16.1.16
|
||||
|
||||
mpirun -npernode 2 lmp_cuda -c on -sf cuda -pk cuda 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.cuda.512K.2.16
|
||||
|
||||
mpirun -npernode 14 lmp_gpu -sf gpu -pk gpu 2 -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.gpu.512K.2.14.16
|
||||
|
||||
mpirun -npernode 2 lmp_kokkos_cuda -k on g 2 t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.kokkos.cuda.512K.2.1.16
|
||||
|
||||
mpirun -np 256 -bind-to core -map-by core -x KMP_AFFINITY=scatter lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos comm device -v x 128 -v y 128 -v z 128 -v t 100 < in.lj
|
||||
mv log.lammps log.28Jun14.lj.kokkos.omp.512K.16.1.16
|
||||
1
bench/POTENTIALS/CH.rebo
Symbolic link
1
bench/POTENTIALS/CH.rebo
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/CH.rebo
|
||||
File diff suppressed because it is too large
Load Diff
@ -11,7 +11,7 @@ neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.airebo C H
|
||||
pair_coeff * * CH.rebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00154901 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.7
|
||||
ghost atom cutoff = 10.7
|
||||
binsize = 5.35, bins = 14 13 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139299.7 0 -138034.03 7998.7287
|
||||
10 161.33916 -138711.85 0 -138031.17 33242.273
|
||||
20 208.59505 -138911.77 0 -138031.73 -3199.2371
|
||||
30 139.73485 -138617.76 0 -138028.23 10890.529
|
||||
40 142.15332 -138628.03 0 -138028.3 14614.022
|
||||
50 114.21945 -138509.87 0 -138027.98 24700.885
|
||||
60 164.9432 -138725.08 0 -138029.19 35135.722
|
||||
70 162.14928 -138714.86 0 -138030.77 5666.4609
|
||||
80 157.17575 -138694.81 0 -138031.7 19838.161
|
||||
90 196.16354 -138859.65 0 -138032.05 -7942.9718
|
||||
100 178.30378 -138783.8 0 -138031.55 31012.15
|
||||
Loop time of 60.9424 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.071 ns/day, 338.569 hours/ns, 1.641 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 | 55.299 | 55.299 | 55.299 | 0.0 | 90.74
|
||||
Neigh | 5.5777 | 5.5777 | 5.5777 | 0.0 | 9.15
|
||||
Comm | 0.027658 | 0.027658 | 0.027658 | 0.0 | 0.05
|
||||
Output | 0.0011463 | 0.0011463 | 0.0011463 | 0.0 | 0.00
|
||||
Modify | 0.024684 | 0.024684 | 0.024684 | 0.0 | 0.04
|
||||
Other | | 0.012 | | | 0.02
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 48190 ave 48190 max 48190 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2.22179e+07 ave 2.22179e+07 max 2.22179e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 22217870
|
||||
Ave neighs/atom = 680.695
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:02
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00070262 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.7
|
||||
ghost atom cutoff = 10.7
|
||||
binsize = 5.35, bins = 14 13 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139299.7 0 -138034.03 7998.7287
|
||||
10 161.33916 -138711.85 0 -138031.17 33242.273
|
||||
20 208.59505 -138911.77 0 -138031.73 -3199.2371
|
||||
30 139.73485 -138617.76 0 -138028.23 10890.529
|
||||
40 142.15332 -138628.03 0 -138028.3 14614.022
|
||||
50 114.21945 -138509.87 0 -138027.98 24700.885
|
||||
60 164.9432 -138725.08 0 -138029.19 35135.722
|
||||
70 162.14928 -138714.86 0 -138030.77 5666.4609
|
||||
80 157.17575 -138694.81 0 -138031.7 19838.161
|
||||
90 196.16354 -138859.65 0 -138032.05 -7942.9718
|
||||
100 178.30378 -138783.8 0 -138031.55 31012.15
|
||||
Loop time of 16.768 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.258 ns/day, 93.156 hours/ns, 5.964 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.538 | 14.589 | 14.654 | 1.3 | 87.00
|
||||
Neigh | 1.8853 | 1.8992 | 1.9159 | 0.8 | 11.33
|
||||
Comm | 0.18073 | 0.25896 | 0.31361 | 10.6 | 1.54
|
||||
Output | 0.00050807 | 0.0040419 | 0.0077746 | 5.6 | 0.02
|
||||
Modify | 0.0094635 | 0.0096973 | 0.0099616 | 0.2 | 0.06
|
||||
Other | | 0.007481 | | | 0.04
|
||||
|
||||
Nlocal: 8160 ave 8174 max 8146 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 22614.5 ave 22629 max 22601 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 5.55447e+06 ave 5.56557e+06 max 5.54193e+06 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 22217870
|
||||
Ave neighs/atom = 680.695
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
@ -1,93 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.reax
|
||||
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
58 atoms
|
||||
|
||||
replicate 7 8 10
|
||||
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32480 atoms
|
||||
Time spent = 0.00162625 secs
|
||||
|
||||
velocity all create 300.0 9999
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
|
||||
timestep 0.1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 12 13 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 1727 | 1727 | 1727 Mbytes
|
||||
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
|
||||
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5637 -3203096.6
|
||||
10 299.37479 28983.59 -3232075.2 21746.778 -23987.41 7610.2967 -3203091.6
|
||||
20 295.5855 28616.735 -3231710.1 18178.568 -10871.882 10603.247 -3203093.3
|
||||
30 289.48845 28026.457 -3231123.2 12146.362 4985.5572 13364.455 -3203096.8
|
||||
40 282.66404 27365.76 -3230467.5 4284.2794 18132.771 14133.719 -3203101.7
|
||||
50 274.97005 26620.876 -3229730.4 -3719.11 25519.692 12551.708 -3203109.5
|
||||
60 266.11301 25763.393 -3228883.8 -9271.4049 27307.216 9753.2509 -3203120.4
|
||||
70 259.3263 25106.346 -3228237.2 -11150.726 24238.382 6578.5306 -3203130.8
|
||||
80 260.33956 25204.444 -3228344.2 -9576.6006 16737.65 3454.5747 -3203139.7
|
||||
90 269.90199 26130.219 -3229275.5 -5906.376 5246.1572 467.31789 -3203145.3
|
||||
100 280.76717 27182.117 -3230330.6 -1363.8281 -8133.2509 -1689.7711 -3203148.5
|
||||
Loop time of 437.886 on 1 procs for 100 steps with 32480 atoms
|
||||
|
||||
Performance: 0.002 ns/day, 12163.512 hours/ns, 0.228 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 | 350.29 | 350.29 | 350.29 | 0.0 | 80.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.026264 | 0.026264 | 0.026264 | 0.0 | 0.01
|
||||
Output | 0.0024614 | 0.0024614 | 0.0024614 | 0.0 | 0.00
|
||||
Modify | 87.55 | 87.55 | 87.55 | 0.0 | 19.99
|
||||
Other | | 0.01296 | | | 0.00
|
||||
|
||||
Nlocal: 32480 ave 32480 max 32480 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 45128 ave 45128 max 45128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12778082
|
||||
Ave neighs/atom = 393.414
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:07:24
|
||||
@ -1,93 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.reax
|
||||
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
58 atoms
|
||||
|
||||
replicate 7 8 10
|
||||
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
32480 atoms
|
||||
Time spent = 0.000803709 secs
|
||||
|
||||
velocity all create 300.0 9999
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
|
||||
timestep 0.1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 12 13 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 647 | 647 | 647 Mbytes
|
||||
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
|
||||
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
|
||||
10 299.37479 28983.59 -3232075.2 21746.773 -23987.409 7610.2911 -3203091.6
|
||||
20 295.58552 28616.737 -3231710.1 18178.576 -10871.874 10603.421 -3203093.3
|
||||
30 289.48843 28026.455 -3231123.3 12146.158 4985.3436 13364.461 -3203096.8
|
||||
40 282.66409 27365.764 -3230467.5 4284.5077 18133.151 14133.949 -3203101.7
|
||||
50 274.97008 26620.879 -3229730.3 -3718.536 25520.328 12552.195 -3203109.5
|
||||
60 266.11301 25763.393 -3228883.7 -9271.0381 27307.591 9753.5339 -3203120.4
|
||||
70 259.32631 25106.348 -3228237.1 -11150.314 24238.962 6578.8636 -3203130.8
|
||||
80 260.33966 25204.453 -3228344.1 -9575.5709 16738.467 3455.2525 -3203139.7
|
||||
90 269.90213 26130.231 -3229275.5 -5906.0456 5246.2122 467.43473 -3203145.2
|
||||
100 280.76727 27182.127 -3230330.6 -1363.1733 -8132.8726 -1689.3275 -3203148.4
|
||||
Loop time of 128.275 on 4 procs for 100 steps with 32480 atoms
|
||||
|
||||
Performance: 0.007 ns/day, 3563.196 hours/ns, 0.780 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 92.314 | 97.932 | 103.53 | 44.1 | 76.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.039458 | 5.6409 | 11.263 | 184.0 | 4.40
|
||||
Output | 0.00086117 | 0.0010868 | 0.0016167 | 0.9 | 0.00
|
||||
Modify | 24.687 | 24.688 | 24.69 | 0.0 | 19.25
|
||||
Other | | 0.01323 | | | 0.01
|
||||
|
||||
Nlocal: 8120 ave 8120 max 8120 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21992 ave 21992 max 21992 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13930976
|
||||
Ave neighs/atom = 428.909
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:02:10
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.rebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.00151849 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.airebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.48 0 -137176.8 2464.5258
|
||||
10 179.38052 -137930.92 0 -137174.12 15656.95
|
||||
20 206.87725 -138046.63 0 -137173.83 -24042.005
|
||||
30 150.80048 -137807.07 0 -137170.86 -16524.069
|
||||
40 173.25027 -137902 0 -137171.07 -5716.7297
|
||||
50 151.80552 -137812.01 0 -137171.55 3481.1096
|
||||
60 199.08762 -138013.46 0 -137173.53 17882.906
|
||||
70 217.8592 -138093.51 0 -137174.38 -12269.648
|
||||
80 202.37612 -138029.05 0 -137175.24 -7622.1573
|
||||
90 194.905 -137996.68 0 -137174.4 -32267.297
|
||||
100 185.17966 -137954.16 0 -137172.9 -6902.1493
|
||||
Loop time of 5.17257 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.835 ns/day, 28.737 hours/ns, 19.333 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 | 3.3427 | 3.3427 | 3.3427 | 0.0 | 64.62
|
||||
Neigh | 1.7764 | 1.7764 | 1.7764 | 0.0 | 34.34
|
||||
Comm | 0.017914 | 0.017914 | 0.017914 | 0.0 | 0.35
|
||||
Output | 0.0011199 | 0.0011199 | 0.0011199 | 0.0 | 0.02
|
||||
Modify | 0.024357 | 0.024357 | 0.024357 | 0.0 | 0.47
|
||||
Other | | 0.01004 | | | 0.19
|
||||
|
||||
Nlocal: 32640 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 26460 ave 26460 max 26460 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4902132
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
@ -1,87 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.rebo
|
||||
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
|
||||
replicate 17 16 2
|
||||
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
Time spent = 0.000838995 secs
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.airebo C H
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.48 0 -137176.8 2464.5258
|
||||
10 179.38052 -137930.92 0 -137174.12 15656.95
|
||||
20 206.87725 -138046.63 0 -137173.83 -24042.005
|
||||
30 150.80048 -137807.07 0 -137170.86 -16524.069
|
||||
40 173.25027 -137902 0 -137171.07 -5716.7297
|
||||
50 151.80552 -137812.01 0 -137171.55 3481.1096
|
||||
60 199.08762 -138013.46 0 -137173.53 17882.906
|
||||
70 217.8592 -138093.51 0 -137174.38 -12269.648
|
||||
80 202.37612 -138029.05 0 -137175.24 -7622.1573
|
||||
90 194.905 -137996.68 0 -137174.4 -32267.297
|
||||
100 185.17966 -137954.16 0 -137172.9 -6902.1493
|
||||
Loop time of 1.52214 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 2.838 ns/day, 8.456 hours/ns, 65.697 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.88531 | 0.90632 | 0.92546 | 1.6 | 59.54
|
||||
Neigh | 0.53954 | 0.54258 | 0.54621 | 0.3 | 35.65
|
||||
Comm | 0.035654 | 0.058364 | 0.079543 | 7.0 | 3.83
|
||||
Output | 0.00048494 | 0.00065351 | 0.0011017 | 0.0 | 0.04
|
||||
Modify | 0.0090034 | 0.0090633 | 0.0091114 | 0.0 | 0.60
|
||||
Other | | 0.005168 | | | 0.34
|
||||
|
||||
Nlocal: 8160 ave 8163 max 8157 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11605.8 ave 11615 max 11593 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4902132
|
||||
Ave neighs/atom = 150.188
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,132 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SPC/E water box benchmark
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
replicate 2 4 1
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
36000 atoms
|
||||
24000 bonds
|
||||
12000 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
Time spent = 0.0105426 secs
|
||||
|
||||
pair_style lj/cut/coul/long 9.8 9.8
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
12000 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
velocity all create 300 432567 dist uniform
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style one
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268801
|
||||
grid = 36 64 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0331015
|
||||
estimated relative force accuracy = 9.96841e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 91977 55296
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.8
|
||||
ghost atom cutoff = 11.8
|
||||
binsize = 5.9, bins = 13 25 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 105.1 | 105.1 | 105.1 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -133281.51 0 -111820.57 516.17807
|
||||
50 264.98553 -136986.74 0 -118030.61 -440.29256
|
||||
100 274.45966 -136364.57 0 -116730.69 -128.61949
|
||||
Loop time of 20.172 on 1 procs for 100 steps with 36000 atoms
|
||||
|
||||
Performance: 0.857 ns/day, 28.017 hours/ns, 4.957 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 | 15.818 | 15.818 | 15.818 | 0.0 | 78.41
|
||||
Bond | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.00
|
||||
Kspace | 1.966 | 1.966 | 1.966 | 0.0 | 9.75
|
||||
Neigh | 2.0639 | 2.0639 | 2.0639 | 0.0 | 10.23
|
||||
Comm | 0.043918 | 0.043918 | 0.043918 | 0.0 | 0.22
|
||||
Output | 0.00025153 | 0.00025153 | 0.00025153 | 0.0 | 0.00
|
||||
Modify | 0.27056 | 0.27056 | 0.27056 | 0.0 | 1.34
|
||||
Other | | 0.009522 | | | 0.05
|
||||
|
||||
Nlocal: 36000 ave 36000 max 36000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 56963 ave 56963 max 56963 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12462451
|
||||
Ave neighs/atom = 346.179
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 6
|
||||
Total wall time: 0:00:20
|
||||
@ -1,132 +0,0 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SPC/E water box benchmark
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
replicate 2 4 1
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
36000 atoms
|
||||
24000 bonds
|
||||
12000 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
Time spent = 0.00535488 secs
|
||||
|
||||
pair_style lj/cut/coul/long 9.8 9.8
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
12000 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
velocity all create 300 432567 dist uniform
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style one
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268801
|
||||
grid = 36 64 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0331015
|
||||
estimated relative force accuracy = 9.96841e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 27993 13824
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.8
|
||||
ghost atom cutoff = 11.8
|
||||
binsize = 5.9, bins = 13 25 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 37.74 | 37.74 | 37.74 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -133281.51 0 -111820.57 516.17807
|
||||
50 264.98553 -136986.74 0 -118030.61 -440.29256
|
||||
100 274.45966 -136364.57 0 -116730.69 -128.61949
|
||||
Loop time of 5.43807 on 4 procs for 100 steps with 36000 atoms
|
||||
|
||||
Performance: 3.178 ns/day, 7.553 hours/ns, 18.389 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0016 | 4.0968 | 4.1706 | 3.3 | 75.34
|
||||
Bond | 7.1049e-05 | 8.5771e-05 | 0.00010586 | 0.0 | 0.00
|
||||
Kspace | 0.56386 | 0.63614 | 0.73036 | 8.3 | 11.70
|
||||
Neigh | 0.52575 | 0.52587 | 0.52594 | 0.0 | 9.67
|
||||
Comm | 0.045847 | 0.047308 | 0.048331 | 0.4 | 0.87
|
||||
Output | 9.1314e-05 | 0.00012183 | 0.00021172 | 0.0 | 0.00
|
||||
Modify | 0.12561 | 0.1258 | 0.12605 | 0.1 | 2.31
|
||||
Other | | 0.005944 | | | 0.11
|
||||
|
||||
Nlocal: 9000 ave 9002 max 8998 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 24134.2 ave 24184 max 24062 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 12462451
|
||||
Ave neighs/atom = 346.179
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 6
|
||||
Total wall time: 0:00:05
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Ni in ADP
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00184107 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style adp
|
||||
pair_coeff * * Ni.adp Ni
|
||||
Reading adp potential file Ni.adp with DATE: 2011-06-20
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -41,35 +41,35 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 27.56 | 27.56 | 27.56 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 27.57 | 27.57 | 27.57 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -142400 0 -135782.09 20259.105
|
||||
100 793.05485 -139023.13 0 -135742.9 32175.694
|
||||
Loop time of 11.9854 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 11.0841 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.604 ns/day, 6.659 hours/ns, 8.344 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 3.897 ns/day, 6.158 hours/ns, 9.022 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.447 | 11.447 | 11.447 | 0.0 | 95.51
|
||||
Neigh | 0.48465 | 0.48465 | 0.48465 | 0.0 | 4.04
|
||||
Comm | 0.019317 | 0.019317 | 0.019317 | 0.0 | 0.16
|
||||
Output | 0.00011063 | 0.00011063 | 0.00011063 | 0.0 | 0.00
|
||||
Modify | 0.025319 | 0.025319 | 0.025319 | 0.0 | 0.21
|
||||
Other | | 0.009125 | | | 0.08
|
||||
Pair | 10.597 | 10.597 | 10.597 | 0.0 | 95.60
|
||||
Neigh | 0.43765 | 0.43765 | 0.43765 | 0.0 | 3.95
|
||||
Comm | 0.018561 | 0.018561 | 0.018561 | 0.0 | 0.17
|
||||
Output | 0.0001123 | 0.0001123 | 0.0001123 | 0.0 | 0.00
|
||||
Modify | 0.023261 | 0.023261 | 0.023261 | 0.0 | 0.21
|
||||
Other | | 0.00792 | | | 0.07
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Nghost: 19911.0 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1337035
|
||||
Ave neighs/atom = 41.7823
|
||||
Ave neighs/atom = 41.782344
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:12
|
||||
Total wall time: 0:00:11
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Ni in ADP
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000586033 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style adp
|
||||
pair_coeff * * Ni.adp Ni
|
||||
Reading adp potential file Ni.adp with DATE: 2011-06-20
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -142400 0 -135782.09 20259.105
|
||||
100 793.05485 -139023.13 0 -135742.9 32175.694
|
||||
Loop time of 3.49752 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 3.54402 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 12.352 ns/day, 1.943 hours/ns, 28.592 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 12.190 ns/day, 1.969 hours/ns, 28.217 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 | 3.3203 | 3.3261 | 3.3317 | 0.3 | 95.10
|
||||
Neigh | 0.12544 | 0.12594 | 0.12634 | 0.1 | 3.60
|
||||
Comm | 0.024059 | 0.03001 | 0.035574 | 2.9 | 0.86
|
||||
Output | 4.8161e-05 | 6.8128e-05 | 0.00011802 | 0.0 | 0.00
|
||||
Modify | 0.010666 | 0.010841 | 0.011109 | 0.2 | 0.31
|
||||
Other | | 0.00457 | | | 0.13
|
||||
Pair | 3.2768 | 3.3041 | 3.339 | 1.2 | 93.23
|
||||
Neigh | 0.11542 | 0.11601 | 0.11661 | 0.1 | 3.27
|
||||
Comm | 0.068218 | 0.10201 | 0.13103 | 7.0 | 2.88
|
||||
Output | 4.4823e-05 | 8.0943e-05 | 0.000175 | 0.0 | 0.00
|
||||
Modify | 0.010904 | 0.011064 | 0.011172 | 0.1 | 0.31
|
||||
Other | | 0.01075 | | | 0.30
|
||||
|
||||
Nlocal: 8000 ave 8044 max 7960 min
|
||||
Nlocal: 8000.00 ave 8044 max 7960 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 9131 ave 9171 max 9087 min
|
||||
Nghost: 9131.00 ave 9171 max 9087 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 334259 ave 336108 max 332347 min
|
||||
Neighs: 334259.0 ave 336108 max 332347 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1337035
|
||||
Ave neighs/atom = 41.7823
|
||||
Ave neighs/atom = 41.782344
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
||||
90
bench/POTENTIALS/log.9Oct20.airebo.1
Normal file
90
bench/POTENTIALS/log.9Oct20.airebo.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
Reading data file ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 17 16 2
|
||||
Replicating atoms ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading airebo potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.7
|
||||
ghost atom cutoff = 10.7
|
||||
binsize = 5.35, bins = 14 13 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139300.72 0 -138035.04 7988.6646
|
||||
10 161.34683 -138712.9 0 -138032.19 33228.921
|
||||
20 208.59504 -138912.79 0 -138032.74 -3211.8806
|
||||
30 139.7513 -138618.85 0 -138029.25 10878.143
|
||||
40 142.14562 -138629.02 0 -138029.32 14601.302
|
||||
50 114.23401 -138510.95 0 -138029 24691.124
|
||||
60 164.92002 -138726 0 -138030.21 35125.541
|
||||
70 162.15256 -138715.9 0 -138031.79 5658.7946
|
||||
80 157.16184 -138695.77 0 -138032.72 19824.698
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8463
|
||||
100 178.31875 -138784.89 0 -138032.57 30997.671
|
||||
Loop time of 58.0757 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.074 ns/day, 322.643 hours/ns, 1.722 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 53.513 | 53.513 | 53.513 | 0.0 | 92.14
|
||||
Neigh | 4.5013 | 4.5013 | 4.5013 | 0.0 | 7.75
|
||||
Comm | 0.026609 | 0.026609 | 0.026609 | 0.0 | 0.05
|
||||
Output | 0.0010192 | 0.0010192 | 0.0010192 | 0.0 | 0.00
|
||||
Modify | 0.02275 | 0.02275 | 0.02275 | 0.0 | 0.04
|
||||
Other | | 0.01074 | | | 0.02
|
||||
|
||||
Nlocal: 32640.0 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 48190.0 ave 48190 max 48190 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2.22178e+07 ave 2.22178e+07 max 2.22178e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 22217840
|
||||
Ave neighs/atom = 680.69363
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:59
|
||||
90
bench/POTENTIALS/log.9Oct20.airebo.4
Normal file
90
bench/POTENTIALS/log.9Oct20.airebo.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIREBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.airebo
|
||||
Reading data file ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 17 16 2
|
||||
Replicating atoms ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style airebo 3.0 1 1
|
||||
pair_coeff * * CH.airebo C H
|
||||
Reading airebo potential file CH.airebo with DATE: 2011-10-25
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.7
|
||||
ghost atom cutoff = 10.7
|
||||
binsize = 5.35, bins = 14 13 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair airebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.43 | 29.81 | 30.19 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -139300.72 0 -138035.04 7988.6646
|
||||
10 161.34683 -138712.9 0 -138032.19 33228.921
|
||||
20 208.59504 -138912.79 0 -138032.74 -3211.8806
|
||||
30 139.7513 -138618.85 0 -138029.25 10878.143
|
||||
40 142.14562 -138629.02 0 -138029.32 14601.302
|
||||
50 114.23401 -138510.95 0 -138029 24691.124
|
||||
60 164.92002 -138726 0 -138030.21 35125.541
|
||||
70 162.15256 -138715.9 0 -138031.79 5658.7946
|
||||
80 157.16184 -138695.77 0 -138032.72 19824.698
|
||||
90 196.15907 -138860.65 0 -138033.07 -7950.8463
|
||||
100 178.31875 -138784.89 0 -138032.57 30997.671
|
||||
Loop time of 17.206 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.251 ns/day, 95.589 hours/ns, 5.812 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 | 14.655 | 14.727 | 14.848 | 1.9 | 85.59
|
||||
Neigh | 1.5571 | 1.6135 | 1.6871 | 3.7 | 9.38
|
||||
Comm | 0.7741 | 0.83422 | 0.90385 | 5.8 | 4.85
|
||||
Output | 0.00047541 | 0.0027475 | 0.009517 | 7.5 | 0.02
|
||||
Modify | 0.0091925 | 0.009367 | 0.0096078 | 0.2 | 0.05
|
||||
Other | | 0.01908 | | | 0.11
|
||||
|
||||
Nlocal: 8160.00 ave 8174 max 8146 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 22614.5 ave 22629 max 22601 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 5.55446e+06 ave 5.56556e+06 max 5.54192e+06 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 22217840
|
||||
Ave neighs/atom = 680.69363
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:17
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk CdTe via BOP
|
||||
|
||||
@ -7,19 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
|
||||
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00191426 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style bop
|
||||
pair_coeff * * CdTe.bop.table Cd Te
|
||||
Reading potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
Reading potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
mass 1 112.4
|
||||
mass 2 127.6
|
||||
|
||||
@ -51,32 +49,32 @@ Per MPI rank memory allocation (min/avg/max) = 19.39 | 19.39 | 19.39 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -69539.487 0 -65403.292 3473.2595
|
||||
100 572.16481 -67769.936 0 -65403.35 1838.6993
|
||||
Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 36.0284 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.240 ns/day, 100.079 hours/ns, 2.776 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 23.355 | 23.355 | 23.355 | 0.0 | 96.63
|
||||
Neigh | 0.7545 | 0.7545 | 0.7545 | 0.0 | 3.12
|
||||
Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.11
|
||||
Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.00
|
||||
Modify | 0.024145 | 0.024145 | 0.024145 | 0.0 | 0.10
|
||||
Other | | 0.009326 | | | 0.04
|
||||
Pair | 35.306 | 35.306 | 35.306 | 0.0 | 97.99
|
||||
Neigh | 0.66375 | 0.66375 | 0.66375 | 0.0 | 1.84
|
||||
Comm | 0.027954 | 0.027954 | 0.027954 | 0.0 | 0.08
|
||||
Output | 9.9182e-05 | 9.9182e-05 | 9.9182e-05 | 0.0 | 0.00
|
||||
Modify | 0.022574 | 0.022574 | 0.022574 | 0.0 | 0.06
|
||||
Other | | 0.008374 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 35071 ave 35071 max 35071 min
|
||||
Nghost: 35071.0 ave 35071 max 35071 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 141288 ave 141288 max 141288 min
|
||||
FullNghs: 141288.0 ave 141288 max 141288 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 141288
|
||||
Ave neighs/atom = 4.41525
|
||||
Ave neighs/atom = 4.4152500
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
Total wall time: 0:00:36
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk CdTe via BOP
|
||||
|
||||
@ -7,19 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
|
||||
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000597477 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style bop
|
||||
pair_coeff * * CdTe.bop.table Cd Te
|
||||
Reading potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
Reading potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
|
||||
mass 1 112.4
|
||||
mass 2 127.6
|
||||
|
||||
@ -47,36 +45,36 @@ Neighbor list info ...
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.495 | 8.495 | 8.495 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -69539.487 0 -65403.292 3473.2595
|
||||
100 572.16481 -67769.936 0 -65403.35 1838.6993
|
||||
Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 10.2579 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.329 ns/day, 18.056 hours/ns, 15.384 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.842 ns/day, 28.494 hours/ns, 9.749 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7879 | 5.975 | 6.1607 | 5.4 | 91.92
|
||||
Neigh | 0.27603 | 0.27621 | 0.27647 | 0.0 | 4.25
|
||||
Comm | 0.049869 | 0.23531 | 0.42241 | 27.2 | 3.62
|
||||
Output | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 | 0.0 | 0.00
|
||||
Modify | 0.0089927 | 0.0090921 | 0.0092406 | 0.1 | 0.14
|
||||
Other | | 0.004665 | | | 0.07
|
||||
Pair | 9.0899 | 9.3839 | 9.6808 | 6.9 | 91.48
|
||||
Neigh | 0.24734 | 0.2533 | 0.25828 | 0.8 | 2.47
|
||||
Comm | 0.30495 | 0.60685 | 0.89832 | 27.5 | 5.92
|
||||
Output | 4.673e-05 | 7.695e-05 | 0.00016189 | 0.0 | 0.00
|
||||
Modify | 0.0092409 | 0.00937 | 0.0094445 | 0.1 | 0.09
|
||||
Other | | 0.004455 | | | 0.04
|
||||
|
||||
Nlocal: 8000 ave 8006 max 7994 min
|
||||
Nlocal: 8000.00 ave 8006 max 7994 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 15171 ave 15177 max 15165 min
|
||||
Nghost: 15171.0 ave 15177 max 15165 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 35322 ave 35412 max 35267 min
|
||||
FullNghs: 35322.0 ave 35412 max 35267 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 141288
|
||||
Ave neighs/atom = 4.41525
|
||||
Ave neighs/atom = 4.4152500
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
Total wall time: 0:00:10
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SiO2 for COMB potential
|
||||
|
||||
@ -7,10 +6,12 @@ units metal
|
||||
atom_style charge
|
||||
|
||||
read_data data.comb
|
||||
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32400 atoms
|
||||
read_data CPU = 0.022 seconds
|
||||
|
||||
mass 1 28.0855
|
||||
group type1 type 1
|
||||
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
|
||||
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
|
||||
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
|
||||
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
|
||||
Loop time of 517.206 on 1 procs for 100 steps with 32400 atoms
|
||||
Loop time of 426.185 on 1 procs for 100 steps with 32400 atoms
|
||||
|
||||
Performance: 0.003 ns/day, 7183.417 hours/ns, 0.193 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.004 ns/day, 5919.239 hours/ns, 0.235 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 114.18 | 114.18 | 114.18 | 0.0 | 22.08
|
||||
Neigh | 0.47558 | 0.47558 | 0.47558 | 0.0 | 0.09
|
||||
Comm | 0.030611 | 0.030611 | 0.030611 | 0.0 | 0.01
|
||||
Output | 0.0024922 | 0.0024922 | 0.0024922 | 0.0 | 0.00
|
||||
Modify | 402.51 | 402.51 | 402.51 | 0.0 | 77.82
|
||||
Other | | 0.006137 | | | 0.00
|
||||
Pair | 87.4 | 87.4 | 87.4 | 0.0 | 20.51
|
||||
Neigh | 0.3908 | 0.3908 | 0.3908 | 0.0 | 0.09
|
||||
Comm | 0.029936 | 0.029936 | 0.029936 | 0.0 | 0.01
|
||||
Output | 0.0024605 | 0.0024605 | 0.0024605 | 0.0 | 0.00
|
||||
Modify | 338.36 | 338.36 | 338.36 | 0.0 | 79.39
|
||||
Other | | 0.005751 | | | 0.00
|
||||
|
||||
Nlocal: 32400 ave 32400 max 32400 min
|
||||
Nlocal: 32400.0 ave 32400 max 32400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 42518 ave 42518 max 42518 min
|
||||
Nghost: 42518.0 ave 42518 max 42518 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.85317e+07 ave 1.85317e+07 max 1.85317e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18531740
|
||||
Ave neighs/atom = 571.967
|
||||
Ave neighs/atom = 571.96728
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:09:18
|
||||
Total wall time: 0:07:40
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SiO2 for COMB potential
|
||||
|
||||
@ -7,10 +6,12 @@ units metal
|
||||
atom_style charge
|
||||
|
||||
read_data data.comb
|
||||
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
|
||||
Reading data file ...
|
||||
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32400 atoms
|
||||
read_data CPU = 0.031 seconds
|
||||
|
||||
mass 1 28.0855
|
||||
group type1 type 1
|
||||
@ -50,7 +51,7 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 32.11 | 32.11 | 32.11 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 32.28 | 32.28 | 32.29 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
|
||||
0 300 -6.8032038 -6.8419806 4.6274455 -11.469426 2.8875895 -1.4437947 13386.415 462016.62
|
||||
10 273.21913 -6.8032489 -6.8385642 4.6221303 -11.460695 2.8872353 -1.4436176 13076.442 462016.62
|
||||
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
|
||||
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
|
||||
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
|
||||
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
|
||||
Loop time of 131.437 on 4 procs for 100 steps with 32400 atoms
|
||||
Loop time of 116.902 on 4 procs for 100 steps with 32400 atoms
|
||||
|
||||
Performance: 0.013 ns/day, 1825.518 hours/ns, 0.761 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.015 ns/day, 1623.637 hours/ns, 0.855 timesteps/s
|
||||
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 28.847 | 28.874 | 28.913 | 0.5 | 21.97
|
||||
Neigh | 0.10981 | 0.11084 | 0.11145 | 0.2 | 0.08
|
||||
Comm | 0.28924 | 0.32866 | 0.3556 | 4.5 | 0.25
|
||||
Output | 0.0010426 | 0.0011656 | 0.0015302 | 0.6 | 0.00
|
||||
Modify | 102.12 | 102.12 | 102.12 | 0.0 | 77.69
|
||||
Other | | 0.003455 | | | 0.00
|
||||
Pair | 22.866 | 23.181 | 23.375 | 4.0 | 19.83
|
||||
Neigh | 0.093812 | 0.094818 | 0.095301 | 0.2 | 0.08
|
||||
Comm | 0.94054 | 1.1329 | 1.4505 | 18.1 | 0.97
|
||||
Output | 0.0011141 | 0.001422 | 0.0023448 | 1.4 | 0.00
|
||||
Modify | 92.485 | 92.488 | 92.494 | 0.0 | 79.12
|
||||
Other | | 0.003673 | | | 0.00
|
||||
|
||||
Nlocal: 8100 ave 8110 max 8090 min
|
||||
Nlocal: 8100.00 ave 8110 max 8090 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 20725.2 ave 20772 max 20694 min
|
||||
Nghost: 20725.2 ave 20772 max 20694 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.63294e+06 ave 4.63866e+06 max 4.62736e+06 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18531740
|
||||
Ave neighs/atom = 571.967
|
||||
Ave neighs/atom = 571.96728
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:21
|
||||
Total wall time: 0:02:06
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD benchmark
|
||||
|
||||
@ -8,14 +7,14 @@ atom_style atomic
|
||||
comm_modify mode single vel yes
|
||||
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.0018332 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.0 87287 loop geom
|
||||
@ -46,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 3.6872574 0 5.1872105 28.880274
|
||||
100 1.0246036 4.5727353 0 6.1095927 23.859969
|
||||
Loop time of 3.09286 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 2.63541 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 111741.340 tau/day, 32.333 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 131137.146 tau/day, 37.945 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5326 | 1.5326 | 1.5326 | 0.0 | 49.55
|
||||
Neigh | 1.4771 | 1.4771 | 1.4771 | 0.0 | 47.76
|
||||
Comm | 0.044292 | 0.044292 | 0.044292 | 0.0 | 1.43
|
||||
Output | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.00
|
||||
Modify | 0.022322 | 0.022322 | 0.022322 | 0.0 | 0.72
|
||||
Other | | 0.01648 | | | 0.53
|
||||
Pair | 1.1841 | 1.1841 | 1.1841 | 0.0 | 44.93
|
||||
Neigh | 1.3737 | 1.3737 | 1.3737 | 0.0 | 52.12
|
||||
Comm | 0.04266 | 0.04266 | 0.04266 | 0.0 | 1.62
|
||||
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00
|
||||
Modify | 0.020128 | 0.020128 | 0.020128 | 0.0 | 0.76
|
||||
Other | | 0.01468 | | | 0.56
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 14981 ave 14981 max 14981 min
|
||||
Nghost: 14981.0 ave 14981 max 14981 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 660587 ave 660587 max 660587 min
|
||||
Neighs: 660587.0 ave 660587 max 660587 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660587
|
||||
Ave neighs/atom = 20.6433
|
||||
Ave neighs/atom = 20.643344
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:02
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD benchmark
|
||||
|
||||
@ -8,14 +7,14 @@ atom_style atomic
|
||||
comm_modify mode single vel yes
|
||||
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000589132 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.0 87287 loop geom
|
||||
@ -42,34 +41,34 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.874 | 3.874 | 3.874 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.875 | 3.875 | 3.875 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 3.6872574 0 5.1872105 28.911346
|
||||
100 1.0219182 4.5817845 0 6.1146139 23.803115
|
||||
Loop time of 0.83904 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.882096 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 411899.440 tau/day, 119.184 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 391793.935 tau/day, 113.366 timesteps/s
|
||||
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.39605 | 0.40101 | 0.40702 | 0.6 | 47.79
|
||||
Neigh | 0.38186 | 0.38494 | 0.38738 | 0.4 | 45.88
|
||||
Comm | 0.032073 | 0.039688 | 0.045953 | 2.9 | 4.73
|
||||
Output | 4.4823e-05 | 5.4002e-05 | 7.844e-05 | 0.0 | 0.01
|
||||
Modify | 0.0056572 | 0.0056887 | 0.0057547 | 0.1 | 0.68
|
||||
Other | | 0.007655 | | | 0.91
|
||||
Pair | 0.31428 | 0.33654 | 0.37754 | 4.4 | 38.15
|
||||
Neigh | 0.36308 | 0.3849 | 0.41542 | 3.1 | 43.63
|
||||
Comm | 0.07276 | 0.14322 | 0.1842 | 11.3 | 16.24
|
||||
Output | 4.22e-05 | 5.2989e-05 | 8.2493e-05 | 0.0 | 0.01
|
||||
Modify | 0.0057678 | 0.0060433 | 0.0065472 | 0.4 | 0.69
|
||||
Other | | 0.01134 | | | 1.29
|
||||
|
||||
Nlocal: 8000 ave 8014 max 7986 min
|
||||
Nlocal: 8000.00 ave 8014 max 7986 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 6744 ave 6764 max 6726 min
|
||||
Nghost: 6744.00 ave 6764 max 6726 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 165107 ave 166433 max 163419 min
|
||||
Neighs: 165107.0 ave 166433 max 163419 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 660428
|
||||
Ave neighs/atom = 20.6384
|
||||
Ave neighs/atom = 20.638375
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Cu in EAM
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00185037 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 16.83 | 16.83 | 16.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
100 801.832 -109957.3 0 -106640.77 51322.821
|
||||
Loop time of 3.92295 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 3.70399 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 11.012 ns/day, 2.179 hours/ns, 25.491 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 11.663 ns/day, 2.058 hours/ns, 26.998 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.3913 | 3.3913 | 3.3913 | 0.0 | 86.45
|
||||
Neigh | 0.48107 | 0.48107 | 0.48107 | 0.0 | 12.26
|
||||
Comm | 0.01729 | 0.01729 | 0.01729 | 0.0 | 0.44
|
||||
Output | 0.00011253 | 0.00011253 | 0.00011253 | 0.0 | 0.00
|
||||
Modify | 0.024349 | 0.024349 | 0.024349 | 0.0 | 0.62
|
||||
Other | | 0.008847 | | | 0.23
|
||||
Pair | 3.2216 | 3.2216 | 3.2216 | 0.0 | 86.98
|
||||
Neigh | 0.43766 | 0.43766 | 0.43766 | 0.0 | 11.82
|
||||
Comm | 0.015404 | 0.015404 | 0.015404 | 0.0 | 0.42
|
||||
Output | 0.000103 | 0.000103 | 0.000103 | 0.0 | 0.00
|
||||
Modify | 0.021604 | 0.021604 | 0.021604 | 0.0 | 0.58
|
||||
Other | | 0.007627 | | | 0.21
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19909 ave 19909 max 19909 min
|
||||
Nghost: 19909.0 ave 19909 max 19909 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1207784
|
||||
Ave neighs/atom = 37.7433
|
||||
Ave neighs/atom = 37.743250
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Cu in EAM
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000595331 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -41,34 +41,34 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.381 | 7.381 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.382 | 7.382 | 7.382 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
100 801.832 -109957.3 0 -106640.77 51322.821
|
||||
Loop time of 1.04497 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.01466 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 41.341 ns/day, 0.581 hours/ns, 95.697 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 42.576 ns/day, 0.564 hours/ns, 98.555 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.88513 | 0.88724 | 0.89191 | 0.3 | 84.91
|
||||
Neigh | 0.12418 | 0.12458 | 0.12511 | 0.1 | 11.92
|
||||
Comm | 0.015654 | 0.020543 | 0.022984 | 2.0 | 1.97
|
||||
Output | 4.8637e-05 | 5.8711e-05 | 8.6546e-05 | 0.0 | 0.01
|
||||
Modify | 0.0085199 | 0.0085896 | 0.0086446 | 0.1 | 0.82
|
||||
Other | | 0.003959 | | | 0.38
|
||||
Pair | 0.86683 | 0.86797 | 0.86877 | 0.1 | 85.54
|
||||
Neigh | 0.11567 | 0.11681 | 0.11992 | 0.5 | 11.51
|
||||
Comm | 0.015399 | 0.017346 | 0.018526 | 0.9 | 1.71
|
||||
Output | 4.6253e-05 | 8.1241e-05 | 0.00017262 | 0.0 | 0.01
|
||||
Modify | 0.0085337 | 0.0085824 | 0.0086181 | 0.0 | 0.85
|
||||
Other | | 0.003876 | | | 0.38
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7993 min
|
||||
Nlocal: 8000.00 ave 8008 max 7993 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9130.25 ave 9138 max 9122 min
|
||||
Nghost: 9130.25 ave 9138 max 9122 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 301946 ave 302392 max 301360 min
|
||||
Neighs: 301946.0 ave 302392 max 301360 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1207784
|
||||
Ave neighs/atom = 37.7433
|
||||
Ave neighs/atom = 37.743250
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# eFF benchmark of H plasma
|
||||
|
||||
@ -7,12 +6,14 @@ units electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.eff
|
||||
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.040 seconds
|
||||
|
||||
pair_style eff/cut 12
|
||||
pair_coeff * *
|
||||
@ -42,7 +43,7 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 370.9 | 370.9 | 370.9 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 371.5 | 371.5 | 371.5 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press
|
||||
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
|
||||
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
|
||||
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
|
||||
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
|
||||
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
|
||||
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
|
||||
Loop time of 323.031 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 344.943 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 26.747 fs/day, 0.897 hours/fs, 0.310 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 25.048 fs/day, 0.958 hours/fs, 0.290 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 322.78 | 322.78 | 322.78 | 0.0 | 99.92
|
||||
Pair | 344.71 | 344.71 | 344.71 | 0.0 | 99.93
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.1876 | 0.1876 | 0.1876 | 0.0 | 0.06
|
||||
Output | 0.0027025 | 0.0027025 | 0.0027025 | 0.0 | 0.00
|
||||
Modify | 0.032475 | 0.032475 | 0.032475 | 0.0 | 0.01
|
||||
Other | | 0.02538 | | | 0.01
|
||||
Comm | 0.1763 | 0.1763 | 0.1763 | 0.0 | 0.05
|
||||
Output | 0.0024362 | 0.0024362 | 0.0024362 | 0.0 | 0.00
|
||||
Modify | 0.030869 | 0.030869 | 0.030869 | 0.0 | 0.01
|
||||
Other | | 0.02272 | | | 0.01
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 114349 ave 114349 max 114349 min
|
||||
Nghost: 114349.0 ave 114349 max 114349 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8.10572e+07 ave 8.10572e+07 max 8.10572e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 81057159
|
||||
Ave neighs/atom = 2533.04
|
||||
Ave neighs/atom = 2533.0362
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:05:27
|
||||
Total wall time: 0:05:49
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# eFF benchmark of H plasma
|
||||
|
||||
@ -7,12 +6,14 @@ units electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.eff
|
||||
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.064 seconds
|
||||
|
||||
pair_style eff/cut 12
|
||||
pair_coeff * *
|
||||
@ -42,7 +43,7 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 101.4 | 104.8 | 108.3 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 102.1 | 105.5 | 109.0 Mbytes
|
||||
Step TotEng PotEng KinEng Temp Press
|
||||
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
|
||||
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
|
||||
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
|
||||
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
|
||||
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
|
||||
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
|
||||
Loop time of 90.1636 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 100.431 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 95.826 fs/day, 0.250 hours/fs, 1.109 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 86.029 fs/day, 0.279 hours/fs, 0.996 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 83.772 | 86.516 | 89.593 | 29.5 | 95.95
|
||||
Pair | 89.149 | 93.787 | 97.971 | 41.9 | 93.38
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.51677 | 3.5934 | 6.3368 | 144.6 | 3.99
|
||||
Output | 0.0012872 | 0.0018208 | 0.0024981 | 1.0 | 0.00
|
||||
Modify | 0.017231 | 0.018405 | 0.01983 | 0.8 | 0.02
|
||||
Other | | 0.03431 | | | 0.04
|
||||
Comm | 2.4073 | 6.5821 | 11.21 | 157.8 | 6.55
|
||||
Output | 0.0014203 | 0.0094504 | 0.019111 | 8.3 | 0.01
|
||||
Modify | 0.016678 | 0.016999 | 0.017425 | 0.2 | 0.02
|
||||
Other | | 0.03524 | | | 0.04
|
||||
|
||||
Nlocal: 8000 ave 8112 max 7875 min
|
||||
Nlocal: 8000.00 ave 8112 max 7875 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 65589 ave 66004 max 65177 min
|
||||
Nghost: 65589.0 ave 66004 max 65177 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 2.02643e+07 ave 2.11126e+07 max 1.94058e+07 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 81057159
|
||||
Ave neighs/atom = 2533.04
|
||||
Ave neighs/atom = 2533.0362
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:31
|
||||
Total wall time: 0:01:42
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# EIM benchmark
|
||||
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
|
||||
@ -9,12 +8,14 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.eim
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
|
||||
Reading data file ...
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.024 seconds
|
||||
|
||||
pair_style eim
|
||||
pair_coeff * * Na Cl ffield.eim Na Cl
|
||||
@ -44,34 +45,34 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.72 | 17.72 | 17.72 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
|
||||
Step PotEng Pxx Pyy Pzz Temp
|
||||
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
|
||||
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
|
||||
Loop time of 11.4536 on 1 procs for 100 steps with 32000 atoms
|
||||
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
|
||||
Loop time of 10.3731 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.377 ns/day, 63.631 hours/ns, 8.731 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.416 ns/day, 57.628 hours/ns, 9.640 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.8277 | 9.8277 | 9.8277 | 0.0 | 85.80
|
||||
Neigh | 1.484 | 1.484 | 1.484 | 0.0 | 12.96
|
||||
Comm | 0.028584 | 0.028584 | 0.028584 | 0.0 | 0.25
|
||||
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
|
||||
Modify | 0.09791 | 0.09791 | 0.09791 | 0.0 | 0.85
|
||||
Other | | 0.0152 | | | 0.13
|
||||
Pair | 8.8937 | 8.8937 | 8.8937 | 0.0 | 85.74
|
||||
Neigh | 1.344 | 1.344 | 1.344 | 0.0 | 12.96
|
||||
Comm | 0.028207 | 0.028207 | 0.028207 | 0.0 | 0.27
|
||||
Output | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.00
|
||||
Modify | 0.093584 | 0.093584 | 0.093584 | 0.0 | 0.90
|
||||
Other | | 0.0134 | | | 0.13
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21505 ave 21505 max 21505 min
|
||||
Nghost: 21505.0 ave 21505 max 21505 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
|
||||
Neighs: 1.58387e+06 ave 1.58387e+06 max 1.58387e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1583901
|
||||
Ave neighs/atom = 49.4969
|
||||
Total # of neighbors = 1583871
|
||||
Ave neighs/atom = 49.495969
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 12
|
||||
Total wall time: 0:00:11
|
||||
Total wall time: 0:00:10
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# EIM benchmark
|
||||
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
|
||||
@ -9,12 +8,14 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.eim
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
|
||||
Reading data file ...
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.023 seconds
|
||||
|
||||
pair_style eim
|
||||
pair_coeff * * Na Cl ffield.eim Na Cl
|
||||
@ -44,34 +45,34 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.285 | 7.285 | 7.285 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.460 | 7.460 | 7.460 Mbytes
|
||||
Step PotEng Pxx Pyy Pzz Temp
|
||||
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
|
||||
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
|
||||
Loop time of 3.12061 on 4 procs for 100 steps with 32000 atoms
|
||||
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
|
||||
Loop time of 3.14457 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.384 ns/day, 17.337 hours/ns, 32.045 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.374 ns/day, 17.470 hours/ns, 31.801 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6504 | 2.6583 | 2.6685 | 0.5 | 85.18
|
||||
Neigh | 0.36996 | 0.37847 | 0.39396 | 1.5 | 12.13
|
||||
Comm | 0.037041 | 0.040586 | 0.04504 | 1.4 | 1.30
|
||||
Output | 7.081e-05 | 8.75e-05 | 0.00012994 | 0.0 | 0.00
|
||||
Modify | 0.029286 | 0.035978 | 0.047942 | 3.9 | 1.15
|
||||
Other | | 0.007206 | | | 0.23
|
||||
Pair | 2.6017 | 2.6264 | 2.6758 | 1.8 | 83.52
|
||||
Neigh | 0.34384 | 0.35308 | 0.36784 | 1.6 | 11.23
|
||||
Comm | 0.039635 | 0.099661 | 0.15326 | 15.0 | 3.17
|
||||
Output | 6.485e-05 | 9.656e-05 | 0.0001905 | 0.0 | 0.00
|
||||
Modify | 0.035666 | 0.055446 | 0.098401 | 10.6 | 1.76
|
||||
Other | | 0.009939 | | | 0.32
|
||||
|
||||
Nlocal: 8000 ave 8000 max 8000 min
|
||||
Nlocal: 8000.00 ave 8000 max 8000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9460.25 ave 9469 max 9449 min
|
||||
Nghost: 9460.25 ave 9469 max 9449 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 395975 ave 397239 max 394616 min
|
||||
Neighs: 395968.0 ave 397233 max 394606 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1583901
|
||||
Ave neighs/atom = 49.4969
|
||||
Total # of neighbors = 1583871
|
||||
Ave neighs/atom = 49.495969
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 12
|
||||
Total wall time: 0:00:03
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# FENE beadspring benchmark
|
||||
|
||||
@ -8,7 +7,8 @@ atom_style bond
|
||||
special_bonds fene
|
||||
|
||||
read_data data.fene
|
||||
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
Reading data file ...
|
||||
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
@ -18,8 +18,13 @@ read_data data.fene
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31680 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 1.0 1.0
|
||||
special bond factors coul: 0.0 1.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.003 seconds
|
||||
read_data CPU = 0.054 seconds
|
||||
|
||||
neighbor 0.4 bin
|
||||
neigh_modify delay 5 every 1
|
||||
@ -49,36 +54,37 @@ Neighbor list info ...
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes
|
||||
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.20 | 13.20 | 13.20 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
|
||||
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
|
||||
Loop time of 0.66285 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.648089 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 156415.445 tau/day, 150.864 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 159978.044 tau/day, 154.300 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.13075 | 0.13075 | 0.13075 | 0.0 | 19.73
|
||||
Bond | 0.046363 | 0.046363 | 0.046363 | 0.0 | 6.99
|
||||
Neigh | 0.3172 | 0.3172 | 0.3172 | 0.0 | 47.85
|
||||
Comm | 0.016553 | 0.016553 | 0.016553 | 0.0 | 2.50
|
||||
Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.02
|
||||
Modify | 0.14515 | 0.14515 | 0.14515 | 0.0 | 21.90
|
||||
Other | | 0.006728 | | | 1.02
|
||||
Pair | 0.12174 | 0.12174 | 0.12174 | 0.0 | 18.78
|
||||
Bond | 0.050688 | 0.050688 | 0.050688 | 0.0 | 7.82
|
||||
Neigh | 0.33136 | 0.33136 | 0.33136 | 0.0 | 51.13
|
||||
Comm | 0.014753 | 0.014753 | 0.014753 | 0.0 | 2.28
|
||||
Output | 9.8467e-05 | 9.8467e-05 | 9.8467e-05 | 0.0 | 0.02
|
||||
Modify | 0.12378 | 0.12378 | 0.12378 | 0.0 | 19.10
|
||||
Other | | 0.005668 | | | 0.87
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9493 ave 9493 max 9493 min
|
||||
Nghost: 9493.00 ave 9493 max 9493 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 155873 ave 155873 max 155873 min
|
||||
Neighs: 155873.0 ave 155873 max 155873 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 155873
|
||||
Ave neighs/atom = 4.87103
|
||||
Ave special neighs/atom = 1.98
|
||||
Ave neighs/atom = 4.8710312
|
||||
Ave special neighs/atom = 1.9800000
|
||||
Neighbor list builds = 20
|
||||
Dangerous builds = 20
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# FENE beadspring benchmark
|
||||
|
||||
@ -8,7 +7,8 @@ atom_style bond
|
||||
special_bonds fene
|
||||
|
||||
read_data data.fene
|
||||
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
Reading data file ...
|
||||
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
@ -18,8 +18,13 @@ read_data data.fene
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31680 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 1.0 1.0
|
||||
special bond factors coul: 0.0 1.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.048 seconds
|
||||
|
||||
neighbor 0.4 bin
|
||||
neigh_modify delay 5 every 1
|
||||
@ -49,36 +54,37 @@ Neighbor list info ...
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.606 Mbytes
|
||||
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.779 | 4.780 | 4.780 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
|
||||
100 0.9736748 0.44378481 20.502389 22.40664 4.7809557
|
||||
Loop time of 0.184782 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.179123 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 561093.346 tau/day, 541.178 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 578819.228 tau/day, 558.275 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.033747 | 0.034391 | 0.035036 | 0.3 | 18.61
|
||||
Bond | 0.012475 | 0.012579 | 0.012812 | 0.1 | 6.81
|
||||
Neigh | 0.083916 | 0.083953 | 0.084022 | 0.0 | 45.43
|
||||
Comm | 0.012409 | 0.01363 | 0.014534 | 0.7 | 7.38
|
||||
Output | 4.1246e-05 | 5.9545e-05 | 0.00010443 | 0.0 | 0.03
|
||||
Modify | 0.036675 | 0.037876 | 0.038357 | 0.4 | 20.50
|
||||
Other | | 0.002294 | | | 1.24
|
||||
Pair | 0.031898 | 0.032311 | 0.032864 | 0.2 | 18.04
|
||||
Bond | 0.01335 | 0.013471 | 0.013588 | 0.1 | 7.52
|
||||
Neigh | 0.087105 | 0.087195 | 0.087282 | 0.0 | 48.68
|
||||
Comm | 0.010541 | 0.011533 | 0.012463 | 0.7 | 6.44
|
||||
Output | 3.8624e-05 | 5.6028e-05 | 0.00010157 | 0.0 | 0.03
|
||||
Modify | 0.031766 | 0.03233 | 0.033015 | 0.3 | 18.05
|
||||
Other | | 0.002227 | | | 1.24
|
||||
|
||||
Nlocal: 8000 ave 8023 max 7978 min
|
||||
Nlocal: 8000.00 ave 8023 max 7978 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 4158.75 ave 4175 max 4145 min
|
||||
Nghost: 4158.75 ave 4175 max 4145 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 38940 ave 39184 max 38640 min
|
||||
Neighs: 38940.0 ave 39184 max 38640 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 155760
|
||||
Ave neighs/atom = 4.8675
|
||||
Ave special neighs/atom = 1.98
|
||||
Ave neighs/atom = 4.8675000
|
||||
Ave special neighs/atom = 1.9800000
|
||||
Neighbor list builds = 20
|
||||
Dangerous builds = 20
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Gay-Berne benchmark
|
||||
# biaxial ellipsoid mesogens in isotropic phase
|
||||
@ -18,13 +17,15 @@ atom_style ellipsoid
|
||||
#set group all quat/random 982381
|
||||
|
||||
read_data data.gb
|
||||
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
|
||||
Reading data file ...
|
||||
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32768 atoms
|
||||
reading velocities ...
|
||||
32768 velocities
|
||||
32768 ellipsoids
|
||||
read_data CPU = 0.097 seconds
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
@ -63,41 +64,41 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.91 | 28.91 | 28.91 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.98 | 28.98 | 28.98 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
|
||||
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
|
||||
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
|
||||
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
|
||||
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
|
||||
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
|
||||
Loop time of 43.7894 on 1 procs for 100 steps with 32768 atoms
|
||||
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
|
||||
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
|
||||
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
|
||||
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
|
||||
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
|
||||
Loop time of 57.1053 on 1 procs for 100 steps with 32768 atoms
|
||||
|
||||
Performance: 394.616 tau/day, 2.284 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 302.599 tau/day, 1.751 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 42.881 | 42.881 | 42.881 | 0.0 | 97.93
|
||||
Neigh | 0.35071 | 0.35071 | 0.35071 | 0.0 | 0.80
|
||||
Comm | 0.065153 | 0.065153 | 0.065153 | 0.0 | 0.15
|
||||
Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.00
|
||||
Modify | 0.47852 | 0.47852 | 0.47852 | 0.0 | 1.09
|
||||
Other | | 0.01337 | | | 0.03
|
||||
Pair | 56.246 | 56.246 | 56.246 | 0.0 | 98.50
|
||||
Neigh | 0.31058 | 0.31058 | 0.31058 | 0.0 | 0.54
|
||||
Comm | 0.066039 | 0.066039 | 0.066039 | 0.0 | 0.12
|
||||
Output | 0.00048757 | 0.00048757 | 0.00048757 | 0.0 | 0.00
|
||||
Modify | 0.46972 | 0.46972 | 0.46972 | 0.0 | 0.82
|
||||
Other | | 0.01198 | | | 0.02
|
||||
|
||||
Nlocal: 32768 ave 32768 max 32768 min
|
||||
Nlocal: 32768.0 ave 32768 max 32768 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 25669 ave 25669 max 25669 min
|
||||
Nghost: 25669.0 ave 25669 max 25669 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.30433e+06 ave 2.30433e+06 max 2.30433e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2304332
|
||||
Ave neighs/atom = 70.3226
|
||||
Total # of neighbors = 2304331
|
||||
Ave neighs/atom = 70.322601
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 3
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:44
|
||||
Total wall time: 0:00:57
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Gay-Berne benchmark
|
||||
# biaxial ellipsoid mesogens in isotropic phase
|
||||
@ -18,13 +17,15 @@ atom_style ellipsoid
|
||||
#set group all quat/random 982381
|
||||
|
||||
read_data data.gb
|
||||
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
|
||||
Reading data file ...
|
||||
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32768 atoms
|
||||
reading velocities ...
|
||||
32768 velocities
|
||||
32768 ellipsoids
|
||||
read_data CPU = 0.079 seconds
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
@ -63,41 +64,41 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.99 | 11.99 | 12.00 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
|
||||
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
|
||||
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
|
||||
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
|
||||
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
|
||||
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
|
||||
Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
|
||||
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
|
||||
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
|
||||
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
|
||||
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
|
||||
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
|
||||
Loop time of 14.9338 on 4 procs for 100 steps with 32768 atoms
|
||||
|
||||
Performance: 1527.522 tau/day, 8.840 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1157.109 tau/day, 6.696 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.778 | 10.849 | 10.934 | 2.0 | 95.90
|
||||
Neigh | 0.088265 | 0.08871 | 0.089238 | 0.1 | 0.78
|
||||
Comm | 0.1384 | 0.22518 | 0.29662 | 14.1 | 1.99
|
||||
Output | 0.00020599 | 0.00024837 | 0.00036836 | 0.0 | 0.00
|
||||
Modify | 0.13828 | 0.13899 | 0.13984 | 0.2 | 1.23
|
||||
Other | | 0.01053 | | | 0.09
|
||||
Pair | 14.317 | 14.457 | 14.545 | 2.5 | 96.81
|
||||
Neigh | 0.080048 | 0.080928 | 0.082009 | 0.3 | 0.54
|
||||
Comm | 0.15948 | 0.24734 | 0.38914 | 18.9 | 1.66
|
||||
Output | 0.00018859 | 0.00034791 | 0.00082254 | 0.0 | 0.00
|
||||
Modify | 0.137 | 0.13804 | 0.13981 | 0.3 | 0.92
|
||||
Other | | 0.01041 | | | 0.07
|
||||
|
||||
Nlocal: 8192 ave 8215 max 8166 min
|
||||
Nlocal: 8192.00 ave 8215 max 8166 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 11972.5 ave 11984 max 11959 min
|
||||
Nghost: 11972.5 ave 11984 max 11959 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 576083 ave 579616 max 572161 min
|
||||
Neighs: 576083.0 ave 579616 max 572161 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2304332
|
||||
Ave neighs/atom = 70.3226
|
||||
Total # of neighbors = 2304331
|
||||
Ave neighs/atom = 70.322601
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 3
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:11
|
||||
Total wall time: 0:00:15
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# granular chute flow
|
||||
|
||||
@ -10,12 +9,14 @@ newton off
|
||||
comm_modify vel yes
|
||||
|
||||
read_data data.granular
|
||||
orthogonal box = (0 0 0) to (40 20 37.2886)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.050 seconds
|
||||
|
||||
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
@ -52,34 +53,34 @@ Neighbor list info ...
|
||||
pair build: half/size/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.36 | 23.36 | 23.36 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.37 | 23.37 | 23.37 Mbytes
|
||||
Step Atoms KinEng c_1 Volume
|
||||
0 32000 784139.13 1601.1263 29833.783
|
||||
100 32000 784292.08 1571.0968 29834.707
|
||||
Loop time of 0.292816 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.274779 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2950.657 tau/day, 341.511 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 3144.341 tau/day, 363.928 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17449 | 0.17449 | 0.17449 | 0.0 | 59.59
|
||||
Neigh | 0.031927 | 0.031927 | 0.031927 | 0.0 | 10.90
|
||||
Comm | 0.010195 | 0.010195 | 0.010195 | 0.0 | 3.48
|
||||
Output | 0.00019121 | 0.00019121 | 0.00019121 | 0.0 | 0.07
|
||||
Modify | 0.064463 | 0.064463 | 0.064463 | 0.0 | 22.01
|
||||
Other | | 0.01155 | | | 3.94
|
||||
Pair | 0.16956 | 0.16956 | 0.16956 | 0.0 | 61.71
|
||||
Neigh | 0.027646 | 0.027646 | 0.027646 | 0.0 | 10.06
|
||||
Comm | 0.010068 | 0.010068 | 0.010068 | 0.0 | 3.66
|
||||
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.06
|
||||
Modify | 0.056372 | 0.056372 | 0.056372 | 0.0 | 20.52
|
||||
Other | | 0.01096 | | | 3.99
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5463 ave 5463 max 5463 min
|
||||
Nghost: 5463.00 ave 5463 max 5463 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 115133 ave 115133 max 115133 min
|
||||
Neighs: 115133.0 ave 115133 max 115133 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 115133
|
||||
Ave neighs/atom = 3.59791
|
||||
Ave neighs/atom = 3.5979062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# granular chute flow
|
||||
|
||||
@ -10,12 +9,14 @@ newton off
|
||||
comm_modify vel yes
|
||||
|
||||
read_data data.granular
|
||||
orthogonal box = (0 0 0) to (40 20 37.2886)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
read_data CPU = 0.052 seconds
|
||||
|
||||
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
@ -52,34 +53,34 @@ Neighbor list info ...
|
||||
pair build: half/size/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.42 | 10.42 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.60 Mbytes
|
||||
Step Atoms KinEng c_1 Volume
|
||||
0 32000 784139.13 1601.1263 29833.783
|
||||
100 32000 784292.08 1571.0968 29834.707
|
||||
Loop time of 0.0903978 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.0952788 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9557.751 tau/day, 1106.221 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 9068.124 tau/day, 1049.551 timesteps/s
|
||||
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.046331 | 0.049088 | 0.052195 | 1.2 | 54.30
|
||||
Neigh | 0.0090401 | 0.0091327 | 0.0091863 | 0.1 | 10.10
|
||||
Comm | 0.0073855 | 0.0080023 | 0.0086699 | 0.6 | 8.85
|
||||
Output | 7.1049e-05 | 0.00010067 | 0.00012088 | 0.0 | 0.11
|
||||
Modify | 0.017226 | 0.017449 | 0.01803 | 0.3 | 19.30
|
||||
Other | | 0.006625 | | | 7.33
|
||||
Pair | 0.044316 | 0.047274 | 0.049681 | 1.0 | 49.62
|
||||
Neigh | 0.0079038 | 0.0079354 | 0.0079608 | 0.0 | 8.33
|
||||
Comm | 0.0082569 | 0.0089372 | 0.0094819 | 0.5 | 9.38
|
||||
Output | 6.9857e-05 | 9.3222e-05 | 0.00010514 | 0.0 | 0.10
|
||||
Modify | 0.015689 | 0.016034 | 0.016789 | 0.4 | 16.83
|
||||
Other | | 0.015 | | | 15.75
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7992 min
|
||||
Nlocal: 8000.00 ave 8008 max 7992 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 2439 ave 2450 max 2428 min
|
||||
Nghost: 2439.00 ave 2450 max 2428 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 29500.5 ave 30488 max 28513 min
|
||||
Neighs: 29500.5 ave 30488 max 28513 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 118002
|
||||
Ave neighs/atom = 3.68756
|
||||
Ave neighs/atom = 3.6875625
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
@ -7,14 +6,14 @@ units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00183916 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
@ -44,30 +43,30 @@ Per MPI rank memory allocation (min/avg/max) = 15.82 | 15.82 | 15.82 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
|
||||
Loop time of 1.721 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.59245 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 25101.720 tau/day, 58.106 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 27127.959 tau/day, 62.796 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2551 | 1.2551 | 1.2551 | 0.0 | 72.93
|
||||
Neigh | 0.41825 | 0.41825 | 0.41825 | 0.0 | 24.30
|
||||
Comm | 0.015347 | 0.015347 | 0.015347 | 0.0 | 0.89
|
||||
Output | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.01
|
||||
Modify | 0.023436 | 0.023436 | 0.023436 | 0.0 | 1.36
|
||||
Other | | 0.008766 | | | 0.51
|
||||
Pair | 1.1654 | 1.1654 | 1.1654 | 0.0 | 73.18
|
||||
Neigh | 0.38321 | 0.38321 | 0.38321 | 0.0 | 24.06
|
||||
Comm | 0.014476 | 0.014476 | 0.014476 | 0.0 | 0.91
|
||||
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.01
|
||||
Modify | 0.021453 | 0.021453 | 0.021453 | 0.0 | 1.35
|
||||
Other | | 0.007799 | | | 0.49
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19669 ave 19669 max 19669 min
|
||||
Nghost: 19669.0 ave 19669 max 19669 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1203176
|
||||
Ave neighs/atom = 37.5992
|
||||
Ave neighs/atom = 37.599250
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
@ -7,14 +6,14 @@ units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000587225 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
@ -40,34 +39,34 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
|
||||
Loop time of 0.469936 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.452443 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 91927.316 tau/day, 212.795 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 95481.741 tau/day, 221.023 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.32713 | 0.32917 | 0.33317 | 0.4 | 70.05
|
||||
Neigh | 0.10836 | 0.10931 | 0.11007 | 0.2 | 23.26
|
||||
Comm | 0.015526 | 0.020355 | 0.022399 | 2.0 | 4.33
|
||||
Output | 4.2439e-05 | 5.8353e-05 | 0.00010061 | 0.0 | 0.01
|
||||
Modify | 0.0071156 | 0.0072448 | 0.007309 | 0.1 | 1.54
|
||||
Other | | 0.003793 | | | 0.81
|
||||
Pair | 0.31149 | 0.3132 | 0.31493 | 0.2 | 69.22
|
||||
Neigh | 0.1006 | 0.10164 | 0.10385 | 0.4 | 22.47
|
||||
Comm | 0.02195 | 0.025904 | 0.028603 | 1.6 | 5.73
|
||||
Output | 4.3631e-05 | 7.534e-05 | 0.00015879 | 0.0 | 0.02
|
||||
Modify | 0.0067751 | 0.0073788 | 0.0088398 | 1.0 | 1.63
|
||||
Other | | 0.004243 | | | 0.94
|
||||
|
||||
Nlocal: 8000 ave 8041 max 7958 min
|
||||
Nlocal: 8000.00 ave 8041 max 7958 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 9011 ave 9065 max 8961 min
|
||||
Nghost: 9011.00 ave 9065 max 8961 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 300794 ave 304843 max 297317 min
|
||||
Neighs: 300794.0 ave 304843 max 297317 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1203176
|
||||
Ave neighs/atom = 37.5992
|
||||
Ave neighs/atom = 37.599250
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Ni in MEAM
|
||||
|
||||
@ -7,17 +6,19 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00184226 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style meam/c
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -47,37 +48,37 @@ Neighbor list info ...
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 55.92 | 55.92 | 55.92 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -142400 0 -135782.09 20259.18
|
||||
50 885.10702 -139411.51 0 -135750.54 32425.431
|
||||
100 895.50973 -139454.3 0 -135750.3 31804.185
|
||||
Loop time of 22.9343 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 21.655 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.884 ns/day, 12.741 hours/ns, 4.360 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.995 ns/day, 12.031 hours/ns, 4.618 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 22.397 | 22.397 | 22.397 | 0.0 | 97.66
|
||||
Neigh | 0.48781 | 0.48781 | 0.48781 | 0.0 | 2.13
|
||||
Comm | 0.013967 | 0.013967 | 0.013967 | 0.0 | 0.06
|
||||
Output | 0.00022793 | 0.00022793 | 0.00022793 | 0.0 | 0.00
|
||||
Modify | 0.025412 | 0.025412 | 0.025412 | 0.0 | 0.11
|
||||
Other | | 0.009448 | | | 0.04
|
||||
Pair | 21.181 | 21.181 | 21.181 | 0.0 | 97.81
|
||||
Neigh | 0.42787 | 0.42787 | 0.42787 | 0.0 | 1.98
|
||||
Comm | 0.013557 | 0.013557 | 0.013557 | 0.0 | 0.06
|
||||
Output | 0.00020766 | 0.00020766 | 0.00020766 | 0.0 | 0.00
|
||||
Modify | 0.023456 | 0.023456 | 0.023456 | 0.0 | 0.11
|
||||
Other | | 0.008504 | | | 0.04
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13576 ave 13576 max 13576 min
|
||||
Nghost: 13576.0 ave 13576 max 13576 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 780360 ave 780360 max 780360 min
|
||||
Neighs: 780360.0 ave 780360 max 780360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1560720
|
||||
Ave neighs/atom = 48.7725
|
||||
Ave neighs/atom = 48.772500
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:23
|
||||
Total wall time: 0:00:21
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Ni in MEAM
|
||||
|
||||
@ -7,17 +6,19 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00058651 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style meam/c
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
@ -47,37 +48,37 @@ Neighbor list info ...
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.42 | 17.42 | 17.42 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -142400 0 -135782.09 20259.18
|
||||
50 885.10702 -139411.51 0 -135750.54 32425.431
|
||||
100 895.50973 -139454.3 0 -135750.3 31804.185
|
||||
Loop time of 6.45947 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 6.34746 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 6.688 ns/day, 3.589 hours/ns, 15.481 timesteps/s
|
||||
Performance: 6.806 ns/day, 3.526 hours/ns, 15.754 timesteps/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.22 | 6.2385 | 6.265 | 0.7 | 96.58
|
||||
Neigh | 0.12657 | 0.12691 | 0.12721 | 0.1 | 1.96
|
||||
Comm | 0.052339 | 0.07915 | 0.097897 | 5.9 | 1.23
|
||||
Output | 9.7752e-05 | 0.0001151 | 0.00016594 | 0.0 | 0.00
|
||||
Modify | 0.010194 | 0.010291 | 0.010442 | 0.1 | 0.16
|
||||
Other | | 0.004529 | | | 0.07
|
||||
Pair | 6.0585 | 6.1109 | 6.1535 | 1.4 | 96.27
|
||||
Neigh | 0.11286 | 0.11651 | 0.12455 | 1.4 | 1.84
|
||||
Comm | 0.058046 | 0.099641 | 0.15569 | 11.7 | 1.57
|
||||
Output | 9.0122e-05 | 0.00016046 | 0.0003624 | 0.0 | 0.00
|
||||
Modify | 0.010822 | 0.011674 | 0.014224 | 1.4 | 0.18
|
||||
Other | | 0.008601 | | | 0.14
|
||||
|
||||
Nlocal: 8000 ave 8045 max 7947 min
|
||||
Nlocal: 8000.00 ave 8045 max 7947 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 6066.75 ave 6120 max 6021 min
|
||||
Nghost: 6066.75 ave 6120 max 6021 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 195090 ave 196403 max 193697 min
|
||||
Neighs: 195090.0 ave 196403 max 193697 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
FullNghs: 390180 ave 392616 max 387490 min
|
||||
FullNghs: 390180.0 ave 392616 max 387490 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1560720
|
||||
Ave neighs/atom = 48.7725
|
||||
Ave neighs/atom = 48.772500
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Crack growth in notched 3D Peridynamic block
|
||||
|
||||
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
|
||||
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
|
||||
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
|
||||
create_box 3 plate
|
||||
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region plate
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00362897 secs
|
||||
create_atoms CPU = 0.004 seconds
|
||||
|
||||
|
||||
pair_style peri/pmb
|
||||
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
|
||||
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
|
||||
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
|
||||
set region topleft type 2
|
||||
Setting atom values ...
|
||||
5000 settings made for type
|
||||
set region topright type 3
|
||||
Setting atom values ...
|
||||
5000 settings made for type
|
||||
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
|
||||
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
|
||||
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
|
||||
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
|
||||
set group all density ${mydensity}
|
||||
set group all density 2440
|
||||
Setting atom values ...
|
||||
32000 settings made for density
|
||||
variable myvolume equal ($h)^3
|
||||
variable myvolume equal (0.0005)^3
|
||||
set group all volume ${myvolume}
|
||||
set group all volume 1.25e-10
|
||||
Setting atom values ...
|
||||
32000 settings made for volume
|
||||
|
||||
velocity all set 0.0 0.0 0.0 sum no units box
|
||||
@ -184,23 +187,23 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
|
||||
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
|
||||
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
|
||||
Loop time of 11.0398 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 10.1036 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.005 | 11.005 | 11.005 | 0.0 | 99.68
|
||||
Pair | 10.07 | 10.07 | 10.07 | 0.0 | 99.67
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 | 0.0 | 0.00
|
||||
Output | 0.00057292 | 0.00057292 | 0.00057292 | 0.0 | 0.01
|
||||
Modify | 0.0256 | 0.0256 | 0.0256 | 0.0 | 0.23
|
||||
Other | | 0.008592 | | | 0.08
|
||||
Comm | 6.6519e-05 | 6.6519e-05 | 6.6519e-05 | 0.0 | 0.00
|
||||
Output | 0.00051737 | 0.00051737 | 0.00051737 | 0.0 | 0.01
|
||||
Modify | 0.024288 | 0.024288 | 0.024288 | 0.0 | 0.24
|
||||
Other | | 0.008486 | | | 0.08
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -208,10 +211,10 @@ FullNghs: 1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13488836
|
||||
Ave neighs/atom = 421.526
|
||||
Ave neighs/atom = 421.52612
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:11
|
||||
Total wall time: 0:00:10
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Crack growth in notched 3D Peridynamic block
|
||||
|
||||
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
|
||||
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
|
||||
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
|
||||
create_box 3 plate
|
||||
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region plate
|
||||
Created 32000 atoms
|
||||
Time spent = 0.0011344 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
|
||||
pair_style peri/pmb
|
||||
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
|
||||
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
|
||||
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
|
||||
set region topleft type 2
|
||||
Setting atom values ...
|
||||
5000 settings made for type
|
||||
set region topright type 3
|
||||
Setting atom values ...
|
||||
5000 settings made for type
|
||||
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
|
||||
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
|
||||
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
|
||||
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
|
||||
set group all density ${mydensity}
|
||||
set group all density 2440
|
||||
Setting atom values ...
|
||||
32000 settings made for density
|
||||
variable myvolume equal ($h)^3
|
||||
variable myvolume equal (0.0005)^3
|
||||
set group all volume ${myvolume}
|
||||
set group all volume 1.25e-10
|
||||
Setting atom values ...
|
||||
32000 settings made for volume
|
||||
|
||||
velocity all set 0.0 0.0 0.0 sum no units box
|
||||
@ -176,7 +179,7 @@ Neighbor list info ...
|
||||
Peridynamic bonds:
|
||||
total # of bonds = 3457032
|
||||
bonds/atom = 108.032
|
||||
Per MPI rank memory allocation (min/avg/max) = 47.63 | 48.11 | 48.78 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 47.70 | 48.18 | 48.85 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
|
||||
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
|
||||
@ -184,34 +187,34 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
|
||||
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
|
||||
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
|
||||
Loop time of 2.8928 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 2.82804 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7472 | 2.7951 | 2.8585 | 2.9 | 96.62
|
||||
Pair | 2.6021 | 2.6599 | 2.7081 | 2.4 | 94.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.019592 | 0.083156 | 0.13278 | 17.0 | 2.87
|
||||
Output | 0.00022125 | 0.00034326 | 0.00058961 | 0.0 | 0.01
|
||||
Modify | 0.0083542 | 0.0089623 | 0.0095983 | 0.5 | 0.31
|
||||
Other | | 0.005276 | | | 0.18
|
||||
Comm | 0.10341 | 0.15313 | 0.21057 | 10.3 | 5.41
|
||||
Output | 0.00020409 | 0.00041658 | 0.00093699 | 0.0 | 0.01
|
||||
Modify | 0.008944 | 0.0092288 | 0.0095088 | 0.3 | 0.33
|
||||
Other | | 0.005395 | | | 0.19
|
||||
|
||||
Nlocal: 8000 ave 8000 max 8000 min
|
||||
Nlocal: 8000.00 ave 8000 max 8000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5125 ave 5125 max 5125 min
|
||||
Nghost: 5125.00 ave 5125 max 5125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
|
||||
Neighs: 1.68610e+06 ave 1.77502e+06 max 1.60625e+06 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
|
||||
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 13488836
|
||||
Ave neighs/atom = 421.526
|
||||
Ave neighs/atom = 421.52612
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:02
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Rhodopsin model
|
||||
|
||||
@ -17,7 +16,8 @@ pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.protein
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
||||
Reading data file ...
|
||||
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
@ -39,16 +39,22 @@ read_data data.protein
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
special bonds CPU = 0.011 seconds
|
||||
read_data CPU = 0.125 seconds
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
find clusters CPU = 0.006 seconds
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
@ -58,13 +64,13 @@ timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.248835
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.24883488
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0355478
|
||||
estimated relative force accuracy = 0.000107051
|
||||
using double precision FFTs
|
||||
estimated absolute RMS force accuracy = 0.035547797
|
||||
estimated relative force accuracy = 0.00010705113
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 41070 25600
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
@ -78,46 +84,46 @@ Neighbor list info ...
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 140.0 | 140.0 | 140.0 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
|
||||
Volume = 307995.0335
|
||||
---------------- Step 100 ----- CPU = 23.7567 (sec) ----------------
|
||||
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
|
||||
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
|
||||
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
|
||||
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
|
||||
Volume = 308133.9933
|
||||
Loop time of 23.7568 on 1 procs for 100 steps with 32000 atoms
|
||||
---------------- Step 100 ----- CPU = 20.0022 (sec) ----------------
|
||||
TotEng = -25290.7304 KinEng = 21591.9084 Temp = 301.0906
|
||||
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
|
||||
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
|
||||
E_coul = 206659.5226 E_long = -270404.9730 Press = 6.7406
|
||||
Volume = 308134.2285
|
||||
Loop time of 20.0022 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.727 ns/day, 32.995 hours/ns, 4.209 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.864 ns/day, 27.781 hours/ns, 4.999 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.905 | 17.905 | 17.905 | 0.0 | 75.37
|
||||
Bond | 0.73417 | 0.73417 | 0.73417 | 0.0 | 3.09
|
||||
Kspace | 1.4676 | 1.4676 | 1.4676 | 0.0 | 6.18
|
||||
Neigh | 2.9907 | 2.9907 | 2.9907 | 0.0 | 12.59
|
||||
Comm | 0.037427 | 0.037427 | 0.037427 | 0.0 | 0.16
|
||||
Output | 0.00011754 | 0.00011754 | 0.00011754 | 0.0 | 0.00
|
||||
Modify | 0.60985 | 0.60985 | 0.60985 | 0.0 | 2.57
|
||||
Other | | 0.01201 | | | 0.05
|
||||
Pair | 15 | 15 | 15 | 0.0 | 74.99
|
||||
Bond | 0.65091 | 0.65091 | 0.65091 | 0.0 | 3.25
|
||||
Kspace | 1.2144 | 1.2144 | 1.2144 | 0.0 | 6.07
|
||||
Neigh | 2.6096 | 2.6096 | 2.6096 | 0.0 | 13.05
|
||||
Comm | 0.035203 | 0.035203 | 0.035203 | 0.0 | 0.18
|
||||
Output | 0.00010848 | 0.00010848 | 0.00010848 | 0.0 | 0.00
|
||||
Modify | 0.48116 | 0.48116 | 0.48116 | 0.0 | 2.41
|
||||
Other | | 0.01032 | | | 0.05
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 47958 ave 47958 max 47958 min
|
||||
Nghost: 47958.0 ave 47958 max 47958 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12028098
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Total # of neighbors = 12028093
|
||||
Ave neighs/atom = 375.87791
|
||||
Ave special neighs/atom = 7.4318750
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
Total wall time: 0:00:20
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Rhodopsin model
|
||||
|
||||
@ -17,7 +16,8 @@ pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.protein
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
||||
Reading data file ...
|
||||
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
@ -39,16 +39,22 @@ read_data data.protein
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
special bonds CPU = 0.005 seconds
|
||||
read_data CPU = 0.210 seconds
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
@ -58,13 +64,13 @@ timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.248835
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.24883488
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0355478
|
||||
estimated relative force accuracy = 0.000107051
|
||||
using double precision FFTs
|
||||
estimated absolute RMS force accuracy = 0.035547797
|
||||
estimated relative force accuracy = 0.00010705113
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 13230 6400
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
@ -78,46 +84,46 @@ Neighbor list info ...
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 49.25 | 49.35 | 49.64 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
|
||||
Volume = 307995.0335
|
||||
---------------- Step 100 ----- CPU = 6.3997 (sec) ----------------
|
||||
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
|
||||
PotEng = -46882.6483 E_bond = 2567.9789 E_angle = 10781.9556
|
||||
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
|
||||
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
|
||||
Volume = 308133.9933
|
||||
Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
|
||||
---------------- Step 100 ----- CPU = 5.5375 (sec) ----------------
|
||||
TotEng = -25290.7303 KinEng = 21591.9085 Temp = 301.0906
|
||||
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
|
||||
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
|
||||
E_coul = 206659.5225 E_long = -270404.9730 Press = 6.7406
|
||||
Volume = 308134.2285
|
||||
Loop time of 5.53765 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 3.120 ns/day, 7.691 hours/ns, 18.058 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4434 | 4.5321 | 4.6846 | 4.3 | 70.82
|
||||
Bond | 0.17894 | 0.18568 | 0.19951 | 1.9 | 2.90
|
||||
Kspace | 0.4651 | 0.61064 | 0.69123 | 11.1 | 9.54
|
||||
Neigh | 0.7739 | 0.77394 | 0.774 | 0.0 | 12.09
|
||||
Comm | 0.057676 | 0.069183 | 0.07901 | 3.0 | 1.08
|
||||
Output | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 | 0.0 | 0.00
|
||||
Modify | 0.21444 | 0.21866 | 0.22524 | 0.9 | 3.42
|
||||
Other | | 0.009451 | | | 0.15
|
||||
Pair | 3.8921 | 3.9427 | 4.0762 | 3.9 | 71.20
|
||||
Bond | 0.16218 | 0.16829 | 0.17972 | 1.7 | 3.04
|
||||
Kspace | 0.35196 | 0.48475 | 0.53996 | 11.1 | 8.75
|
||||
Neigh | 0.69975 | 0.69981 | 0.69988 | 0.0 | 12.64
|
||||
Comm | 0.04908 | 0.049445 | 0.049767 | 0.1 | 0.89
|
||||
Output | 5.1737e-05 | 8.5056e-05 | 0.00018382 | 0.0 | 0.00
|
||||
Modify | 0.18393 | 0.18474 | 0.18528 | 0.1 | 3.34
|
||||
Other | | 0.007858 | | | 0.14
|
||||
|
||||
Nlocal: 8000 ave 8143 max 7933 min
|
||||
Nlocal: 8000.00 ave 8143 max 7933 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 22733.5 ave 22769 max 22693 min
|
||||
Nghost: 22733.5 ave 22769 max 22693 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
|
||||
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 12028098
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Total # of neighbors = 12028093
|
||||
Ave neighs/atom = 375.87791
|
||||
Ave special neighs/atom = 7.4318750
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
Total wall time: 0:00:05
|
||||
96
bench/POTENTIALS/log.9Oct20.reaxc.1
Normal file
96
bench/POTENTIALS/log.9Oct20.reaxc.1
Normal file
@ -0,0 +1,96 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.reax
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
58 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 7 8 10
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32480 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
velocity all create 300.0 9999
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
|
||||
|
||||
timestep 0.1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 12 13 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 1727.0 | 1727.0 | 1727.0 Mbytes
|
||||
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
|
||||
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
|
||||
10 299.37479 28983.59 -3232075.2 21746.783 -23987.396 7610.3039 -3203091.6
|
||||
20 295.58549 28616.733 -3231710.1 18178.443 -10872.027 10603.19 -3203093.3
|
||||
30 289.48845 28026.456 -3231123.3 12146.101 4985.2572 13364.258 -3203096.8
|
||||
40 282.66408 27365.763 -3230467.5 4284.1187 18132.512 14133.51 -3203101.7
|
||||
50 274.97007 26620.878 -3229730.4 -3718.933 25520.016 12551.903 -3203109.5
|
||||
60 266.11301 25763.393 -3228883.8 -9271.3498 27307.451 9753.2362 -3203120.4
|
||||
70 259.32635 25106.351 -3228237.2 -11150.623 24238.509 6578.531 -3203130.8
|
||||
80 260.33969 25204.456 -3228344.2 -9576.4144 16737.758 3454.6426 -3203139.7
|
||||
90 269.9021 26130.229 -3229275.5 -5905.8652 5246.3236 467.53439 -3203145.2
|
||||
100 280.76723 27182.123 -3230330.6 -1363.6002 -8133.2093 -1689.6535 -3203148.5
|
||||
Loop time of 213.234 on 1 procs for 100 steps with 32480 atoms
|
||||
|
||||
Performance: 0.004 ns/day, 5923.154 hours/ns, 0.469 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 157 | 157 | 157 | 0.0 | 73.63
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.024997 | 0.024997 | 0.024997 | 0.0 | 0.01
|
||||
Output | 0.0022025 | 0.0022025 | 0.0022025 | 0.0 | 0.00
|
||||
Modify | 56.19 | 56.19 | 56.19 | 0.0 | 26.35
|
||||
Other | | 0.01211 | | | 0.01
|
||||
|
||||
Nlocal: 32480.0 ave 32480 max 32480 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 45128.0 ave 45128 max 45128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12778082
|
||||
Ave neighs/atom = 393.41385
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:03:37
|
||||
96
bench/POTENTIALS/log.9Oct20.reaxc.4
Normal file
96
bench/POTENTIALS/log.9Oct20.reaxc.4
Normal file
@ -0,0 +1,96 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.reax
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
58 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 7 8 10
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
32480 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
velocity all create 300.0 9999
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H O N
|
||||
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
|
||||
|
||||
timestep 0.1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp ke pe pxx pyy pzz etotal
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 12 13 12
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 647.0 | 647.0 | 647.0 Mbytes
|
||||
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
|
||||
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
|
||||
10 299.37479 28983.59 -3232075.2 21746.771 -23987.411 7610.2901 -3203091.6
|
||||
20 295.58551 28616.736 -3231710.1 18178.439 -10871.954 10603.303 -3203093.3
|
||||
30 289.48844 28026.456 -3231123.2 12146.289 4985.5678 13364.519 -3203096.8
|
||||
40 282.66406 27365.762 -3230467.4 4284.8179 18133.406 14134.156 -3203101.7
|
||||
50 274.97009 26620.88 -3229730.3 -3718.6796 25520.338 12552.205 -3203109.5
|
||||
60 266.11302 25763.394 -3228883.8 -9271.5644 27307.146 9753.1034 -3203120.4
|
||||
70 259.32636 25106.352 -3228237.1 -11150.66 24238.705 6578.7141 -3203130.8
|
||||
80 260.33966 25204.454 -3228344.1 -9576.2474 16737.753 3454.7607 -3203139.7
|
||||
90 269.90207 26130.226 -3229275.5 -5905.8809 5246.1687 467.42114 -3203145.2
|
||||
100 280.76722 27182.122 -3230330.6 -1363.4752 -8133.2096 -1689.5922 -3203148.5
|
||||
Loop time of 69.1187 on 4 procs for 100 steps with 32480 atoms
|
||||
|
||||
Performance: 0.013 ns/day, 1919.965 hours/ns, 1.447 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 45.964 | 48.533 | 51.423 | 29.3 | 70.22
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.19604 | 3.0913 | 5.6647 | 116.3 | 4.47
|
||||
Output | 0.00074649 | 0.0011722 | 0.0023553 | 2.0 | 0.00
|
||||
Modify | 17.48 | 17.485 | 17.489 | 0.1 | 25.30
|
||||
Other | | 0.008528 | | | 0.01
|
||||
|
||||
Nlocal: 8120.00 ave 8120 max 8120 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21992.0 ave 21992 max 21992 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13930976
|
||||
Ave neighs/atom = 428.90936
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:10
|
||||
90
bench/POTENTIALS/log.9Oct20.rebo.1
Normal file
90
bench/POTENTIALS/log.9Oct20.rebo.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.rebo
|
||||
Reading data file ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 17 16 2
|
||||
Replicating atoms ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.rebo C H
|
||||
Reading rebo potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0748
|
||||
10 179.37985 -137931.27 0 -137174.48 15655.936
|
||||
20 206.87654 -138046.99 0 -137174.19 -24042.627
|
||||
30 150.80122 -137807.43 0 -137171.21 -16524.118
|
||||
40 173.24945 -137902.35 0 -137171.42 -5716.9119
|
||||
50 151.80455 -137812.36 0 -137171.91 3480.4584
|
||||
60 199.08777 -138013.82 0 -137173.88 17881.372
|
||||
70 217.85748 -138093.86 0 -137174.73 -12270.999
|
||||
80 202.37482 -138029.39 0 -137175.59 -7622.7319
|
||||
90 194.90628 -137997.05 0 -137174.75 -32267.471
|
||||
100 185.17818 -137954.51 0 -137173.26 -6901.7499
|
||||
Loop time of 4.83649 on 1 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 0.893 ns/day, 26.869 hours/ns, 20.676 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.3248 | 3.3248 | 3.3248 | 0.0 | 68.74
|
||||
Neigh | 1.4583 | 1.4583 | 1.4583 | 0.0 | 30.15
|
||||
Comm | 0.01934 | 0.01934 | 0.01934 | 0.0 | 0.40
|
||||
Output | 0.0011871 | 0.0011871 | 0.0011871 | 0.0 | 0.02
|
||||
Modify | 0.023516 | 0.023516 | 0.023516 | 0.0 | 0.49
|
||||
Other | | 0.009316 | | | 0.19
|
||||
|
||||
Nlocal: 32640.0 ave 32640 max 32640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 26460.0 ave 26460 max 26460 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.18793
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
90
bench/POTENTIALS/log.9Oct20.rebo.4
Normal file
90
bench/POTENTIALS/log.9Oct20.rebo.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REBO polyethelene benchmark
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
read_data data.rebo
|
||||
Reading data file ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
60 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
replicate 17 16 2
|
||||
Replicating atoms ...
|
||||
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32640 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
pair_style rebo
|
||||
pair_coeff * * CH.rebo C H
|
||||
Reading rebo potential file CH.rebo with DATE: 2018-7-3
|
||||
|
||||
velocity all create 300.0 761341
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.5
|
||||
ghost atom cutoff = 6.5
|
||||
binsize = 3.25, bins = 22 21 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair rebo, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.80 | 12.00 | 12.19 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -138442.83 0 -137177.16 2463.0748
|
||||
10 179.37985 -137931.27 0 -137174.48 15655.936
|
||||
20 206.87654 -138046.99 0 -137174.19 -24042.627
|
||||
30 150.80122 -137807.43 0 -137171.21 -16524.118
|
||||
40 173.24945 -137902.35 0 -137171.42 -5716.9119
|
||||
50 151.80455 -137812.36 0 -137171.91 3480.4584
|
||||
60 199.08777 -138013.82 0 -137173.88 17881.372
|
||||
70 217.85748 -138093.86 0 -137174.73 -12270.999
|
||||
80 202.37482 -138029.39 0 -137175.59 -7622.7319
|
||||
90 194.90628 -137997.05 0 -137174.75 -32267.471
|
||||
100 185.17818 -137954.51 0 -137173.26 -6901.7499
|
||||
Loop time of 1.74701 on 4 procs for 100 steps with 32640 atoms
|
||||
|
||||
Performance: 2.473 ns/day, 9.706 hours/ns, 57.241 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.89836 | 0.96998 | 1.054 | 6.0 | 55.52
|
||||
Neigh | 0.453 | 0.47091 | 0.50316 | 2.8 | 26.96
|
||||
Comm | 0.15706 | 0.27291 | 0.36547 | 14.5 | 15.62
|
||||
Output | 0.00047016 | 0.00073808 | 0.0015287 | 0.0 | 0.04
|
||||
Modify | 0.0093558 | 0.010209 | 0.011958 | 1.0 | 0.58
|
||||
Other | | 0.02227 | | | 1.27
|
||||
|
||||
Nlocal: 8160.00 ave 8163 max 8157 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11605.8 ave 11615 max 11593 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4902134
|
||||
Ave neighs/atom = 150.18793
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
147
bench/POTENTIALS/log.9Oct20.spce.1
Normal file
147
bench/POTENTIALS/log.9Oct20.spce.1
Normal file
@ -0,0 +1,147 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SPC/E water box benchmark
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
Reading data file ...
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.009 seconds
|
||||
|
||||
replicate 2 4 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
36000 atoms
|
||||
24000 bonds
|
||||
12000 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
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 = 0.005 seconds
|
||||
replicate CPU = 0.012 seconds
|
||||
|
||||
pair_style lj/cut/coul/long 9.8 9.8
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.005 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
12000 = # of frozen angles
|
||||
find clusters CPU = 0.005 seconds
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
velocity all create 300 432567 dist uniform
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style one
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.2688011
|
||||
grid = 36 64 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.033101471
|
||||
estimated relative force accuracy = 9.9684097e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 91977 55296
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.8
|
||||
ghost atom cutoff = 11.8
|
||||
binsize = 5.9, bins = 13 25 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 105.4 | 105.4 | 105.4 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -133281.51 0 -111820.57 516.17807
|
||||
50 264.98553 -136986.74 0 -118030.61 -440.29256
|
||||
100 274.45966 -136364.57 0 -116730.69 -128.61948
|
||||
Loop time of 18.5133 on 1 procs for 100 steps with 36000 atoms
|
||||
|
||||
Performance: 0.933 ns/day, 25.713 hours/ns, 5.402 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.557 | 14.557 | 14.557 | 0.0 | 78.63
|
||||
Bond | 7.1764e-05 | 7.1764e-05 | 7.1764e-05 | 0.0 | 0.00
|
||||
Kspace | 1.7651 | 1.7651 | 1.7651 | 0.0 | 9.53
|
||||
Neigh | 1.8703 | 1.8703 | 1.8703 | 0.0 | 10.10
|
||||
Comm | 0.042219 | 0.042219 | 0.042219 | 0.0 | 0.23
|
||||
Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.00
|
||||
Modify | 0.26983 | 0.26983 | 0.26983 | 0.0 | 1.46
|
||||
Other | | 0.008397 | | | 0.05
|
||||
|
||||
Nlocal: 36000.0 ave 36000 max 36000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 56963.0 ave 56963 max 56963 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12462451
|
||||
Ave neighs/atom = 346.17919
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 6
|
||||
Total wall time: 0:00:19
|
||||
147
bench/POTENTIALS/log.9Oct20.spce.4
Normal file
147
bench/POTENTIALS/log.9Oct20.spce.4
Normal file
@ -0,0 +1,147 @@
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SPC/E water box benchmark
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
Reading data file ...
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
replicate 2 4 1
|
||||
Replicating atoms ...
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
36000 atoms
|
||||
24000 bonds
|
||||
12000 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
replicate CPU = 0.005 seconds
|
||||
|
||||
pair_style lj/cut/coul/long 9.8 9.8
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
pair_coeff * 2 0.0000 0.0000
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.004 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
12000 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
velocity all create 300 432567 dist uniform
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style one
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.2688011
|
||||
grid = 36 64 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.033101471
|
||||
estimated relative force accuracy = 9.9684097e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 27993 13824
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.8
|
||||
ghost atom cutoff = 11.8
|
||||
binsize = 5.9, bins = 13 25 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 37.90 | 37.90 | 37.90 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -133281.51 0 -111820.57 516.17807
|
||||
50 264.98553 -136986.74 0 -118030.61 -440.29255
|
||||
100 274.45966 -136364.57 0 -116730.69 -128.61954
|
||||
Loop time of 5.44355 on 4 procs for 100 steps with 36000 atoms
|
||||
|
||||
Performance: 3.174 ns/day, 7.560 hours/ns, 18.370 timesteps/s
|
||||
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.82 | 3.8744 | 3.9155 | 1.8 | 71.17
|
||||
Bond | 7.8917e-05 | 8.6784e-05 | 9.4891e-05 | 0.0 | 0.00
|
||||
Kspace | 0.79192 | 0.83671 | 0.88328 | 3.5 | 15.37
|
||||
Neigh | 0.51754 | 0.5178 | 0.51789 | 0.0 | 9.51
|
||||
Comm | 0.069774 | 0.078783 | 0.088247 | 2.3 | 1.45
|
||||
Output | 9.0361e-05 | 0.00015712 | 0.00035048 | 0.0 | 0.00
|
||||
Modify | 0.12822 | 0.13016 | 0.13486 | 0.8 | 2.39
|
||||
Other | | 0.005435 | | | 0.10
|
||||
|
||||
Nlocal: 9000.00 ave 9002 max 8998 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 24134.2 ave 24184 max 24062 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 12462451
|
||||
Ave neighs/atom = 346.17919
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 6
|
||||
Total wall time: 0:00:05
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Si via Stillinger-Weber
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00191712 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -138771.2 0 -134635 6866.6499
|
||||
100 508.80533 -136736.12 0 -134631.6 6361.7858
|
||||
Loop time of 5.66634 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 3.9309 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.525 ns/day, 15.740 hours/ns, 17.648 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 2.198 ns/day, 10.919 hours/ns, 25.439 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.5464 | 5.5464 | 5.5464 | 0.0 | 97.88
|
||||
Neigh | 0.075834 | 0.075834 | 0.075834 | 0.0 | 1.34
|
||||
Comm | 0.0092049 | 0.0092049 | 0.0092049 | 0.0 | 0.16
|
||||
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
|
||||
Modify | 0.024666 | 0.024666 | 0.024666 | 0.0 | 0.44
|
||||
Other | | 0.01014 | | | 0.18
|
||||
Pair | 3.8206 | 3.8206 | 3.8206 | 0.0 | 97.19
|
||||
Neigh | 0.067368 | 0.067368 | 0.067368 | 0.0 | 1.71
|
||||
Comm | 0.0091503 | 0.0091503 | 0.0091503 | 0.0 | 0.23
|
||||
Output | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.00
|
||||
Modify | 0.023839 | 0.023839 | 0.023839 | 0.0 | 0.61
|
||||
Other | | 0.009882 | | | 0.25
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12495 ave 12495 max 12495 min
|
||||
Nghost: 12495.0 ave 12495 max 12495 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 894818 ave 894818 max 894818 min
|
||||
FullNghs: 894818.0 ave 894818 max 894818 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 894818
|
||||
Ave neighs/atom = 27.9631
|
||||
Ave neighs/atom = 27.963062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
Total wall time: 0:00:03
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Si via Stillinger-Weber
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000604153 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 4.104 | 4.104 | 4.104 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -138771.2 0 -134635 6866.6499
|
||||
100 508.80533 -136736.12 0 -134631.6 6361.7858
|
||||
Loop time of 1.47105 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.04386 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 5.873 ns/day, 4.086 hours/ns, 67.978 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 8.277 ns/day, 2.900 hours/ns, 95.798 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3788 | 1.3929 | 1.4053 | 0.8 | 94.69
|
||||
Neigh | 0.019134 | 0.019502 | 0.019816 | 0.2 | 1.33
|
||||
Comm | 0.024183 | 0.035734 | 0.049122 | 4.7 | 2.43
|
||||
Output | 5.1975e-05 | 6.6102e-05 | 0.00010204 | 0.0 | 0.00
|
||||
Modify | 0.0063825 | 0.0064374 | 0.0064764 | 0.0 | 0.44
|
||||
Other | | 0.01638 | | | 1.11
|
||||
Pair | 0.96496 | 0.97632 | 0.9978 | 1.3 | 93.53
|
||||
Neigh | 0.01732 | 0.017998 | 0.019718 | 0.7 | 1.72
|
||||
Comm | 0.012035 | 0.036398 | 0.049588 | 7.7 | 3.49
|
||||
Output | 4.5061e-05 | 5.5015e-05 | 7.7248e-05 | 0.0 | 0.01
|
||||
Modify | 0.0070148 | 0.0070775 | 0.0071096 | 0.0 | 0.68
|
||||
Other | | 0.006012 | | | 0.58
|
||||
|
||||
Nlocal: 8000 ave 8015 max 7978 min
|
||||
Nlocal: 8000.00 ave 8015 max 7978 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 4995 ave 5017 max 4980 min
|
||||
Nghost: 4995.00 ave 5017 max 4980 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 223704 ave 224108 max 223131 min
|
||||
FullNghs: 223704.0 ave 224108 max 223131 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 894818
|
||||
Ave neighs/atom = 27.9631
|
||||
Ave neighs/atom = 27.963062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Si via Tersoff
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.0019412 secs
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -42,36 +42,36 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.1 | 11.1 | 11.1 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.11 | 11.11 | 11.11 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -148173.19 0 -144036.99 7019.4434
|
||||
100 430.57813 -145815.61 0 -144034.65 -14550.734
|
||||
Loop time of 8.53088 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 4.71424 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.013 ns/day, 23.697 hours/ns, 11.722 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.833 ns/day, 13.095 hours/ns, 21.212 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.4236 | 8.4236 | 8.4236 | 0.0 | 98.74
|
||||
Neigh | 0.065852 | 0.065852 | 0.065852 | 0.0 | 0.77
|
||||
Comm | 0.0078607 | 0.0078607 | 0.0078607 | 0.0 | 0.09
|
||||
Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.00
|
||||
Modify | 0.023968 | 0.023968 | 0.023968 | 0.0 | 0.28
|
||||
Other | | 0.009521 | | | 0.11
|
||||
Pair | 4.612 | 4.612 | 4.612 | 0.0 | 97.83
|
||||
Neigh | 0.060618 | 0.060618 | 0.060618 | 0.0 | 1.29
|
||||
Comm | 0.008847 | 0.008847 | 0.008847 | 0.0 | 0.19
|
||||
Output | 9.9659e-05 | 9.9659e-05 | 9.9659e-05 | 0.0 | 0.00
|
||||
Modify | 0.023234 | 0.023234 | 0.023234 | 0.0 | 0.49
|
||||
Other | | 0.00941 | | | 0.20
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Nlocal: 32000.0 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11537 ave 11537 max 11537 min
|
||||
Nghost: 11537.0 ave 11537 max 11537 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 530500 ave 530500 max 530500 min
|
||||
FullNghs: 530500.0 ave 530500 max 530500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 530500
|
||||
Ave neighs/atom = 16.5781
|
||||
Ave neighs/atom = 16.578125
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
Total wall time: 0:00:04
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (16 Mar 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (9 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# bulk Si via Tersoff
|
||||
|
||||
@ -7,17 +6,18 @@ units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
region box block 0 20 0 20 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000605822 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -42,36 +42,36 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.754 | 3.754 | 3.754 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1000 -148173.19 0 -144036.99 7019.4434
|
||||
100 430.57813 -145815.61 0 -144034.65 -14550.734
|
||||
Loop time of 2.16161 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.32053 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.997 ns/day, 6.004 hours/ns, 46.262 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.543 ns/day, 3.668 hours/ns, 75.727 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1122 | 2.1165 | 2.122 | 0.2 | 97.91
|
||||
Neigh | 0.016894 | 0.016915 | 0.016955 | 0.0 | 0.78
|
||||
Comm | 0.012348 | 0.017858 | 0.022105 | 2.7 | 0.83
|
||||
Output | 4.7684e-05 | 6.2048e-05 | 9.9421e-05 | 0.0 | 0.00
|
||||
Modify | 0.0064063 | 0.0064579 | 0.0065169 | 0.0 | 0.30
|
||||
Other | | 0.003793 | | | 0.18
|
||||
Pair | 1.1729 | 1.2118 | 1.2453 | 2.3 | 91.77
|
||||
Neigh | 0.015989 | 0.016319 | 0.016708 | 0.3 | 1.24
|
||||
Comm | 0.046884 | 0.078767 | 0.11602 | 8.9 | 5.96
|
||||
Output | 3.9816e-05 | 7.0453e-05 | 0.00015831 | 0.0 | 0.01
|
||||
Modify | 0.0070612 | 0.0071967 | 0.0073555 | 0.1 | 0.54
|
||||
Other | | 0.006331 | | | 0.48
|
||||
|
||||
Nlocal: 8000 ave 8005 max 7993 min
|
||||
Nlocal: 8000.00 ave 8005 max 7993 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 4580.25 ave 4593 max 4567 min
|
||||
Nghost: 4580.25 ave 4593 max 4567 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 132625 ave 132785 max 132562 min
|
||||
FullNghs: 132625.0 ave 132785 max 132562 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 530500
|
||||
Ave neighs/atom = 16.5781
|
||||
Ave neighs/atom = 16.578125
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
Total wall time: 0:00:01
|
||||
@ -379,6 +379,13 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
# optionally enable building script wrappers using swig
|
||||
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
|
||||
if(WITH_SWIG)
|
||||
get_filename_component(LAMMPS_SWIG_DIR ${LAMMPS_SOURCE_DIR}/../tools/swig ABSOLUTE)
|
||||
add_subdirectory(${LAMMPS_SWIG_DIR} swig)
|
||||
endif()
|
||||
|
||||
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
|
||||
separate_arguments(CMAKE_TUNE_FLAGS)
|
||||
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
|
||||
@ -584,7 +591,7 @@ endif()
|
||||
|
||||
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
|
||||
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
|
||||
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
|
||||
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
|
||||
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
|
||||
@ -613,48 +620,7 @@ if(BUILD_SHARED_LIBS)
|
||||
endif()
|
||||
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
|
||||
|
||||
if(BUILD_TOOLS)
|
||||
add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
|
||||
target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||
install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
|
||||
include(CheckGeneratorSupport)
|
||||
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
|
||||
include(CheckLanguage)
|
||||
check_language(Fortran)
|
||||
if(CMAKE_Fortran_COMPILER)
|
||||
enable_language(Fortran)
|
||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
||||
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
else()
|
||||
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
|
||||
endif()
|
||||
else()
|
||||
message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
|
||||
endif()
|
||||
|
||||
enable_language(C)
|
||||
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
|
||||
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
|
||||
add_executable(msi2lmp ${MSI2LMP_SOURCES})
|
||||
target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
|
||||
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
|
||||
endif()
|
||||
|
||||
if(BUILD_LAMMPS_SHELL)
|
||||
find_package(PkgConfig REQUIRED)
|
||||
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
|
||||
if(NOT LAMMPS_EXCEPTIONS)
|
||||
message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
|
||||
endif()
|
||||
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp)
|
||||
target_compile_definitions(lammps-shell PRIVATE -DLAMMPS_LIB_NO_MPI)
|
||||
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
|
||||
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
endif()
|
||||
|
||||
include(Tools)
|
||||
include(Documentation)
|
||||
|
||||
###############################################################################
|
||||
@ -737,23 +703,31 @@ include(Testing)
|
||||
include(CodeCoverage)
|
||||
include(CodingStandard)
|
||||
|
||||
###############################################################################
|
||||
# Print package summary
|
||||
###############################################################################
|
||||
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||
if(PKG_${PKG})
|
||||
message(STATUS "Building package: ${PKG}")
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
|
||||
include(FeatureSummary)
|
||||
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
|
||||
message(STATUS "<<< Build configuration >>>
|
||||
Operating System: ${CMAKE_SYSTEM_NAME}
|
||||
Build type: ${CMAKE_BUILD_TYPE}
|
||||
Install path: ${CMAKE_INSTALL_PREFIX}
|
||||
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
|
||||
-- <<< Compilers and Flags: >>>
|
||||
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
|
||||
###############################################################################
|
||||
# Print package summary
|
||||
###############################################################################
|
||||
set(ENABLED_PACKAGES)
|
||||
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||
if(PKG_${PKG})
|
||||
list(APPEND ENABLED_PACKAGES ${PKG})
|
||||
endif()
|
||||
endforeach()
|
||||
if(ENABLED_PACKAGES)
|
||||
list(SORT ENABLED_PACKAGES)
|
||||
else()
|
||||
set(ENABLED_PACKAGES "<None>")
|
||||
endif()
|
||||
message(STATUS "Enabled packages: ${ENABLED_PACKAGES}")
|
||||
|
||||
message(STATUS "<<< Compilers and Flags: >>>
|
||||
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
|
||||
Type: ${CMAKE_CXX_COMPILER_ID}
|
||||
Version: ${CMAKE_CXX_COMPILER_VERSION}
|
||||
@ -849,3 +823,15 @@ endif()
|
||||
if(BUILD_DOC)
|
||||
message(STATUS "<<< Building HTML Manual >>>")
|
||||
endif()
|
||||
if(BUILD_TOOLS)
|
||||
message(STATUS "<<< Building Tools >>>")
|
||||
endif()
|
||||
if(BUILD_LAMMPS_SHELL)
|
||||
message(STATUS "<<< Building LAMMPS Shell >>>")
|
||||
endif()
|
||||
if(ENABLE_TESTING)
|
||||
message(STATUS "<<< Building Unit Tests >>>")
|
||||
if(ENABLE_COVERAGE)
|
||||
message(STATUS "Collecting code coverage data")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
@ -57,20 +57,14 @@ if(BUILD_DOC)
|
||||
|
||||
# download mathjax distribution and unpack to folder "mathjax"
|
||||
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
|
||||
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
|
||||
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
|
||||
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
|
||||
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
|
||||
EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
|
||||
endif()
|
||||
|
||||
# for increased browser compatibility
|
||||
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
|
||||
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
|
||||
"${DOC_BUILD_STATIC_DIR}/polyfill.js")
|
||||
endif()
|
||||
|
||||
# set up doxygen and add targets to run it
|
||||
file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
|
||||
file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)
|
||||
|
||||
@ -59,7 +59,6 @@ function(CreateStyleHeader path filename)
|
||||
set(temp "${temp}#include \"${FNAME}\"\n")
|
||||
endforeach()
|
||||
endif()
|
||||
message(STATUS "Generating ${filename}...")
|
||||
file(WRITE "${path}/${filename}.tmp" "${temp}" )
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
|
||||
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
|
||||
@ -142,6 +141,7 @@ function(RegisterStylesExt search_path extension sources)
|
||||
endfunction(RegisterStylesExt)
|
||||
|
||||
function(GenerateStyleHeaders output_path)
|
||||
message(STATUS "Generating style headers...")
|
||||
GenerateStyleHeader(${output_path} ANGLE angle ) # force
|
||||
GenerateStyleHeader(${output_path} ATOM_VEC atom ) # atom atom_vec_hybrid
|
||||
GenerateStyleHeader(${output_path} BODY body ) # atom_vec_body
|
||||
@ -232,7 +232,6 @@ function(CreatePackagesHeader path filename)
|
||||
set(temp "${temp}#include \"${DNAME}/${FNAME}\"\n")
|
||||
endforeach()
|
||||
endif()
|
||||
message(STATUS "Generating ${filename}...")
|
||||
file(WRITE "${path}/${filename}.tmp" "${temp}" )
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
|
||||
set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
|
||||
@ -244,6 +243,7 @@ function(GeneratePackagesHeader path property style)
|
||||
endfunction(GeneratePackagesHeader)
|
||||
|
||||
function(GeneratePackagesHeaders output_path)
|
||||
message(STATUS "Generating package headers...")
|
||||
GeneratePackagesHeader(${output_path} PKGANGLE angle ) # force
|
||||
GeneratePackagesHeader(${output_path} PKGATOM_VEC atom ) # atom atom_vec_hybrid
|
||||
GeneratePackagesHeader(${output_path} PKGBODY body ) # atom_vec_body
|
||||
|
||||
57
cmake/Modules/Tools.cmake
Normal file
57
cmake/Modules/Tools.cmake
Normal file
@ -0,0 +1,57 @@
|
||||
if(BUILD_TOOLS)
|
||||
add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
|
||||
target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
|
||||
install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
|
||||
include(CheckGeneratorSupport)
|
||||
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
|
||||
include(CheckLanguage)
|
||||
check_language(Fortran)
|
||||
if(CMAKE_Fortran_COMPILER)
|
||||
enable_language(Fortran)
|
||||
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
|
||||
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
else()
|
||||
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
|
||||
endif()
|
||||
else()
|
||||
message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
|
||||
endif()
|
||||
|
||||
enable_language(C)
|
||||
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
|
||||
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
|
||||
add_executable(msi2lmp ${MSI2LMP_SOURCES})
|
||||
target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
|
||||
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
|
||||
endif()
|
||||
|
||||
if(BUILD_LAMMPS_SHELL)
|
||||
find_package(PkgConfig REQUIRED)
|
||||
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
|
||||
if(NOT LAMMPS_EXCEPTIONS)
|
||||
message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
|
||||
endif()
|
||||
|
||||
# include resource compiler to embed icons into the executable on Windows
|
||||
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
|
||||
enable_language(RC)
|
||||
set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
|
||||
endif()
|
||||
|
||||
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
|
||||
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
|
||||
|
||||
# workaround for broken readline pkg-config file on FreeBSD
|
||||
if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
|
||||
target_include_directories(lammps-shell PRIVATE /usr/local/include)
|
||||
endif()
|
||||
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
|
||||
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
|
||||
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
|
||||
endif()
|
||||
|
||||
|
||||
32
cmake/Modules/YAML.cmake
Normal file
32
cmake/Modules/YAML.cmake
Normal file
@ -0,0 +1,32 @@
|
||||
message(STATUS "Downloading and building YAML library")
|
||||
|
||||
include(ExternalProject)
|
||||
set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
|
||||
mark_as_advanced(YAML_URL)
|
||||
ExternalProject_Add(libyaml
|
||||
URL ${YAML_URL}
|
||||
URL_MD5 bb15429d8fb787e7d3f1c83ae129a999
|
||||
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
|
||||
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
|
||||
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
|
||||
CXX=${CMAKE_CXX_COMPILER}
|
||||
CC=${CMAKE_C_COMPILER}
|
||||
--prefix=<INSTALL_DIR> --disable-shared
|
||||
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
|
||||
TEST_COMMAND "")
|
||||
|
||||
ExternalProject_Get_Property(libyaml INSTALL_DIR)
|
||||
set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
|
||||
set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
|
||||
|
||||
# workaround for CMake 3.10 on ubuntu 18.04
|
||||
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
|
||||
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
|
||||
|
||||
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
|
||||
|
||||
add_library(Yaml::Yaml UNKNOWN IMPORTED)
|
||||
set_target_properties(Yaml::Yaml PROPERTIES
|
||||
IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
|
||||
INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
|
||||
add_dependencies(Yaml::Yaml libyaml)
|
||||
@ -7,17 +7,20 @@ set(temp_git_info "false")
|
||||
message(STATUS "Git Directory: ${LAMMPS_DIR}/.git")
|
||||
if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
|
||||
set(temp_git_info "true")
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse HEAD
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
|
||||
OUTPUT_VARIABLE temp_git_commit
|
||||
ERROR_QUIET
|
||||
WORKING_DIRECTORY ${LAMMPS_DIR}
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse --abbrev-ref HEAD
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
|
||||
OUTPUT_VARIABLE temp_git_branch
|
||||
ERROR_QUIET
|
||||
WORKING_DIRECTORY ${LAMMPS_DIR}
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} describe --dirty=-modified
|
||||
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
|
||||
OUTPUT_VARIABLE temp_git_describe
|
||||
ERROR_QUIET
|
||||
WORKING_DIRECTORY ${LAMMPS_DIR}
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
|
||||
|
||||
@ -2,7 +2,8 @@
|
||||
|
||||
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
|
||||
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
@ -14,4 +15,3 @@ set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
|
||||
17
cmake/presets/gcc.cmake
Normal file
17
cmake/presets/gcc.cmake
Normal file
@ -0,0 +1,17 @@
|
||||
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
|
||||
|
||||
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
|
||||
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX "g++" CACHE STRING "" FORCE)
|
||||
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)
|
||||
@ -2,11 +2,11 @@
|
||||
|
||||
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
|
||||
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
||||
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||
unset(HAVE_OMP_H_INCLUDE CACHE)
|
||||
|
||||
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
|
||||
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
|
||||
|
||||
|
||||
@ -23,7 +23,7 @@ set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
|
||||
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
|
||||
set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
|
||||
set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
|
||||
set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
|
||||
set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
|
||||
set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
|
||||
set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
|
||||
set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
|
||||
set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")
|
||||
|
||||
14
doc/Makefile
14
doc/Makefile
@ -14,7 +14,6 @@ TXT2RST = $(VENV)/bin/txt2rst
|
||||
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
|
||||
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
|
||||
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
|
||||
POLYFILL = $(SPHINXCONFIG)/_static/polyfill.js
|
||||
|
||||
PYTHON = $(shell which python3)
|
||||
DOXYGEN = $(shell which doxygen)
|
||||
@ -65,7 +64,7 @@ DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+
|
||||
help:
|
||||
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
|
||||
@echo "Please use \`make <target>' where <target> is one of"
|
||||
@echo " html create HTML doc pages in html dir"
|
||||
@echo " html create HTML pages in html dir"
|
||||
@echo " pdf create Manual.pdf in this dir"
|
||||
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
|
||||
@echo " epub create ePUB format manual for e-book readers"
|
||||
@ -81,7 +80,7 @@ help:
|
||||
# ------------------------------------------
|
||||
|
||||
clean-all: clean
|
||||
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(POLYFILL) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
|
||||
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
|
||||
|
||||
clean: clean-spelling
|
||||
rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
|
||||
@ -95,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
|
||||
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
|
||||
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
|
||||
|
||||
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
|
||||
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
|
||||
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
|
||||
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||
@(\
|
||||
@ -237,13 +236,6 @@ $(VENV):
|
||||
$(MATHJAX):
|
||||
@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
|
||||
|
||||
# fall back to using wget and/or unencrypted download, if curl fails
|
||||
$(POLYFILL): $(MATHJAX)
|
||||
@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
|
||||
curl -s -o $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
|
||||
wget -O $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \
|
||||
wget -O $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1
|
||||
|
||||
$(TXT2RST) $(ANCHORCHECK): $(VENV)
|
||||
@( \
|
||||
. $(VENV)/bin/activate; \
|
||||
|
||||
@ -41,11 +41,17 @@ The layout and formatting of added files should follow the example
|
||||
of the existing files. Since those are directly derived from their
|
||||
former .txt format versions and the manual has been maintained in
|
||||
that format for many years, there is a large degree of consistency
|
||||
already, so comparision with similar files should give you a good
|
||||
already, so comparison with similar files should give you a good
|
||||
idea what kind of information and sections are needed.
|
||||
|
||||
## Formatting conventions
|
||||
|
||||
For headlines we try to follow the conventions posted here:
|
||||
https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings
|
||||
It seems to be sufficient to have this consistent only within
|
||||
any single file and it is not (yet) enforced strictly, but making
|
||||
this globally consistent makes it easier to move sections around.
|
||||
|
||||
Filenames, folders, paths, (shell) commands, definitions, makefile
|
||||
settings and similar should be formatted as "literals" with
|
||||
double backward quotes bracketing the item: \`\`path/to/some/file\`\`
|
||||
@ -67,8 +73,19 @@ a `.. parsed-literal::` block can be used, which allows some
|
||||
formatting directives, which means that related characters need
|
||||
to be escaped with a preceding backslash: `\*`.
|
||||
|
||||
For more compact display of alternatives (e.g. compilation or
|
||||
configuration directions for CMake versus GNU make) a `.. tabs::`
|
||||
block can be used, followed by multiple `.. tab::` blocks, one
|
||||
for each alternative. This is only used for HTML output. For other
|
||||
outputs, the `.. tabs::` directive is transparently removed and
|
||||
the individual `.. tab::` blocks will be replaced with an
|
||||
`.. admonition::`` block. Thus in PDF and ePUB output those will
|
||||
be realized as sequential and plain notes.
|
||||
|
||||
Special remarks can be highlighted with a `.. note::` block and
|
||||
strong warnings can be put into a `.. warning::` block.
|
||||
For notes with a title, use `.. admonition:: title text` followed
|
||||
by ` :class: note`.
|
||||
|
||||
## Required steps when adding a custom style to LAMMPS
|
||||
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 13 KiB After Width: | Height: | Size: 22 KiB |
@ -95,7 +95,7 @@ on the pull request discussion page on GitHub, so that other developers
|
||||
can later review the entire discussion after the fact and understand the
|
||||
rationale behind choices made. Exceptions to this policy are technical
|
||||
discussions, that are centered on tools or policies themselves
|
||||
(git, github, c++) rather than on the content of the pull request.
|
||||
(git, GitHub, c++) rather than on the content of the pull request.
|
||||
|
||||
### Checklist for Pull Requests
|
||||
|
||||
|
||||
@ -17,7 +17,7 @@ clean:
|
||||
|
||||
ifeq ($(HAS_DOT),YES)
|
||||
$(IMGDIR)/%.png: %.dot
|
||||
dot -Tpng -o $@ $<
|
||||
dot -Tpng -Kneato -o $@ $<
|
||||
endif
|
||||
|
||||
ifeq ($(HAS_DOT),NO)
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
// LAMMPS Class topology
|
||||
digraph lammps {
|
||||
rankdir="LR"
|
||||
La [shape=circle label="LAMMPS"]
|
||||
overlap=false
|
||||
splines=true
|
||||
La [shape=circle label="LAMMPS" pos="0,0"]
|
||||
At [shape=box label="Atom" color=blue]
|
||||
Ci [shape=box label="CiteMe"]
|
||||
Co [shape=box label="Comm" color=blue]
|
||||
@ -10,17 +11,14 @@ digraph lammps {
|
||||
Fo [shape=box label="Force" color=blue]
|
||||
Gr [shape=box label="Group" color=blue]
|
||||
In [shape=box label="Input" color=blue]
|
||||
Ko [shape=box label="KokkosLMP"]
|
||||
Ak [shape=box label="AtomKK" color=blue]
|
||||
Mk [shape=box label="MemoryKK" color=blue]
|
||||
Me [shape=box label="Memory" color=blue]
|
||||
Mo [shape=box label="Modify" color=blue]
|
||||
Ne [shape=box label="Neighbor" color=blue]
|
||||
Ou [shape=box label="Output" color=blue]
|
||||
Py [shape=box label="Python" color=blue]
|
||||
Up [shape=box label="Update" color=blue]
|
||||
Un [shape=box label="Universe" color=blue]
|
||||
Ti [shape=box label="Timer" color=blue]
|
||||
Lt [label="Lattice"]
|
||||
Rg [label="Region" color=red]
|
||||
Rb [shape=box label="RegionBlock"]
|
||||
Rs [shape=box label="RegionSphere"]
|
||||
@ -43,48 +41,70 @@ digraph lammps {
|
||||
Ff [label="FFT3d"]
|
||||
Re [label="Remap"]
|
||||
Gc [label="GridComm"]
|
||||
Bn [label="Bonus"]
|
||||
Cb [shape=box label="CommBrick"]
|
||||
Ct [shape=box label="CommTiled"]
|
||||
Aa [shape=box label="AtomVecAtomic"]
|
||||
Am [shape=box label="AtomVecMolecular"]
|
||||
Ae [shape=box label="AtomVecEllipsoid"]
|
||||
Lj [shape=box label="PairLJCut"]
|
||||
Lo [shape=box label="PairLJCutOMP"]
|
||||
Lg [shape=box label="PairLJCutGPU"]
|
||||
Li [shape=box label="PairLJCutIntel"]
|
||||
Lk [shape=box label="PairLJCutKokkos"]
|
||||
Te [shape=box label="PairTersoff"]
|
||||
Bh [shape=box label="BondHarmonic"]
|
||||
Bp [shape=box label="BondHarmonicOMP"]
|
||||
Bf [shape=box label="BondFENE"]
|
||||
Fa [shape=box label="FixAveTime"]
|
||||
Fn [shape=box label="FixNVE"]
|
||||
Fh [shape=box label="FixNH"]
|
||||
Fp [shape=box label="FixNPT"]
|
||||
Ft [shape=box label="FixNVT"]
|
||||
Ce [shape=box label="ComputeTemp"]
|
||||
Ca [shape=box label="ComputeTempAtom"]
|
||||
Cr [shape=box label="ComputeReduce"]
|
||||
Cg [shape=box label="ComputeReduceRegion"]
|
||||
Ck [shape=box label="ComputeTempKokkos"]
|
||||
Da [shape=box label="DumpAtom"]
|
||||
Dc [shape=box label="DumpCustom"]
|
||||
Dg [shape=box label="DumpCFG"]
|
||||
Ve [shape=box label="Verlet"]
|
||||
Rr [shape=box label="Respa"]
|
||||
Po [shape=box label="PPPMOmp"]
|
||||
La -> {At Ci Co Do Er Fo Gr In Ko Ak Mk Me Mo Ne Ou Py Ti Up Un} [penwidth=2]
|
||||
Do -> {Rg} [penwidth=2]
|
||||
Co -> {Cb Ct} [style=dashed penwidth=2]
|
||||
Pt [shape=box label="PPPMTIP4P"]
|
||||
Vs [shape=box label="VerletSplit"]
|
||||
Ro [shape=box label="RespaOMP"]
|
||||
Mc [shape=box label="MinCG"]
|
||||
Mf [shape=box label="MinFire"]
|
||||
La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
|
||||
Do -> {Lt Rg} [penwidth=2]
|
||||
Rg -> {Rb Rs} [style=dashed penwidth=2]
|
||||
Co -> {Cb Ct} [style=dashed penwidth=2]
|
||||
In -> Va [penwidth=2]
|
||||
Mo -> {Fi Cp} [penwidth=2]
|
||||
Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
|
||||
Ks -> {Ew Pp} [style=dashed penwidth=2]
|
||||
Pp -> {Ff Re Gc} [penwidth=2]
|
||||
Pp -> {Po} [style=dashed penwidth=2]
|
||||
Pp -> {Pt} [style=dashed penwidth=2]
|
||||
Up -> {It Mi} [penwidth=2]
|
||||
It -> {Ve Rr} [style=dashed penwidth=2]
|
||||
Ou -> {Du Th} [penwidth=2]
|
||||
Du -> {Da Dc} [style=dashed penwidth=2]
|
||||
Dc -> {Dg} [style=dashed penwidth=2]
|
||||
At -> Av [penwidth=2]
|
||||
Av -> {Aa Am} [style=dashed penwidth=2]
|
||||
Av -> {Aa Am Ae} [style=dashed penwidth=2]
|
||||
Ae -> Bn [penwidth=2]
|
||||
Pa -> {Lj Te} [style=dashed penwidth=2]
|
||||
Lj -> {Lo Lg} [style=dashed penwidth=2]
|
||||
Lj -> {Lo Lg Li Lk} [style=dashed penwidth=2]
|
||||
Bo -> {Bh Bf} [style=dashed penwidth=2]
|
||||
Bh -> Bp [style=dashed penwidth=2]
|
||||
Fi -> {Fa Fn Fh} [style=dashed penwidth=2]
|
||||
Fh -> {Fp Ft} [style=dashed penwidth=2]
|
||||
Cp -> {Ce Ca Cr} [style=dashed penwidth=2]
|
||||
Ce -> Ck [style=dashed penwidth=2]
|
||||
Cr -> Cg [style=dashed penwidth=2]
|
||||
Ve -> Vs [style=dashed penwidth=2]
|
||||
Rr -> Ro [style=dashed penwidth=2]
|
||||
Mi -> {Mc Mf} [style=dashed penwidth=2]
|
||||
}
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
.TH LAMMPS "18 September 2020" "2020-09-18"
|
||||
.TH LAMMPS "29 October 2020" "2020-10-29"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
Build LAMMPS
|
||||
************
|
||||
============
|
||||
|
||||
LAMMPS is built as a library and an executable from source code using
|
||||
either traditional makefiles for use with GNU make (which may require
|
||||
@ -8,7 +8,7 @@ Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
|
||||
|
||||
As an alternative you can download a package with pre-built executables
|
||||
or automated build trees as described on the :doc:`Install <Install>`
|
||||
doc page.
|
||||
page.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
@ -20,5 +20,6 @@ doc page.
|
||||
Build_settings
|
||||
Build_package
|
||||
Build_extras
|
||||
Build_manual
|
||||
Build_windows
|
||||
Build_development
|
||||
|
||||
@ -8,7 +8,6 @@ CMake and make:
|
||||
* :ref:`Choice of compiler and compile/link options <compile>`
|
||||
* :ref:`Build the LAMMPS executable and library <exe>`
|
||||
* :ref:`Including and removing debug support <debug>`
|
||||
* :ref:`Build the LAMMPS documentation <doc>`
|
||||
* :ref:`Install LAMMPS after a build <install>`
|
||||
|
||||
----------
|
||||
@ -134,8 +133,8 @@ support included as well. These are commands in the ``MPIIO``,
|
||||
``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages. In addition
|
||||
some packages support OpenMP threading indirectly through the libraries
|
||||
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
|
||||
See the :doc:`Packages details <Packages_details>` doc page for more
|
||||
info on these packages and the doc pages for their respective commands
|
||||
See the :doc:`Packages details <Packages_details>` page for more
|
||||
info on these packages and the pages for their respective commands
|
||||
for OpenMP threading info.
|
||||
|
||||
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
|
||||
@ -300,17 +299,18 @@ LAMMPS.
|
||||
|
||||
then you have either an unsupported (old) compiler or you have
|
||||
to turn on C++11 mode. The latter applies to GCC 4.8.x shipped
|
||||
with RHEL 7.x and CentOS 7.x. For those compilers, you need to
|
||||
add the ``-std=c++11`` flag. Otherwise, you would have to
|
||||
install a newer compiler that supports C++11; either as a
|
||||
binary package or through compiling from source.
|
||||
with RHEL 7.x and CentOS 7.x or GCC 5.4.x shipped with Ubuntu16.04.
|
||||
For those compilers, you need to add the ``-std=c++11`` flag.
|
||||
If there is no compiler that supports this flag (or equivalent),
|
||||
you would have to install a newer compiler that supports C++11;
|
||||
either as a binary package or through compiling from source.
|
||||
|
||||
If you build LAMMPS with any :doc:`Speed_packages` included,
|
||||
there may be specific compiler or linker flags that are either
|
||||
required or recommended to enable required features and to
|
||||
achieve optimal performance. You need to include these in the
|
||||
CCFLAGS and LINKFLAGS settings above. For details, see the
|
||||
individual package doc pages listed on the
|
||||
documentation for the individual packages listed on the
|
||||
:doc:`Speed_packages` page. Or examine these files in the
|
||||
src/MAKE/OPTIONS directory. They correspond to each of the 5
|
||||
accelerator packages and their hardware variants:
|
||||
@ -341,7 +341,7 @@ will then process commands provided via a file or from the console
|
||||
input. The LAMMPS library can also be called from another application
|
||||
or a scripting language. See the :doc:`Howto couple <Howto_couple>` doc
|
||||
page for more info on coupling LAMMPS to other codes. See the
|
||||
:doc:`Python <Python_head>` doc page for more info on wrapping and
|
||||
:doc:`Python <Python_head>` page for more info on wrapping and
|
||||
running LAMMPS from Python via its library interface.
|
||||
|
||||
.. tabs::
|
||||
@ -466,68 +466,6 @@ the debug information from the LAMMPS executable:
|
||||
|
||||
----------
|
||||
|
||||
.. _doc:
|
||||
|
||||
Build the LAMMPS documentation
|
||||
----------------------------------------
|
||||
|
||||
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
|
||||
can be translated to different output format using the `Sphinx <sphinx_>`_
|
||||
document generator tool. Currently the translation to HTML and PDF (via
|
||||
LaTeX) are supported. For that to work a Python 3 interpreter and
|
||||
internet access is required. For the documentation build a python
|
||||
based virtual environment is set up in the folder doc/docenv and various
|
||||
python packages are installed into that virtual environment via the pip
|
||||
tool. The actual translation is then done via make commands.
|
||||
|
||||
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
|
||||
.. _sphinx: https://www.sphinx-doc.org
|
||||
|
||||
Documentation makefile options
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
The following make commands can be issued in the doc folder of the
|
||||
LAMMPS source distribution.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
make html # create HTML doc pages in html directory
|
||||
make pdf # create Manual.pdf in this directory
|
||||
make fetch # fetch HTML and PDF files from LAMMPS web site
|
||||
make clean # remove all intermediate files
|
||||
make clean-all # reset the entire doc build environment
|
||||
make anchor_check # scan for duplicate anchor labels
|
||||
make style_check # check for complete and consistent style lists
|
||||
make package_check # check for complete and consistent package lists
|
||||
make spelling # spell-check the manual
|
||||
|
||||
Thus "make html" will create a "doc/html" directory with the HTML format
|
||||
manual pages so that you can browse them with a web browser locally on
|
||||
your system.
|
||||
|
||||
.. note::
|
||||
|
||||
You can also download a tarball of the documentation for the
|
||||
current LAMMPS version (HTML and PDF files), from the website
|
||||
`download page <https://lammps.sandia.gov/download.html>`_.
|
||||
|
||||
CMake build options
|
||||
^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
It is also possible to create the HTML version (and only the HTML
|
||||
version) of the manual within the :doc:`CMake build directory
|
||||
<Build_cmake>`. The reason for this option is to include the
|
||||
installation of the HTML manual pages into the "install" step when
|
||||
installing LAMMPS after the CMake build via ``make install``. The
|
||||
documentation build is included in the default build target, but can
|
||||
also be requested independently with ``make doc``.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D BUILD_DOC=value # yes or no (default)
|
||||
|
||||
----------
|
||||
|
||||
.. _tools:
|
||||
|
||||
Build LAMMPS tools
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
Build LAMMPS with CMake
|
||||
=======================
|
||||
-----------------------
|
||||
|
||||
This page describes how to use `CMake <https://cmake.org>`_ in general
|
||||
to build LAMMPS. Details for specific compile time settings and options
|
||||
|
||||
@ -111,8 +111,10 @@ error margin). The status of this automated testing can be viewed on
|
||||
The unit testing facility is integrated into the CMake build process
|
||||
of the LAMMPS source code distribution itself. It can be enabled by
|
||||
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
|
||||
It requires the `PyYAML <http://pyyaml.org/>`_ library and development
|
||||
headers to compile and will download and compile a recent version of the
|
||||
It requires the `YAML <http://pyyaml.org/>`_ library and development
|
||||
headers (if not found locally a recent version will be downloaded
|
||||
and compiled transparently) to compile and will download and compile
|
||||
a specific recent version of the
|
||||
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
|
||||
for implementing the tests.
|
||||
|
||||
|
||||
@ -18,7 +18,7 @@ in addition to
|
||||
|
||||
$ make yes-name
|
||||
|
||||
as described on the :doc:`Build_package <Build_package>` doc page.
|
||||
as described on the :doc:`Build_package <Build_package>` page.
|
||||
|
||||
For a CMake build there may be additional optional or required
|
||||
variables to set. For a build with make, a provided library under the
|
||||
|
||||
@ -27,14 +27,14 @@ additional tools to be available and functioning.
|
||||
* a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
|
||||
* python (optional, required for ``make lib-<pkg>`` in the src folder).
|
||||
python scripts are currently tested with python 2.7 and 3.6. The procedure
|
||||
for :doc:`building the documentation <Manual_build>` requires python 3.
|
||||
for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
|
||||
|
||||
Getting started
|
||||
^^^^^^^^^^^^^^^
|
||||
|
||||
To include LAMMPS packages (i.e. optional commands and styles) you must
|
||||
enable (or "install") them first, as discussed on the :doc:`Build
|
||||
package <Build_package>` doc page. If a packages requires (provided or
|
||||
package <Build_package>` page. If a packages requires (provided or
|
||||
external) libraries, you must configure and build those libraries
|
||||
**before** building LAMMPS itself and especially **before** enabling
|
||||
such a package with ``make yes-<package>``. :doc:`Building LAMMPS with
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
Building the LAMMPS manual
|
||||
**************************
|
||||
Build the LAMMPS documentation
|
||||
==============================
|
||||
|
||||
Depending on how you obtained LAMMPS and whether you have built the
|
||||
manual yourself, this directory has a number of sub-directories and
|
||||
@ -32,37 +32,59 @@ and PDF files are not included. Instead you need to create them, in one
|
||||
of two ways:
|
||||
|
||||
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
|
||||
site. Just type ``make fetch``. This should download a html_www
|
||||
directory and a Manual_www.pdf file. Note that if new LAMMPS features
|
||||
site. Just type ``make fetch``. This should download a ``html_www``
|
||||
directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features
|
||||
have been added more recently than the date of your LAMMPS version, the
|
||||
fetched documentation will include those changes (but your source code
|
||||
will not, unless you update your local repository).
|
||||
|
||||
b. You can build the HTML or PDF files yourself, by typing ``make html``
|
||||
or ``make pdf``. This requires various tools and files. Some of them
|
||||
have to be installed (more on that below). For the rest the build
|
||||
process will attempt to download and install them into a python
|
||||
virtual environment and local folders. This download is required
|
||||
only once, unless you type ``make clean-all``. After that, viewing and
|
||||
processing of the documentation can be done without internet access.
|
||||
or ``make pdf`` in the ``doc`` folder. This requires various tools
|
||||
and files. Some of them have to be installed (see below). For the
|
||||
rest the build process will attempt to download and install them into
|
||||
a python virtual environment and local folders.
|
||||
|
||||
A current version of the manual (latest patch release, aka unstable branch)
|
||||
is is available online at: `https://lammps.sandia.gov/doc/Manual.html <https://lammps.sandia.gov/doc/Manual.html>`_
|
||||
A version of the manual corresponding to the ongoing development
|
||||
(aka master branch) is available online at: `https://docs.lammps.org/ <https://docs.lammps.org/>`_
|
||||
A current version of the manual (latest patch release, aka unstable
|
||||
branch) is is available online at:
|
||||
`https://lammps.sandia.gov/doc/Manual.html
|
||||
<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
|
||||
corresponding to the ongoing development (aka master branch) is
|
||||
available online at: `https://docs.lammps.org/
|
||||
<https://docs.lammps.org/>`_
|
||||
|
||||
----------
|
||||
Build using GNU make
|
||||
--------------------
|
||||
|
||||
The generation of all documentation is managed by the Makefile in the
|
||||
doc directory. The following documentation related make commands are
|
||||
available:
|
||||
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
|
||||
can be translated to different output format using the `Sphinx
|
||||
<sphinx_>`_ document generator tool. It also incorporates programmer
|
||||
documentation extracted from the LAMMPS C++ sources through the `Doxygen
|
||||
<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
|
||||
(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
|
||||
readers) are supported. For that to work a Python 3 interpreter, the
|
||||
``doxygen`` tools and internet access to download additional files and
|
||||
tools are required. This download is usually only required once or
|
||||
after the documentation folder is returned to a pristine state with
|
||||
``make clean-all``.
|
||||
|
||||
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
|
||||
.. _sphinx: https://www.sphinx-doc.org
|
||||
|
||||
For the documentation build a python virtual environment is set up in
|
||||
the folder ``doc/docenv`` and various python packages are installed into
|
||||
that virtual environment via the ``pip`` tool. For rendering embedded
|
||||
LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
|
||||
engine needs to be downloaded.
|
||||
|
||||
The actual translation is then done via ``make`` commands in the doc
|
||||
folder. The following ``make`` commands are available:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
make html # generate HTML in html dir using Sphinx
|
||||
make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex
|
||||
make fetch # fetch HTML doc pages and PDF file from web site
|
||||
# as a tarball and unpack into html dir and PDF
|
||||
make fetch # fetch HTML pages and PDF files from LAMMPS web site
|
||||
# and unpack into the html_www folder and Manual_www.pdf
|
||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
|
||||
@ -76,66 +98,79 @@ available:
|
||||
|
||||
----------
|
||||
|
||||
Installing prerequisites for HTML build
|
||||
=======================================
|
||||
Build using CMake
|
||||
-----------------
|
||||
|
||||
It is also possible to create the HTML version (and **only** the HTML
|
||||
version) of the manual within the :doc:`CMake build directory
|
||||
<Build_cmake>`. The reason for this option is to include the
|
||||
installation of the HTML manual pages into the "install" step when
|
||||
installing LAMMPS after the CMake build via ``cmake --build . --target
|
||||
install``. The documentation build is included in the default build
|
||||
target, but can also be requested independently with
|
||||
``cmake --build . --target doc``.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D BUILD_DOC=value # yes or no (default)
|
||||
|
||||
----------
|
||||
|
||||
Prerequisites for HTML
|
||||
----------------------
|
||||
|
||||
To run the HTML documentation build toolchain, python 3, git, doxygen,
|
||||
and virtualenv have to be installed locally. Here are instructions for
|
||||
common setups:
|
||||
|
||||
Ubuntu
|
||||
------
|
||||
.. tabs::
|
||||
|
||||
.. code-block:: bash
|
||||
.. tab:: Ubuntu
|
||||
|
||||
sudo apt-get install python-virtualenv git doxygen
|
||||
.. code-block:: bash
|
||||
|
||||
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
|
||||
------------------------------------------------------------------------------------
|
||||
sudo apt-get install python-virtualenv git doxygen
|
||||
|
||||
.. code-block:: bash
|
||||
.. tab:: RHEL or CentOS (Version 7.x)
|
||||
|
||||
sudo yum install python3-virtualenv git doxygen
|
||||
.. code-block:: bash
|
||||
|
||||
Fedora (since version 22)
|
||||
-------------------------
|
||||
sudo yum install python3-virtualenv git doxygen
|
||||
|
||||
.. code-block:: bash
|
||||
.. tab:: Fedora or RHEL/CentOS (8.x or later)
|
||||
|
||||
sudo dnf install python3-virtualenv git doxygen
|
||||
.. code-block:: bash
|
||||
|
||||
MacOS X
|
||||
-------
|
||||
sudo dnf install python3-virtualenv git doxygen
|
||||
|
||||
Python 3
|
||||
^^^^^^^^
|
||||
.. tab:: MacOS X
|
||||
|
||||
Download the latest Python 3 MacOS X package from
|
||||
`https://www.python.org <https://www.python.org>`_
|
||||
and install it. This will install both Python 3
|
||||
and pip3.
|
||||
*Python 3*
|
||||
|
||||
virtualenv
|
||||
^^^^^^^^^^
|
||||
Download the latest Python 3 MacOS X package from
|
||||
`https://www.python.org <https://www.python.org>`_ and install it.
|
||||
This will install both Python 3 and pip3.
|
||||
|
||||
Once Python 3 is installed, open a Terminal and type
|
||||
*virtualenv*
|
||||
|
||||
.. code-block:: bash
|
||||
Once Python 3 is installed, open a Terminal and type
|
||||
|
||||
pip3 install virtualenv
|
||||
.. code-block:: bash
|
||||
|
||||
This will install virtualenv from the Python Package Index.
|
||||
pip3 install virtualenv
|
||||
|
||||
Installing prerequisites for PDF build
|
||||
======================================
|
||||
This will install virtualenv from the Python Package Index.
|
||||
|
||||
Prerequisites for PDF
|
||||
---------------------
|
||||
|
||||
In addition to the tools needed for building the HTML format manual,
|
||||
a working LaTeX installation with support for PDFLaTeX and a selection
|
||||
of LaTeX styles/packages are required. To run the PDFLaTeX translation
|
||||
the ``latexmk`` script needs to be installed as well.
|
||||
|
||||
Installing prerequisites for e-book reader builds
|
||||
=================================================
|
||||
Prerequisites for ePUB and MOBI
|
||||
-------------------------------
|
||||
|
||||
In addition to the tools needed for building the HTML format manual,
|
||||
a working LaTeX installation with a few add-on LaTeX packages
|
||||
@ -152,12 +187,12 @@ files, so you could download and view the PDF version as an alternative.
|
||||
|
||||
|
||||
Instructions for Developers
|
||||
===========================
|
||||
---------------------------
|
||||
|
||||
When adding new styles or options to the LAMMPS code, corresponding
|
||||
documentation is required and either existing files in the ``src``
|
||||
folder need to be updated or new files added. These files are written
|
||||
in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
|
||||
folder need to be updated or new files added. These files are written in
|
||||
`reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
|
||||
|
||||
Before contributing any documentation, please check that both the HTML
|
||||
and the PDF format documentation can translate without errors. Please also
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user