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Merge pull request #35 from lammps/master

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rebase
This commit is contained in:
Jacob Gissinger
2018-11-30 21:36:01 -07:00
committed by GitHub
parent d7abb8cf4d 67041a5446
commit 482e120af4
695 changed files with 207399 additions and 30240 deletions
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1
.gitignore vendored
View File

@ -22,6 +22,7 @@ log.cite
.*.swp
*.orig
*.rej
vgcore.*
.vagrant
\#*#
.#*

152
cmake/CMakeLists.txt
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@ -11,6 +11,10 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
endif()
# To avoid conflicts with the conventional Makefile build system, we build everything here
file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
@ -75,6 +79,7 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
#release comes with -O3 by default
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
# check for files auto-generated by make-based buildsystem
# this is fast, so check for it all the time
@ -422,16 +427,30 @@ if(WITH_FFMPEG)
add_definitions(-DLAMMPS_FFMPEG)
endif()
if(BUILD_SHARED_LIBS)
set(CONFIGURE_REQUEST_PIC "--with-pic")
set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}")
set(CUDA_REQUEST_PIC "-Xcompiler ${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
else()
set(CONFIGURE_REQUEST_PIC)
set(CMAKE_REQUEST_PIC)
set(CUDA_REQUEST_PIC)
endif()
if(PKG_VORONOI)
option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
if(DOWNLOAD_VORO)
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
if(BUILD_SHARED_LIBS)
set(VORO_BUILD_OPTIONS "CFLAGS=-fPIC")
set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
else()
set(VORO_BUILD_OPTIONS)
set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
endif()
string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
ExternalProject_Add(voro_build
URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
@ -445,7 +464,7 @@ if(PKG_VORONOI)
else()
find_package(VORO)
if(NOT VORO_FOUND)
message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
endif()
include_directories(${VORO_INCLUDE_DIRS})
@ -453,26 +472,26 @@ if(PKG_VORONOI)
endif()
if(PKG_LATTE)
option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
if(DOWNLOAD_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
message(STATUS "LATTE not found - we will build our own")
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
URL_MD5 85ac414fdada2d04619c8f936344df14
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
)
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
list(APPEND LAMMPS_DEPS latte_build)
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
@ -480,24 +499,22 @@ endif()
if(PKG_USER-SCAFACOS)
find_package(GSL REQUIRED)
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
URL_MD5 bd46d74e3296bd8a444d731bb10c1738
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
--disable-doc
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw
--with-internal-pfft
--with-internal-pnfft
$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
--with-internal-fftw --with-internal-pfft
--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
F77=
)
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
@ -537,15 +554,15 @@ if(PKG_USER-PLUMED)
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
if(DOWNLOAD_PLUMED)
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
URL_MD5 b1be7c48971627febc11c61b70767fc5
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic> )
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
list(APPEND LAMMPS_DEPS plumed_build)
@ -592,11 +609,12 @@ if(PKG_USER-NETCDF)
endif()
if(PKG_USER-SMD)
option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
URL_MD5 1a47e78efe365a97de0c022d127607c3
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
@ -633,8 +651,9 @@ if(PKG_USER-VTK)
endif()
if(PKG_KIM)
option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
if(DOWNLOAD_KIM)
message(STATUS "KIM-API v1 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
@ -649,7 +668,7 @@ if(PKG_KIM)
else()
find_package(KIM)
if(NOT KIM_FOUND)
message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
@ -662,12 +681,7 @@ if(PKG_MESSAGE)
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
if(BUILD_SHARED_LIBS)
add_library(cslib SHARED ${cslib_SOURCES})
else()
add_library(cslib STATIC ${cslib_SOURCES})
endif()
add_library(cslib STATIC ${cslib_SOURCES})
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
@ -692,10 +706,10 @@ endif()
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
if(DOWNLOAD_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
@ -705,7 +719,7 @@ if(PKG_MSCG)
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
URL_MD5 8c45e269ee13f60b303edd7823866a91
SOURCE_SUBDIR src/CMake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
BUILD_COMMAND make mscg INSTALL_COMMAND ""
)
ExternalProject_get_property(mscg_build BINARY_DIR)
@ -753,7 +767,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
include(CheckLibraryExists)
if (CMAKE_VERSION VERSION_LESS "3.4")
enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
endif()
# RB: disabled this check because it breaks with KOKKOS CUDA enabled
#foreach(FUNC sin cos)
@ -791,6 +805,13 @@ foreach(PKG ${DEFAULT_PACKAGES})
endif()
endforeach()
# packages that need defines set
foreach(PKG MPIIO)
if(PKG_${PKG})
add_definitions(-DLMP_${PKG})
endif()
endforeach()
# dedicated check for entire contents of accelerator packages
foreach(PKG ${ACCEL_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
@ -1019,7 +1040,7 @@ if(PKG_USER-INTEL)
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
if(NOT BUILD_OMP)
@ -1084,7 +1105,7 @@ if(PKG_USER-INTEL)
endif()
if(PKG_GPU)
if (CMAKE_VERSION VERSION_LESS "3.1")
if (CMAKE_VERSION VERSION_LESS "3.1")
message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
@ -1119,11 +1140,11 @@ if(PKG_GPU)
find_package(CUDA REQUIRED)
find_program(BIN2C bin2c)
if(NOT BIN2C)
message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
endif()
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@ -1136,11 +1157,39 @@ if(PKG_GPU)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
endif()
# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
if(CUDA_VERSION VERSION_GREATER "4.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER "5.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER "7.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER "8.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER "9.9")
string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
endif()
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
-DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@ -1288,7 +1337,7 @@ if(BUILD_EXE)
add_dependencies(lmp ${LAMMPS_DEPS})
endif()
endif()
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
@ -1409,7 +1458,6 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
endif()
endforeach()
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
include(FeatureSummary)
feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
@ -1425,14 +1473,14 @@ message(STATUS "<<< Build configuration >>>
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if (${_index} GREATER -1)
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
Type ${CMAKE_Fortran_COMPILER_ID}
Version ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
list (FIND LANGUAGES "C" _index)
if (${_index} GREATER -1)
message(STATUS "C Compiler ${CMAKE_C_COMPILER}
message(STATUS "C Compiler ${CMAKE_C_COMPILER}
Type ${CMAKE_C_COMPILER_ID}
Version ${CMAKE_C_COMPILER_VERSION}
C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
@ -1440,7 +1488,7 @@ endif()
if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Linker flags:
Executable ${CMAKE_EXE_LINKER_FLAGS}")
endif()
endif()
if(BUILD_SHARED_LIBS)
message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}")
else()

1
cmake/README.md
View File

@ -195,6 +195,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
<td><code>CMAKE_INSTALL_PREFIX</code></td>
<td>Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do.</td>
<td>
Default setting is <code>$HOME/.local</code>.
</td>
</tr>
<tr>

1
doc/Makefile
View File

@ -176,7 +176,6 @@ $(VENV):
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install Sphinx; \
pip install sphinxcontrib-images; \
deactivate;\
)

11
doc/github-development-workflow.md
View File

@ -55,11 +55,11 @@ required changes or ask the submitter of the pull request to implement
them. Even though, all LAMMPS developers may have write access to pull
requests (if enabled by the submitter, which is the default), only the
submitter or the assignee of a pull request may do so. During this
period the "work_in_progress" label shall be applied to the pull
period the `work_in_progress` label shall be applied to the pull
request. The assignee gets to decide what happens to the pull request
next, e.g. whether it should be assigned to a different developer for
additional checks and changes, or is recommended to be merged. Removing
the "work_in_progress" label and assigning the pull request to the
the `work_in_progress` label and assigning the pull request to the
developer tasked with merging signals that a pull request is ready to be
merged.
@ -107,7 +107,9 @@ Here are some items to check:
* new style docs should be added to the "overview" files in
`doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
and `doc/src/lammps.book`
* new files in packages should be added to `src/.gitignore`
* check whether manual cleanly translates with `make html` and `make pdf`
* check spelling of manual with `make spelling` in doc folder
* new source files in packages should be added to `src/.gitignore`
* removed or renamed files in packages should be added to `src/Purge.list`
* C++ source files should use C++ style include files for accessing
C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
@ -143,6 +145,9 @@ Here are some items to check:
compiling LAMMPS with `-DLAMMPS_BIGBIG`.
* when including both `lmptype.h` (and using defines or macros from it)
and `mpi.h`, `lmptype.h` must be included first.
* when pair styles are added, check if settings for flags like
`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
and others are correctly set and supported.
## GitHub Issues

6
doc/src/Build_basics.txt
View File

@ -49,7 +49,7 @@ make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre
Serial build (see src/MAKE/Makefile.serial):
MPI_INC = -I../STUBS
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs :pre
@ -172,7 +172,7 @@ want.
Parallel build (see src/MAKE/Makefile.mpi):
CC = mpicxx
CCFLAGS = -g -O3
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O :pre
@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
NOTE: You can also download a tarball of the documention for the
NOTE: You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
"download page"_http://lammps.sandia.gov/download.html.

4
doc/src/Build_cmake.txt
View File

@ -27,7 +27,7 @@ make command to build LAMMPS, which uses the created
Makefile(s). Example:
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
mkdir build; cd build # create a new directory (folder) for build
cmake ../cmake \[options ...\] # configuration with (command-line) cmake
make # compilation :pre
@ -44,7 +44,7 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
After compilation, you can optionally copy the LAMMPS executable and
library into your system folders (by default under /usr/local) with:
library into your system folders (by default under $HOME/.local) with:
make install # optional, copy LAMMPS executable & library elsewhere :pre

74
doc/src/Build_extras.txt
View File

@ -64,7 +64,7 @@ available on your system.
If CMake cannot find the library, you can set these variables:
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre
[Traditional make]:
@ -87,22 +87,30 @@ which GPU hardware to build for.
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # hardware choice for GPU_API=cuda
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is Cuda-compiler dependent, but typically sm_20
-D CUDPP_OPT=value # optimization setting for GPU_API=cudea
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# yes (default) or no :pre
GPU_ARCH settings for different GPU hardware is as follows:
sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
sm_30 for Kepler (K10)
sm_35 for Kepler (K40) or GeForce GTX Titan or similar
sm_37 for Kepler (dual K80)
sm_50 for Maxwell
sm_60 for Pascal (P100)
sm_70 for Volta :ul
sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
sm_50 or sm_52 for Maxwell (supported since CUDA 6)
sm_60 or sm_61 for Pascal (supported since CUDA 8)
sm_70 for Volta (supported since CUDA 9)
sm_75 for Turing (supported since CUDA 10) :ul
A more detailed list can be found, for example,
at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported
CMake can detect which version of the CUDA toolkit is used and thus can
include support for [all] major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
[Traditional make]:
@ -137,6 +145,11 @@ CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
CUDA_PRECISION = precision (double, mixed, single)
EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
The file Makefile.linux_multi is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
If the library build is successful, 3 files should be created:
lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and
lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS
@ -150,8 +163,9 @@ re-build LAMMPS. This is because the compilation of files in the GPU
package uses the library settings from the lib/gpu/Makefile.machine
used to build the GPU library.
:line
KIM package :h4,link(kim)
To build with this package, the KIM library must be downloaded and
@ -178,7 +192,7 @@ package?" page.
[CMake build]:
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
@ -255,7 +269,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables:
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
# archGPU = GPU from list above
-D KOKKOS_ENABLE_CUDA=yes
-D KOKKOS_ENABLE_OPENMP=yes
-D KOKKOS_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre
The wrapper value is the Cuda nvcc compiler wrapper provided in the
@ -297,7 +311,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx :pre
:line
LATTE package :h4,link(latte)
To build with this package, you must download and build the LATTE
@ -325,7 +339,7 @@ args:
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
:pre
@ -336,7 +350,7 @@ also check that the Makefile.lammps file you create is appropriate for
the compiler you use on your system to build LATTE.
:line
MEAM package :h4,link(meam)
NOTE: the use of the MEAM package is discouraged, as it has been
@ -379,7 +393,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
file.
:line
MESSAGE package :h4,link(message)
This package can optionally include support for messaging via sockets,
@ -408,7 +422,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ
library if requested in the build.
:line
MSCG package :h4,link(mscg)
To build with this package, you must download and build the MS-CG
@ -420,7 +434,7 @@ lib/mscg/README and MSCG/Install files for more details.
[CMake build]:
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre
If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
@ -465,7 +479,7 @@ line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
an example.
:line
POEMS package :h4,link(poems)
[CMake build]:
@ -494,7 +508,7 @@ for your system, which should define an EXTRAMAKE variable to specify
a corresponding Makefile.lammps.machine file.
:line
PYTHON package :h4,link(python)
Building with the PYTHON package requires you have a Python shared
@ -521,7 +535,7 @@ Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
build fails.
:line
REAX package :h4,link(reax)
NOTE: the use of the REAX package and its "pair_style
@ -571,7 +585,7 @@ library"_voro-home.
[CMake build]:
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre
If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
@ -732,7 +746,7 @@ can be shared across multiple MD packages and can be updated, for as
long as the shared PLUMED library is ABI-compatible. The third linkage
mode is "runtime" which allows to switch the PLUMED kernel at runtime
between different variants through setting the PLUMED_KERNEL environment
varible, which has to point to the location of the libplumedKernel.so
variable, which has to point to the location of the libplumedKernel.so
dynamical shared object, which is then loaded at runtime. This is
particularly convenient for doing PLUMED development and comparing
multiple PLUMED versions without having to recompile the hosting MD
@ -750,7 +764,7 @@ a global PLUMED installation or downloading it during building LAMMPS.
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
downloaded (the version of that is hardcoded to a vetted version of
downloaded (the version of that is hard-coded to a vetted version of
PLUMED, usually a recent stable release version) and built inside the
CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default),
CMake will try to detect an installed version of PLUMED and link to
@ -788,10 +802,10 @@ Note that 2 symbolic (soft) links, "includelink" and "liblink" are
created in lib/plumed to point into the location of the PLUMED build to
use and also a new file lib/plumed/Makefile.lammps is created with
settings suitable for LAMMPS to compile and link PLUMED in the desired
linkage mode. After this step is compleded, you can install the
linkage mode. After this step is completed, you can install the
USER-PLUMED package and compile LAMMPS in the usual manner:
make yes-user-plumed
make yes-user-plumed
make machine :pre
Once this compilation completes you should be able to run LAMMPS in the
@ -804,7 +818,7 @@ operating systems, using the static linkage is expected to be the most
portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings [and] do a reinstall if the
lib-plumed" with the desired settings [and] do a re-install if the
USER-PLUMED package with "make yes-user-plumed" to update the required
makefile settings with the changes in the lib/plumed folder.
@ -967,7 +981,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version
[CMake build]:
The CMake build system currently does not support building the full
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
You must use the traditional make build for this package.
[Traditional make]:
@ -1037,7 +1051,7 @@ Coulomb solver library"_scafacos-home
[CMake build]:
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre
If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded

24
doc/src/Build_settings.txt
View File

@ -22,7 +22,7 @@ explain how to do this for building both with CMake and make.
"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
:line
FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the
@ -73,7 +73,7 @@ FFT_LIB with the appropriate FFT libraries to include in the link.
The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the
size of the FFTs and the number of processors used, the other
libraries listed here can be faster.
libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
@ -92,7 +92,7 @@ Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
various options.
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT_LIB setting above).
@ -139,16 +139,16 @@ adequate.
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
# default is LAMMMPS_SMALLBIG if not specified
# default is LAMMPS_SMALLBIG if not specified
[CMake and make info]:
The default "smallbig" setting allows for simulations with:
total atom count = 2^63 atoms (about 9e18)
total timesteps = 2^63 (about 9e18)
atom IDs = 2^31 (about 2 billion)
image flags = roll over at 512 :ul
The "bigbig" setting increases the latter two limits. It allows for:
total atom count = 2^63 atoms (about 9e18)
@ -209,12 +209,12 @@ Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre
[Makefile.machine settings]:

8
doc/src/Build_windows.txt
View File

@ -53,20 +53,20 @@ are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. The CMake build system is untested
for this; you will have to request that makefiles are generated and
manually set the compiler.
manually set the compiler.
When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
this up automatically, but is untested.
this up automatically, but is untested.
In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems
requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS github project.
them as an issue or pull request on the LAMMPS GitHub project.
Using a cross-compiler :h4,link(cross)

8
doc/src/Commands.txt
View File

@ -42,10 +42,10 @@ END_RST -->
"Input script structure"_Commands_structure.html
"Commands by category"_Commands_category.html :all(b)
"All commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"General commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"Bond, angle, dihedral, improper commands"_Commands_bond.html
"KSpace solvers"_Commands_kspace.html :all(b)

6
doc/src/Commands_all.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
All commands :h3
General commands :h3
An alphabetic list of all LAMMPS commands.
An alphabetic list of all general LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,

2
doc/src/Commands_bond.txt
View File

@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(ld,Manual.html)
:link(lc,Commands_all.html)
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

7
doc/src/Commands_category.txt
View File

@ -10,10 +10,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Commands by category :h3
This page lists most of the LAMMPS commands, grouped by category. The
"Commands all"_Commands_all.html doc page lists all commands
alphabetically. It also includes long lists of style options for
entries that appear in the following categories as a single command
(fix, compute, pair, etc).
"General commands"_Commands_all.html doc page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:

2
doc/src/Commands_compute.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

4
doc/src/Commands_fix.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
@ -235,4 +235,4 @@ OPT.
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/region/ees"_fix_wall_ees.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

2
doc/src/Commands_kspace.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

2
doc/src/Commands_pair.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

2
doc/src/Commands_parse.txt
View File

@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
(4) The line is broken into "words" separated by white-space (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.

3
doc/src/Developer/.gitignore vendored Normal file
View File

@ -0,0 +1,3 @@
/developer.aux
/developer.log
/developer.toc

2
doc/src/Errors.txt
View File

@ -32,7 +32,7 @@ END_RST -->
"Common problems"_Errors_common.html
"Reporting bugs"_Errors_bugs.html
"Error messages"_Errors_messages.html
"Error messages"_Errors_messages.html
"Warning messages"_Errors_warnings.html :all(b)
<!-- END_HTML_ONLY -->

48
doc/src/Errors_messages.txt
View File

@ -279,12 +279,6 @@ multibody joint). The bodies you have defined exceed this limit. :dd
This is an internal LAMMPS error. Please report it to the
developers. :dd
{Atom sorting has bin size = 0.0} :dt
The neighbor cutoff is being used as the bin size, but it is zero.
Thus you must explicitly list a bin size in the atom_modify sort
command or turn off sorting. :dd
{Atom style hybrid cannot have hybrid as an argument} :dt
Self-explanatory. :dd
@ -421,9 +415,9 @@ This is an internal error. It should normally not occur. :dd
This is an internal error. It should normally not occur. :dd
{Bad real space Coulomb cutoff in fix tune/kspace} :dt
{Bad real space Coulombic cutoff in fix tune/kspace} :dt
Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd
{Balance command before simulation box is defined} :dt
@ -460,7 +454,7 @@ compute. :dd
{Big particle in fix srd cannot be point particle} :dt
Big particles must be extended spheriods or ellipsoids. :dd
Big particles must be extended spheroids or ellipsoids. :dd
{Bigint setting in lmptype.h is invalid} :dt
@ -780,7 +774,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd
Self-explanatory. :dd
{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt
{Cannot change box z boundary to non-periodic for a 2d simulation} :dt
Self-explanatory. :dd
@ -1288,7 +1282,7 @@ are defined. :dd
You cannot reset the timestep when a fix that keeps track of elapsed
time is in place. :dd
{Cannot run 2d simulation with nonperiodic Z dimension} :dt
{Cannot run 2d simulation with non-periodic Z dimension} :dt
Use the boundary command to make the z dimension periodic in order to
run a 2d simulation. :dd
@ -2116,29 +2110,29 @@ Self-explanatory. :dd
Fix setforce cannot be used in this manner. Use fix addforce
instead. :dd
{Cannot use nonperiodic boundares with fix ttm} :dt
{Cannot use non-periodic boundares with fix ttm} :dt
This fix requires a fully periodic simulation box. :dd
{Cannot use nonperiodic boundaries with Ewald} :dt
{Cannot use non-periodic boundaries with Ewald} :dt
For kspace style ewald, all 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with EwaldDisp} :dt
{Cannot use non-periodic boundaries with EwaldDisp} :dt
For kspace style ewald/disp, all 3 dimensions must have periodic
boundaries unless you use the kspace_modify command to define a 2d
slab with a non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with PPPM} :dt
{Cannot use non-periodic boundaries with PPPM} :dt
For kspace style pppm, all 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with PPPMDisp} :dt
{Cannot use non-periodic boundaries with PPPMDisp} :dt
For kspace style pppm/disp, all 3 dimensions must have periodic
boundaries unless you use the kspace_modify command to define a 2d
@ -3351,21 +3345,21 @@ probably due to errors in the Python code. :dd
The default minimum order is 2. This can be reset by the
kspace_modify minorder command. :dd
{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt
{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cut not supported in pair_style lj/long/coul/long} :dt
{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt
{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt
If using a Kspace solver, all Coulomb cutoffs of long pair styles must
If using a Kspace solver, all Coulombic cutoffs of long pair styles must
be the same. :dd
{Coulombic cut not supported in pair_style lj/long/dipole/long} :dt
@ -5938,9 +5932,9 @@ map command will force an atom map to be created. :dd
Self-explanatory. :dd
{Input line quote not followed by whitespace} :dt
{Input line quote not followed by white-space} :dt
An end quote must be followed by whitespace. :dd
An end quote must be followed by white-space. :dd
{Insertion region extends outside simulation box} :dt
@ -7014,7 +7008,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd
{KSpace accuracy too large to estimate G vector} :dt
Reduce the accuracy request or specify gwald explicitly
Reduce the accuracy request or specify gewald explicitly
via the kspace_modify command. :dd
{KSpace accuracy too low} :dt
@ -8014,7 +8008,7 @@ Self-explanatory. :dd
{Package command after simulation box is defined} :dt
The package command cannot be used afer a read_data, read_restart, or
The package command cannot be used after a read_data, read_restart, or
create_box command. :dd
{Package gpu command without GPU package installed} :dt
@ -9198,7 +9192,7 @@ creates one large file for all processors. :dd
{Restart file byte ordering is not recognized} :dt
The file does not appear to be a LAMMPS restart file since it doesn't
contain a recognized byte-orderomg flag at the beginning. :dd
contain a recognized byte-ordering flag at the beginning. :dd
{Restart file byte ordering is swapped} :dt
@ -9410,7 +9404,7 @@ You may also want to boost the page size. :dd
{Small to big integers are not sized correctly} :dt
This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
This error occurs when the sizes of smallint, imageint, tagint, bigint,
as defined in src/lmptype.h are not what is expected. Contact
the developers if this occurs. :dd

6
doc/src/Errors_warnings.txt
View File

@ -757,7 +757,7 @@ Self-explanatory. :dd
This may indicate the shell command did not operate as expected. :dd
{Should not allow rigid bodies to bounce off relecting walls} :dt
{Should not allow rigid bodies to bounce off reflecting walls} :dt
LAMMPS allows this, but their dynamics are not computed correctly. :dd
@ -850,10 +850,10 @@ Most FENE models need this setting for the special_bonds command. :dd
Most FENE models need this setting for the special_bonds command. :dd
{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt
{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt
This is likely not what you want to do. The exclusion settings will
eliminate neighbors in the neighbor list, which the manybody potential
eliminate neighbors in the neighbor list, which the many-body potential
needs to calculated its terms correctly. :dd
{Using compute temp/deform with inconsistent fix deform remap option} :dt

2
doc/src/Examples.txt
View File

@ -78,7 +78,7 @@ micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
nb3b: use of non-bonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel

2
doc/src/Howto.txt
View File

@ -45,7 +45,7 @@ General howto :h3
<!-- RST
.. toctree::
:name: general
:name: general_howto
:maxdepth: 1
Howto_restart

2
doc/src/Howto_barostat.txt
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@ -19,7 +19,7 @@ barostat attempts to equilibrate the system to the requested T and/or
P.
Barostatting in LAMMPS is performed by "fixes"_fix.html. Two
barosttating methods are currently available: Nose-Hoover (npt and
barostatting methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
"fix npt"_fix_nh.html

6
doc/src/Howto_bash.txt
View File

@ -40,7 +40,7 @@ Install Windows Subsystem for Linux :h5
Next you must ensure that the Window Subsystem for Linux is installed. Again,
search for "enable windows features" in the Settings dialog. This opens a
dialog with a list of features you can install. Add a checkmark to Windows
Subsystem for Linux (Beta) and press OK.
Subsystem for Linux (Beta) and press OK.
:image(JPG/bow_tutorial_04_small.png,JPG/bow_tutorial_04.png)
:image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
@ -54,12 +54,12 @@ enter. This will then download Ubuntu for Windows.
:image(JPG/bow_tutorial_06.png)
:image(JPG/bow_tutorial_07.png)
During installation, you will be asked for a new password. This will be used
for installing new software and running commands with sudo.
:image(JPG/bow_tutorial_08.png)
Type exit to close the command-line window.
Go to the Start menu and type "bash" again. This time you will see a "Bash on

4
doc/src/Howto_body.txt
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@ -132,7 +132,7 @@ x1 y1 z1
xN yN zN :pre
where M = 6 + 3*N, and N is the number of sub-particles in the body
particle.
particle.
The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
@ -315,7 +315,7 @@ x1 y1 z1
...
xN yN zN
0 1
1 2
1 2
2 3
...
0 1 2 -1

4
doc/src/Howto_chunk.txt
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@ -22,8 +22,8 @@ commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 4 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
Here a brief overview for each of the 4 kinds of chunk-related commands
is provided. Then some examples are given of how to compute different
properties with chunk commands.
Compute chunk/atom command: :h4

12
doc/src/Howto_client_server.txt
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@ -64,7 +64,7 @@ client or server.
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
The server doc files give details of the message protocols
for data that is exchanged bewteen the client and server.
for data that is exchanged between the client and server.
These example directories illustrate how to use LAMMPS as either a
client or server code:
@ -75,7 +75,7 @@ examples/COUPLE/lammps_mc
examples/COUPLE/lammps_vasp :ul
The examples/message dir couples a client instance of LAMMPS to a
server instance of LAMMPS.
server instance of LAMMPS.
The lammps_mc dir shows how to couple LAMMPS as a server to a simple
Monte Carlo client code as the driver.
@ -87,7 +87,7 @@ DFT forces, thru a Python wrapper script on VASP.
Here is how to launch a client and server code together for any of the
4 modes of message exchange that the "message"_message.html command
and the CSlib support. Here LAMMPS is used as both the client and
server code. Another code could be subsitituted for either.
server code. Another code could be substituted for either.
The examples below show launching both codes from the same window (or
batch script), using the "&" character to launch the first code in the
@ -106,13 +106,13 @@ together to exchange MPI messages between them.
For message exchange in {file}, {zmq}, or {mpi/two} modes:
% mpirun -np 1 lmp_mpi -log log.client < in.client &
% mpirun -np 1 lmp_mpi -log log.client < in.client &
% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
% mpirun -np 4 lmp_mpi -log log.client < in.client &
% mpirun -np 4 lmp_mpi -log log.client < in.client &
% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
% mpirun -np 2 lmp_mpi -log log.client < in.client &
% mpirun -np 2 lmp_mpi -log log.client < in.client &
% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
For message exchange in {mpi/one} mode:

6
doc/src/Howto_coreshell.txt
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@ -19,7 +19,7 @@ polarizable"_Howto_polarizable.html doc page for a discussion of all
the polarizable models available in LAMMPS.
Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
k*r where k is a parameterized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
add up to the ion charge, thus q(ion) = q(core) + q(shell). This
setup introduces the ion polarizability (alpha) given by
@ -111,7 +111,7 @@ the core and shell particles corresponds to the polarization,
hereby an instantaneous relaxation of the shells is approximated
and a fast core/shell spring frequency ensures a nearly constant
internal kinetic energy during the simulation.
Thermostats can alter this polarization behaviour, by scaling the
Thermostats can alter this polarization behavior, by scaling the
internal kinetic energy, meaning the shell will not react freely to
its electrostatic environment.
Therefore it is typically desirable to decouple the relative motion of
@ -165,7 +165,7 @@ fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification
If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small
momentum to the system, which is noticable over long trajectories.
momentum to the system, which is noticeable over long trajectories.
Therefore it is recommendable to use the "fix
momentum"_fix_momentum.html command in combination with "compute
temp/cs"_compute_temp_cs.html when equilibrating the system to

2
doc/src/Howto_dispersion.txt
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@ -74,7 +74,7 @@ command.
A reasonable approach that combines the upsides of both methods is to
make the first run using the {kspace_modify force/disp/real} and
{kspace_modify force/disp/kspace} commands, write down the PPPM
parameters from the outut, and specify these parameters using the
parameters from the output, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).

2
doc/src/Howto_drude.txt
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@ -17,7 +17,7 @@ for a discussion of all the polarizable models available in LAMMPS.
The Drude model has a number of features aimed at its use in
molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
Thermostating of the additional degrees of freedom associated with the
Thermostatting of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles. :ulb,l

8
doc/src/Howto_drude2.txt
View File

@ -82,7 +82,7 @@ decouple the degrees of freedom associated with the Drude oscillators
from those of the normal atoms. Thermalizing the Drude dipoles at
temperatures comparable to the rest of the simulation leads to several
problems (kinetic energy transfer, very short timestep, etc.), which
can be remediate by the "cold Drude" technique ("Lamoureux and
can be remedied by the "cold Drude" technique ("Lamoureux and
Roux"_#Lamoureux2).
Two closely related models are used to represent polarization through
@ -213,7 +213,7 @@ of mass of the DC-DP pairs, with relaxation time 100 and with random
seed 12345. This fix applies also a Langevin thermostat at temperature
1. to the relative motion of the DPs around their DCs, with relaxation
time 20 and random seed 13977. Only the DCs and non-polarizable
atoms need to be in this fix's group. LAMMPS will thermostate the DPs
atoms need to be in this fix's group. LAMMPS will thermostat the DPs
together with their DC. For this, ghost atoms need to know their
velocities. Thus you need to add the following command:
@ -360,7 +360,7 @@ fix NPH all nph iso 1. 1. 500 :pre
It is also possible to use a Nose-Hoover instead of a Langevin
thermostat. This requires to use "{fix
drude/transform}"_fix_drude_transform.html just before and after the
time intergation fixes. The {fix drude/transform/direct} converts the
time integration fixes. The {fix drude/transform/direct} converts the
atomic masses, positions, velocities and forces into a reduced
representation, where the DCs transform into the centers of mass of
the DC-DP pairs and the DPs transform into their relative position
@ -396,7 +396,7 @@ global pressure and thus a global temperature whatever the fix group.
We do want the pressure to correspond to the whole system, but we want
the temperature to correspond to the fix group only. We must then use
the {fix_modify} command for this. In the end, the block of
instructions for thermostating and barostating will look like
instructions for thermostatting and barostatting will look like
compute TATOMS ATOMS temp
fix DIRECT all drude/transform/direct

2
doc/src/Howto_elastic.txt
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@ -30,7 +30,7 @@ examples/elastic directory described on the "Examples"_Examples.html
doc page.
Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
challenging, because it is necessary to run a simulation that performs
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance

50
doc/src/Howto_github.txt
View File

@ -96,7 +96,7 @@ machine to a directory with the name you chose. If none is given, it will
default to "lammps". Typical names are "mylammps" or something similar.
You can use this local clone to make changes and
test them without interfering with the repository on Github.
test them without interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory
and use git pull:
@ -150,7 +150,7 @@ After the commit, the changes can be pushed to the same branch on GitHub:
$ git push :pre
Git will ask you for your user name and password on GitHub if you have
not configured anything. If your local branch is not present on Github yet,
not configured anything. If your local branch is not present on GitHub yet,
it will ask you to add it by running
$ git push --set-upstream origin github-tutorial-update :pre
@ -254,20 +254,53 @@ them, or if a developer has requested that something needs to be changed
before the feature can be accepted into the official LAMMPS version.
After each push, the automated checks are run again.
[Labels]
LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are
important: needs_work, work_in_progress, test-for-regression, and
full-regression-test. The first two indicate, that your pull request
is not considered to be complete. With "needs_work" the burden is on
exclusively on you; while "work_in_progress" can also mean, that a
LAMMPS developer may want to add changes. Please watch the comments
to the pull requests. The two "test" labels are used to trigger
extended tests before the code is merged. This is sometimes done by
LAMMPS developers, if they suspect that there may be some subtle
side effects from your changes. It is not done by default, because
those tests are very time consuming.
[Reviews]
As of Summer 2018, a pull request needs at least 1 approving review
from a LAMMPS developer with write access to the repository.
In case your changes touch code that certain developers are associated
with, they are auto-requested by the GitHub software. Those associations
are set in the file
".github/CODEOWNERS"_https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS
Thus if you want to be automatically notified to review when anybody
changes files or packages, that you have contributed to LAMMPS, you can
add suitable patterns to that file, or a LAMMPS developer may add you.
Otherwise, you can also manually request reviews from specific developers,
or LAMMPS developers - in their assessment of your pull request - may
determine who else should be reviewing your contribution and add that person.
Through reviews, LAMMPS developers also may request specific changes from you.
If those are not addressed, your pull requests cannot be merged.
[Assignees]
There is an assignee label for pull requests. If the request has not
There is an assignee property for pull requests. If the request has not
been reviewed by any developer yet, it is not assigned to anyone. After
revision, a developer can choose to assign it to either a) you, b) a
LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
Case a) happens if changes are required on your part :ulb,l
Case b) means that at the moment, it is being tested and reviewed by a
LAMMPS developer with the expectation that some changes would be required.
After the review, the developer can choose to implement changes directly
or suggest them to you. :l
Case c) means that the pull request has been assigned to the lead
developer Steve Plimpton and means it is considered ready for merging. :ule,l
Case c) means that the pull request has been assigned to the developer
overseeing the merging of pull requests into the master branch. :ule,l
In this case, Axel assigned the tutorial to Steve:
@ -336,7 +369,7 @@ commit and push again:
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps :pre
This merge also shows up on the lammps Github page:
This merge also shows up on the lammps GitHub page:
:c,image(JPG/tutorial_reverse_pull_request7.png)
@ -381,3 +414,6 @@ Furthermore, the naming of the patches now follow the pattern
"patch_<Day><Month><Year>" to simplify comparisons between releases.
Finally, all patches and submissions are subject to automatic testing
and code checks to make sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file
"doc/github-development-workflow.md"_https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md

2
doc/src/Howto_library.txt
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@ -185,7 +185,7 @@ by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
If the count is specified as 1, they are returned
If the count is specified as 1, they are returned
in a packed format with all three image flags stored in a single integer.
If the count is specified as 3, the values are unpacked into xyz flags
by the library before returning them.

4
doc/src/Howto_manifold.txt
View File

@ -31,8 +31,8 @@ plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with norma
plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R
spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine
spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine
spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendritic spine
spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendritic spine
thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)

2
doc/src/Howto_nemd.txt
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@ -55,5 +55,5 @@ using the "fix flow/gauss"_fix_flow_gauss.html command.
:line
:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

6
doc/src/Howto_polarizable.txt
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@ -45,8 +45,8 @@ high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
complex in order to remedy this and other issues. Specifically, the
Drude model includes specific thermostatting of the core-Drude pairs
and short-range damping of the induced dipoles.
The three polarization methods can be implemented through a
@ -77,5 +77,5 @@ motion of the Drude particles with respect to their cores is kept
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
relative core-Drude particle motion is thermostatted separately as
well.

8
doc/src/Howto_pylammps.txt
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@ -141,16 +141,16 @@ Python code if {L} was a lammps instance:
L.command("region box block 0 10 0 5 -0.5 0.5") :pre
With the PyLammps interface, any command can be split up into arbitrary parts
separated by whitespace, passed as individual arguments to a region method.
separated by white-space, passed as individual arguments to a region method.
L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre
Note that each parameter is set as Python literal floating-point number. In the
PyLammps interface, each command takes an arbitrary parameter list and transparently
merges it to a single command string, separating individual parameters by whitespace.
merges it to a single command string, separating individual parameters by white-space.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parametrization needed to be done
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre
@ -328,7 +328,7 @@ jupyter notebook :pre
IPyLammps Examples :h4
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
sub-directory. To open these notebooks launch {jupyter notebook} inside this
directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.

2
doc/src/Howto_replica.txt
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@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Multi-replica simulations :h3
Several commands in LAMMPS run mutli-replica simulations, meaning
Several commands in LAMMPS run multi-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.

2
doc/src/Howto_spc.txt
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@ -30,7 +30,7 @@ r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
Angstrom cutoff for both LJ and Coulombic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.

4
doc/src/Howto_spherical.txt
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@ -35,7 +35,7 @@ There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
The sphere style defines particles that are spheriods and each
The sphere style defines particles that are spheroids and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
@ -236,7 +236,7 @@ particles are point masses.
Also note that body particles cannot be modeled with the "fix
rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
list of sub-particles. Individual body particles are typically treated
as rigid bodies, and their motion integrated with a command like "fix
nve/body"_fix_nve_body.html. Interactions between pairs of body
particles are computed via a command like "pair_style

54
doc/src/Howto_spins.txt
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@ -12,48 +12,48 @@ Magnetic spins :h3
The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
materials.
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
materials.
The magnetic spins are interacting with each others and with the
lattice via pair interactions. Typically, the magnetic exchange
interaction can be defined using the
The magnetic spins are interacting with each others and with the
lattice via pair interactions. Typically, the magnetic exchange
interaction can be defined using the
"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
applies a magnetic torque to a given spin, considering the orientation
of its neighboring spins and their relative distances.
It also applies a force on the atoms as a function of the spin
orientations and their associated inter-atomic distances.
of its neighboring spins and their relative distances.
It also applies a force on the atoms as a function of the spin
orientations and their associated inter-atomic distances.
The command "fix precession/spin"_fix_precession_spin.html allows to
apply a constant magnetic torque on all the spins in the system. This
torque can be an external magnetic field (Zeeman interaction), or an
uniaxial magnetic anisotropy.
uniaxial magnetic anisotropy.
A Langevin thermostat can be applied to those magnetic spins using
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
can be coupled to another Langevin thermostat applied to the atoms
using "fix langevin"_fix_langevin.html in order to simulate
thermostated spin-lattice system.
A Langevin thermostat can be applied to those magnetic spins using
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
can be coupled to another Langevin thermostat applied to the atoms
using "fix langevin"_fix_langevin.html in order to simulate
thermostatted spin-lattice system.
The magnetic Gilbert damping can also be applied using "fix
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
The magnetic Gilbert damping can also be applied using "fix
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or
the magnetic energy. The second command is "compute
the magnetic energy. The second command is "compute
property/atom"_compute_property_atom.html. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
:line
:link(Tranchida7)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
arXiv preprint arXiv:1801.10233, (2018).

2
doc/src/Howto_thermostat.txt
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@ -96,5 +96,5 @@ temperature compute is used for default thermodynamic output.
:line
:link(Daivis-thermostat)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

2
doc/src/Howto_triclinic.txt
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@ -200,7 +200,7 @@ used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
"create_atoms"_create_atoms.html command.
A second use is to run Parinello-Rahman dynamics via the "fix
A second use is to run Parrinello-Rahman dynamics via the "fix
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analog for an "energy minimization"_minimize.html is

2
doc/src/Howto_viscosity.txt
View File

@ -140,5 +140,5 @@ with time at sufficiently long times.
:line
:link(Daivis-viscosity)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

2
doc/src/Install_git.txt
View File

@ -45,7 +45,7 @@ git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre
where "mylammps" is the name of the directory you wish to create on
your machine and "unstable" is one of the 3 branches listed above.
(Note that you actually download all 3 branches; you can switch
between them at any time using "git checkout <branchname>".)
between them at any time using "git checkout <branch name>".)
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with two exceptions:

2
doc/src/Install_linux.txt
View File

@ -89,7 +89,7 @@ the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is {lmp} in all 3 cases.
By default, {lmp} will refer to the serial executable, unless
one of the MPI environment modules is loaded
one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable is used.
The same mechanism applies when loading the LAMMPS python module.

2
doc/src/Install_patch.txt
View File

@ -17,7 +17,7 @@ how to stay current are on the "Install git"_Install_git.html and
If you prefer to download a tarball, as described on the "Install
git"_Install_tarball.html doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the "bug and feature
a patch file is posted on the "bug and feature
page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local

4
doc/src/Intro_authors.txt
View File

@ -48,7 +48,7 @@ Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
Mike Parks (Sandia), PERI package for Peridynamics
Roy Pollock (LLNL), Ewald and PPPM solvers
Christian Trott (Sandia), USER-CUDA and KOKKOS packages
Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
:line
@ -58,7 +58,7 @@ page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)

10
doc/src/Intro_features.txt
View File

@ -68,7 +68,7 @@ commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
long-range interactions for charge, point-dipoles, and LJ dispersion: \
@ -110,11 +110,11 @@ Atom creation :h4,link(create)
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4,link(ensemble)
("fix"_fix.html command)
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)
@ -128,7 +128,7 @@ Ensembles, constraints, and boundary conditions :h4,link(ensemble)
variety of additional boundary conditions and constraints :ul
Integrators :h4,link(integrate)
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
Brownian dynamics
@ -142,7 +142,7 @@ Diagnostics :h4,link(diag)
see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4,link(output)
("dump"_dump.html, "restart"_restart.html commands)
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities

32
doc/src/Intro_nonfeatures.txt
View File

@ -13,15 +13,19 @@ LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of
functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS does not:
Specifically, LAMMPS was not conceived and designed for:
run thru a GUI
build molecular systems
being run thru a GUI
build molecular systems, or building molecular topologies
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
perform sophisticated analysis of your MD simulation
visualize your MD simulation interactively
plot your output data :ul
Although over the years these limitations have been somewhat
reduced through features added to LAMMPS or external tools
that either interface with LAMMPS or extend LAMMPS.
Here are suggestions on how to perform these tasks:
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
@ -29,7 +33,7 @@ the library interface is provided. Thus, GUI interfaces can be
written in Python (or C or C++ if desired) that run LAMMPS and
visualize or plot its output. Examples of this are provided in the
python directory and described on the "Python"_Python_head.html doc
page. :ulb,l
page. Also, there are several external wrappers or GUI front ends.:ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
of them convert input files in formats produced by other MD codes such
@ -40,28 +44,36 @@ molecular builder that will generate complex molecular models. See
the "Tools"_Tools.html doc page for details on tools packaged with
LAMMPS. The "Pre/post processing
page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
describes a variety of 3rd party tools for this task. :l
describes a variety of 3rd party tools for this task. Furthermore,
some LAMMPS internal commands to reconstruct topology, as well as
the option to insert molecule templates instead of atoms.:l
Force-field assignment: The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
or Accelerys force field files. :l
or BIOVIA (formerly Accelrys) force field files. :l
Simulation analyses: If you want to perform analyses on-the-fly as
Simulation analysis: If you want to perform analysis on-the-fly as
your simulation runs, see the "compute"_compute.html and
"fix"_fix.html doc pages, which list commands that can be used in a
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
info on how to add your own analysis code or algorithms to LAMMPS.
For post-processing, LAMMPS output such as "dump file
snapshots"_dump.html can be converted into formats used by other MD or
post-processing codes. Some post-processing tools packaged with
post-processing codes. To some degree, that conversion can be done
directly inside of LAMMPS by interfacing to the VMD molfile plugins.
The "rerun"_rerun.html command also allows to do some post-processing
of existing trajectories, and through being able to read a variety
of file formats, this can also be used for analyzing trajectories
from other MD codes. Some post-processing tools packaged with
LAMMPS will do these conversions. Scripts provided in the
tools/python directory can extract and massage data in dump files to
make it easier to import into other programs. See the
"Tools"_Tools.html doc page for details on these various options. :l
Visualization: LAMMPS can produce JPG or PNG snapshot images
on-the-fly via its "dump image"_dump_image.html command. For
on-the-fly via its "dump image"_dump_image.html command and pass
them to an external program FFmpeg to generate movies from them. For
high-quality, interactive visualization there are many excellent and
free tools available. See the "Other Codes
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="15 Nov 2018 version">
<META NAME="docnumber" CONTENT="27 Nov 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
15 Nov 2018 version :c,h2
27 Nov 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

2
doc/src/Manual_build.txt
View File

@ -61,7 +61,7 @@ make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data :pre

4
doc/src/Modify_contribute.txt
View File

@ -33,11 +33,11 @@ how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
typical requirements. Once you have prepared everything, see the
"Howto github"_Howto_github.html doc page for instructions on how to
"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to
submit your changes or new files through a GitHub pull request. If you
prefer to submit patches or full files, you should first make certain,
that your code works correctly with the latest patch-level version of
LAMMPS and contains all bugfixes from it. Then create a gzipped tar
LAMMPS and contains all bug fixes from it. Then create a gzipped tar
file of all changed or added files or a corresponding patch file using
'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.

2
doc/src/Modify_pair.txt
View File

@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Pair styles :h3
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
class. In LAMMPS, pairwise calculation include many-body potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.

4
doc/src/Modify_region.txt
View File

@ -20,6 +20,6 @@ Here is a brief description of methods you define in your new derived
class. See region.h for details.
inside: determine whether a point is in the region
surface_interior: determine if a point is within a cutoff distance inside of surc
surface_exterior: determine if a point is within a cutoff distance outside of surf
surface_interior: determine if a point is within a cutoff distance inside of surface
surface_exterior: determine if a point is within a cutoff distance outside of surface
shape_update : change region shape if set by time-dependent variable :tb(s=:)

62
doc/src/Packages_details.txt
View File

@ -205,7 +205,7 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -286,7 +286,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -354,7 +354,7 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -400,7 +400,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -494,7 +494,7 @@ MANYBODY package :link(PKG-MANYBODY),h4
[Contents:]
A variety of manybody and bond-order potentials. These include
A variety of many-body and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
[Supporting info:]
@ -518,7 +518,7 @@ MC package :link(PKG-MC),h4
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
(GCMC) in conjunction with dynamics.
[Supporting info:]
@ -548,7 +548,7 @@ and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -681,7 +681,7 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -713,7 +713,7 @@ have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -770,7 +770,7 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -802,7 +802,7 @@ shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
lib/python/README for more details.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -850,7 +850,7 @@ as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1023,7 +1023,7 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1050,7 +1050,7 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1077,7 +1077,7 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1100,7 +1100,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
of "fix npt"_fix_nh.html which includes the pressure correction to
the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
@ -1185,7 +1185,7 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#user-colvars on the "Build
@ -1207,7 +1207,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
[Contents:]
The fix plumed command allows you to use the PLUMED free energy plugin
for molecular dynamics to analyse and bias your LAMMPS trajectory on
for molecular dynamics to analyze and bias your LAMMPS trajectory on
the fly. The PLUMED library is called from within the LAMMPS input
script by using the "fix plumed _fix_plumed.html command.
@ -1395,7 +1395,7 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1433,7 +1433,7 @@ NOTE: the USER-INTEL package contains styles that require using the
[Author:] Mike Brown (Intel).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1603,17 +1603,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
Pair, angle and improper styles needed to employ the MOF-FF
force field by Schmid and coworkers with LAMMPS.
force field by Schmid and coworkers with LAMMPS.
MOF-FF is a first principles derived force field with the primary aim
to simulate MOFs and related porous framework materials, using spherical
to simulate MOFs and related porous framework materials, using spherical
Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
2013, 250, 1128-1141.
For the usage of MOF-FF see the example in the example directory as
For the usage of MOF-FF see the example in the example directory as
well as the "MOF+"_MOFplus website.
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
[Author:] Hendrik Heenen (Technical U of Munich),
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
[Supporting info:]
@ -1654,7 +1654,7 @@ at
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1694,7 +1694,7 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1738,7 +1738,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1817,7 +1817,7 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1875,7 +1875,7 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1994,7 +1994,7 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -2120,7 +2120,7 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build

4
doc/src/Packages_user.txt
View File

@ -38,8 +38,8 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no

2
doc/src/Python_call.txt
View File

@ -79,7 +79,7 @@ of Python and your machine to successfully build LAMMPS. See the
lib/python/README file for more info.
If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps overviewed in the "Python
must also follow the steps summarized in the "Python
run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared
library and insure that Python can find the python/lammps.py file and
the shared library.

2
doc/src/Python_examples.txt
View File

@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
The latter link is to AtomEye 3 which has the scriping
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
Note that for PyMol, you need to have built and installed the

53
doc/src/Run_options.txt
View File

@ -354,29 +354,31 @@ the LAMMPS simulation domain.
:line
[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
[-restart2data restartfile \[remap\] datafile keyword value ...]
:link(restart2data)
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
read_restart restartfile \[remap\]
write_data datafile keyword value ... :pre
Note that the specified restartfile and/or datafile can have the
wild-card character "*". The restartfile can also have the wild-card
The specified restartfile and/or datafile name may contain the wild-card
character "*". The restartfile name may also contain the wild-card
character "%". The meaning of these characters is explained on the
"read_restart"_read_restart.html and "write_data"_write_data.html doc
pages. The use of "%" means that a parallel restart file can be read.
Note that a filename such as file.* will need to be enclosed in quotes
to avoid shell expansion of the "*" character.
Note that a filename such as file.* may need to be enclosed in quotes or
the "*" character prefixed with a backslash ("\") to avoid shell
expansion of the "*" character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect of adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the data file to still be produced.
Following restartfile argument, the optional word "remap" may be used.
This has the same effect like adding it to a
"read_restart"_read_restart.html command, and operates as explained on
its doc page. This is useful if reading the restart file triggers an
error that atoms have been lost. In that case, use of the remap flag
should allow the data file to still be produced.
The syntax following restartfile (or remap), namely
@ -388,29 +390,30 @@ optional keyword/value settings.
:line
[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile (remap)
read_restart restartfile \[remap\]
write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
Note that the specified restartfile and dumpfile can have wild-card
characters ("*","%") as explained on the
Note that the specified restartfile and dumpfile names may contain
wild-card characters ("*","%") as explained on the
"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
pages. The use of "%" means that a parallel restart file and/or
parallel dump file can be read and/or written. Note that a filename
such as file.* will need to be enclosed in quotes to avoid shell
expansion of the "*" character.
such as file.* may need to be enclosed in quotes or the "*" character
prefixed with a backslash ("\") to avoid shell expansion of the "*"
character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the dump file to still be produced.
Note that following the restartfile argument, the optional word "remap"
can be used. This has the effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc page.
This is useful if reading the restart file triggers an error that atoms
have been lost. In that case, use of the remap flag should allow the
dump file to still be produced.
The syntax following restartfile (or remap), namely
@ -524,7 +527,7 @@ option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined.
re-defined.
See the "variable"_variable.html command for more info on defining
index and other kinds of variables and the "Commands

2
doc/src/Run_windows.txt
View File

@ -41,7 +41,7 @@ path for the default location of this MPI package. After the
installation of the MPICH2 software, it needs to be integrated into
the system. For this you need to start a Command Prompt in
{Administrator Mode} (right click on the icon and select it). Change
into the MPICH2 installation directory, then into the subdirectory
into the MPICH2 installation directory, then into the sub-directory
[bin] and execute [smpd.exe -install]. Exit the command window.
Get a new, regular command prompt by going to Start->Run... ,

2
doc/src/Speed.txt
View File

@ -19,7 +19,7 @@ using code options that implement alternate algorithms that can
speed-up a simulation. The second is to use one of the several
accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi coprocessors.
Intel Xeon Phi co-processors.
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator

96
doc/src/Speed_intel.txt
View File

@ -14,11 +14,11 @@ Corporation. It provides two methods for accelerating simulations,
depending on the hardware you have. The first is acceleration on
Intel CPUs by running in single, mixed, or double precision with
vectorization. The second is acceleration on Intel Xeon Phi
coprocessors via offloading neighbor list and non-bonded force
co-processors via offloading neighbor list and non-bonded force
calculations to the Phi. The same C++ code is used in both cases.
When offloading to a coprocessor from a CPU, the same routine is run
When offloading to a co-processor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
LAMMPS to run on the CPU cores and co-processor cores simultaneously.
[Currently Available USER-INTEL Styles:]
@ -27,9 +27,9 @@ Bond Styles: fene, fourier, harmonic :l
Dihedral Styles: charmm, harmonic, opls :l
Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
Improper Styles: cvff, harmonic :l
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
rebo, sw, tersoff :l
K-Space Styles: pppm, pppm/disp :l
:ule
@ -47,7 +47,7 @@ These are scalable in size; the results given are with 512K
particles (524K for Liquid Crystal). Most of the simulations are
standard LAMMPS benchmarks (indicated by the filename extension in
parenthesis) with modifications to the run length and to add a
warmup run (for use with offload benchmarks).
warm-up run (for use with offload benchmarks).
:c,image(JPG/user_intel.png)
@ -134,19 +134,19 @@ Do not use thread affinity (set KMP_AFFINITY=none) :l
The "newton off" setting may provide better scalability :l
:ule
For Intel Xeon Phi coprocessors (Offload):
For Intel Xeon Phi co-processors (Offload):
Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l
"-pk intel N omp 1" added to command-line where N is the number of
coprocessors per node. :l
co-processors per node. :l
:ule
:line
[Required hardware/software:]
In order to use offload to coprocessors, an Intel Xeon Phi
coprocessor and an Intel compiler are required. For this, the
In order to use offload to co-processors, an Intel Xeon Phi
co-processor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
@ -214,7 +214,7 @@ Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
Makefile.knl # Intel Compiler, Intel MPI, No Offload
Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload
Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre
Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload :pre
Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
it explicitly specifies that vectorization should be for Intel Xeon
@ -227,18 +227,18 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
However, if you do not have coprocessors on your system, building
Note that if you build with support for a Phi co-processor, the same
binary can be used on nodes with or without co-processors installed.
However, if you do not have co-processors on your system, building
without offload support will produce a smaller binary.
The general requirements for Makefiles with the USER-INTEL package
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
are as follows. When using Intel compilers, "-restrict" is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS.
CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
(unless Intel Math Kernel Library (MKL) is not available in the build
environment). For Intel compilers, LIB should include "-ltbbmalloc"
environment). For Intel compilers, LIB should include "-ltbbmalloc"
or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
@ -272,7 +272,7 @@ Advanced performance tuning options are also described below to get
the best performance.
When running on a single node (including runs using offload to a
coprocessor), best performance is normally obtained by using 1 MPI
co-processor), best performance is normally obtained by using 1 MPI
task per physical core and additional OpenMP threads with SMT. For
Intel Xeon processors, 2 OpenMP threads should be used for SMT.
For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
@ -290,7 +290,7 @@ NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
threads to a core or group of cores so that memory access can be
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host (CPU) will be set by default on the host
{when using offload to a coprocessor}. In this case, it is unnecessary
{when using offload to a co-processor}. In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl,
I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
option to the "package intel"_package.html command or by disabling the
@ -310,15 +310,15 @@ editing the input script. This switch will automatically append
options for the USER-INTEL package. The default package command will
specify that USER-INTEL calculations are performed in mixed precision,
that the number of OpenMP threads is specified by the OMP_NUM_THREADS
environment variable, and that if coprocessors are present and the
binary was built with offload support, that 1 coprocessor per node
environment variable, and that if co-processors are present and the
binary was built with offload support, that 1 co-processor per node
will be used with automatic balancing of work between the CPU and the
coprocessor.
co-processor.
You can specify different options for the USER-INTEL package by using
the "-pk intel Nphi" "command-line switch"_Run_options.html with
keyword/value pairs as specified in the documentation. Here, Nphi = #
of Xeon Phi coprocessors/node (ignored without offload
of Xeon Phi co-processors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
override any OMP_NUM_THREADS setting and specify the number of OpenMP
threads, {mode} to set the floating-point precision mode, and {lrt} to
@ -332,7 +332,7 @@ Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision :pre
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre
[Or run with the USER-INTEL package by editing an input script:]
@ -364,7 +364,7 @@ intel"_package.html command that can improve performance when using
"PPPM"_kspace_style.html for long-range electrostatics on processors
with SMT. It generates an extra pthread for each MPI task. The thread
is dedicated to performing some of the PPPM calculations and MPI
communications. This feature requires setting the preprocessor flag
communications. This feature requires setting the pre-processor flag
-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but
it is set in all makefiles tuned for the USER-INTEL package. On Intel
@ -399,7 +399,7 @@ the "suffix hybrid intel omp"_suffix.html command can also be used
within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html to the beginning of the input script for
better scalability.
@ -422,29 +422,29 @@ that MPI runs are performed in MCDRAM.
The default settings for offload should give good performance.
When using LAMMPS with offload to Intel coprocessors, best performance
When using LAMMPS with offload to Intel co-processors, best performance
will typically be achieved with concurrent calculations performed on
both the CPU and the coprocessor. This is achieved by offloading only
a fraction of the neighbor and pair computations to the coprocessor or
both the CPU and the co-processor. This is achieved by offloading only
a fraction of the neighbor and pair computations to the co-processor or
using "hybrid"_pair_hybrid.html pair styles where only one style uses
the "intel" suffix. For simulations with long-range electrostatics or
bond, angle, dihedral, improper calculations, computation and data
transfer to the coprocessor will run concurrently with computations
transfer to the co-processor will run concurrently with computations
and MPI communications for these calculations on the host CPU. This
is illustrated in the figure below for the rhodopsin protein benchmark
running on E5-2697v2 processors with a Intel Xeon Phi 7120p
coprocessor. In this plot, the vertical access is time and routines
co-processor. In this plot, the vertical access is time and routines
running at the same time are running concurrently on both the host and
the coprocessor.
the co-processor.
:c,image(JPG/offload_knc.png)
The fraction of the offloaded work is controlled by the {balance}
keyword in the "package intel"_package.html command. A balance of 0
runs all calculations on the CPU. A balance of 1 runs all
supported calculations on the coprocessor. A balance of 0.5 runs half
of the calculations on the coprocessor. Setting the balance to -1
(the default) will enable dynamic load balancing that continously
supported calculations on the co-processor. A balance of 0.5 runs half
of the calculations on the co-processor. Setting the balance to -1
(the default) will enable dynamic load balancing that continuously
adjusts the fraction of offloaded work throughout the simulation.
Because data transfer cannot be timed, this option typically produces
results within 5 to 10 percent of the optimal fixed balance.
@ -455,23 +455,23 @@ near-optimal setting that will carry over to additional runs.
The default for the "package intel"_package.html command is to have
all the MPI tasks on a given compute node use a single Xeon Phi
coprocessor. In general, running with a large number of MPI tasks on
co-processor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
automatically get affinity to a subset of the hardware threads
available on the coprocessor. For example, if your card has 61 cores,
available on the co-processor. For example, if your card has 61 cores,
with 60 cores available for offload and 4 hardware threads per core
(240 total threads), running with 24 MPI tasks per node will cause
each MPI task to use a subset of 10 threads on the coprocessor. Fine
each MPI task to use a subset of 10 threads on the co-processor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the "package intel"_package.html command.
The USER-INTEL package has two modes for deciding which atoms will be
handled by the coprocessor. This choice is controlled with the {ghost}
handled by the co-processor. This choice is controlled with the {ghost}
keyword of the "package intel"_package.html command. When set to 0,
ghost atoms (atoms at the borders between MPI tasks) are not offloaded
to the card. This allows for overlap of MPI communication of forces
with computation on the coprocessor when the "newton"_newton.html
with computation on the co-processor when the "newton"_newton.html
setting is "on". The default is dependent on the style being used,
however, better performance may be achieved by setting this option
explicitly.
@ -482,21 +482,21 @@ cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks.
If pair computations are being offloaded to an Intel Xeon Phi
coprocessor, a diagnostic line is printed to the screen (not to the
co-processor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
mode is being used and indicating the number of co-processor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for "atom
sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
available co-processor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
switch"_Run_options.html is used to limit the coprocessor threads per
switch"_Run_options.html is used to limit the co-processor threads per
MPI task.
[Restrictions:]
When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
When offloading to a co-processor, "hybrid"_pair_hybrid.html styles
that require skip lists for neighbor builds cannot be offloaded.
Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel
accelerated style may be used with hybrid styles when offloading.
@ -510,7 +510,7 @@ supported.
[References:]
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l

46
doc/src/Speed_kokkos.txt
View File

@ -13,11 +13,11 @@ Kokkos is a templated C++ library that provides abstractions to allow
a single implementation of an application kernel (e.g. a pair style)
to run efficiently on different kinds of hardware, such as GPUs, Intel
Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
different backend languages such as CUDA, OpenMP, or Pthreads. The
different back end languages such as CUDA, OpenMP, or Pthreads. The
Kokkos library also provides data abstractions to adjust (at compile
time) the memory layout of data structures like 2d and 3d arrays to
optimize performance on different hardware. For more information on
Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part
of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
library was written primarily by Carter Edwards, Christian Trott, and
Dan Sunderland (all Sandia).
@ -106,10 +106,10 @@ modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.
NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
backend (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
@ -127,21 +127,21 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
If the "newton"_newton.html command is used in the input
script, it can also override the Newton flag defaults.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomics, which
don't require duplication. The use of atomics can be forced by compiling
with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
Kokkos-enabled pair_styles support data duplication. Alternatively, full
neighbor lists avoid the need for duplication or atomics but require
more compute operations per atom. When using the Kokkos Serial backend
or the OpenMP backend with a single thread, no duplication or atomics are
used. For CUDA and half neighbor lists, the KOKKOS package always uses
atomics.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomic operations
which do not require data duplication. The use of atomic operations can
be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS"
pre-processor flag. Most but not all Kokkos-enabled pair_styles support
data duplication. Alternatively, full neighbor lists avoid the need for
duplication or atomic operations but require more compute operations per
atom. When using the Kokkos Serial back end or the OpenMP back end with
a single thread, no duplication or atomic operations are used. For CUDA
and half neighbor lists, the KOKKOS package always uses atomic operations.
[Core and Thread Affinity:]
@ -193,7 +193,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. When running on KNL, this will
typically be best for pair-wise potentials. For manybody potentials,
typically be best for pair-wise potentials. For many-body potentials,
using "half" neighbor lists and setting the Newton flag to "on" may be
faster. It can also be faster to use non-threaded communication. Use
the "-pk kokkos" "command-line switch"_Run_options.html to change the
@ -207,7 +207,7 @@ mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half co
NOTE: MPI tasks and threads should be bound to cores as described
above for CPUs.
NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
NOTE: To build with Kokkos support for Intel Xeon Phi co-processors
such as Knight's Corner (KNC), your system must be configured to use
them in "native" mode, not "offload" mode like the USER-INTEL package
supports.

4
doc/src/Speed_omp.txt
View File

@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l
The system has a spatially inhomogeneous particle density which does
not map well to the "domain decomposition scheme"_processors.html or
"load-balancing"_balance.html options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
because multi-threading achieves parallelism over the number of
particles, not via their distribution in space. :l
A machine is being used in "capability mode", i.e. near the point
@ -143,7 +143,7 @@ the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
sometimes be achieved by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
"run_style verlet/split"_run_style.html command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number

4
doc/src/Speed_packages.txt
View File

@ -14,7 +14,7 @@ Accelerated versions of various "pair_style"_pair_style.html,
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
co-processors.
All of these commands are in packages provided with LAMMPS. An
overview of packages is give on the "Packages"_Packages.html doc
@ -161,7 +161,7 @@ package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
co-processors. This can result in additional speedup over 2x depending
on the hardware configuration. :l
Styles with a "kk" suffix are part of the KOKKOS package, and can be

10
doc/src/Tools.txt
View File

@ -163,7 +163,7 @@ for the "chain benchmark"_Speed_bench.html.
colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
The colvars directory contains a collection of tools for post-processing
data produced by the colvars collective variable library.
To compile the tools, edit the makefile for your system and run "make".
@ -263,7 +263,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
emacs tool :h4,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
with various highlighting options set up.
@ -406,15 +406,15 @@ supports it. It has its own WWW page at
msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
Insight MD code, formerly MSI/Biosym and its Discover MD code).
input and data files from BIOVIA's Materias Studio files (formerly
Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code).
This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). Several people contributed changes
to remove bugs and adapt its output to changes in LAMMPS.
This tool has several known limitations and is no longer under active
development, so there are no changes except for the occasional bugfix.
development, so there are no changes except for the occasional bug fix.
See the README file in the tools/msi2lmp folder for more information.

24
doc/src/angle_coeff.txt
View File

@ -60,26 +60,14 @@ doc page for details.
:line
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The full list of all
angle styles is on the "Commands bond"_Commands_bond.html#angle doc
The list of all angle styles defined in LAMMPS is given on the
"angle_style"_angle_style.html doc page. They are also listed in more
compact form on the "Commands angle"_Commands_bond.html#angle doc
page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle
"angle_style table"_angle_table.html - tabulated by angle :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
angle_coeff command.
:line

12
doc/src/angle_cosine_buck6d.txt
View File

@ -23,19 +23,19 @@ The {cosine/buck6d} angle style uses the potential
:c,image(Eqs/angle_cosine_buck6d.jpg)
where K is the energy constant, n is the periodic multiplicity and
where K is the energy constant, n is the periodic multiplicity and
Theta0 is the equilibrium angle.
The coefficients must be defined for each angle type via the
The coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands in the following order:
K (energy)
n
n
Theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
Additional to the cosine term the {cosine/buck6d} angle style computes
@ -51,8 +51,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
[Restrictions:]
{cosine/buck6d} can only be used in combination with the
"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the
USER-MOFFF package. See the "Build package"_Build_package.html doc

2
doc/src/angle_cosine_shift.txt
View File

@ -63,7 +63,7 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER-MISC package.
USER-MISC package.
[Related commands:]

2
doc/src/angle_sdk.txt
View File

@ -28,7 +28,7 @@ The {sdk} angle style is a combination of the harmonic angle potential,
where theta0 is the equilibrium value of the angle and K a prefactor,
with the {repulsive} part of the non-bonded {lj/sdk} pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parametrization using the
coarse grained MD simulations with the CMM parameterization using the
"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style
{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.

13
doc/src/angle_style.txt
View File

@ -57,10 +57,15 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The full list of all
angle styles are is on the "Commands bond"_Commands_bond.html#angle
doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the angle_style command, and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
angle"_Commands_bond.html#angle doc page are followed by one or more
of (g,i,k,o,t) to indicate which accelerated styles exist.
"none"_angle_none.html - turn off angle interactions
"zero"_angle_zero.html - topology but no interactions

3
doc/src/atom_modify.txt
View File

@ -166,7 +166,8 @@ info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
"first" group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size.
cutoff will be used to set the bin size. If no neighbor cutoff is
defined, sorting will be turned off.
:line

10
doc/src/atom_style.txt
View File

@ -39,7 +39,7 @@ atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style spin
atom_style template myMols
atom_style template myMols
atom_style tdpd 2 :pre
[Description:]
@ -87,7 +87,7 @@ quantities.
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{peri} | mass, volume | mesoscopic Peridynamic models |
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
{sphere} | diameter, mass, angular velocity | granular models |
{spin} | magnetic moment | system with magnetic particles |
@ -309,9 +309,9 @@ force fields"_pair_eff.html.
The {dpd} style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The {meso} style is part of the USER-SPH package for smoothed particle

13
doc/src/balance.txt
View File

@ -247,7 +247,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the {stopthresh}
criterion is met.
A rebalance operation in a single dimension is performed using a
A re-balance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning for a single value, except
@ -261,11 +261,11 @@ information, so that they become closer together over time. Thus as
the recursion progresses, the count of particles on either side of the
plane gets closer to the target value.
Once the rebalancing is complete and final processor sub-domains
Once the re-balancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and
the balance procedure ends.
NOTE: At each rebalance operation, the bisectioning for each cutting
NOTE: At each re-balance operation, the bisectioning for each cutting
plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
@ -348,7 +348,7 @@ specified groups, its weight is not changed. If it belongs to
multiple groups, its weight is the product of the weight factors.
This weight style is useful in combination with pair style
"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody
"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body
potential with a fast pair-wise potential. It is also useful when
using "run_style respa"_run_style.html where some portions of the
system have many bonded interactions and others none. It assumes that
@ -510,10 +510,13 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES".
For 2d simulations, the {z} style cannot be used. Nor can a "z"
appear in {dimstr} for the {shift} style.
Balancing through recursive bisectioning ({rcb} style) requires
"comm_style tiled"_comm_style.html
[Related commands:]
"group"_group.html, "processors"_processors.html,
"fix balance"_fix_balance.html
"fix balance"_fix_balance.html, "comm_style"_comm_style.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

24
doc/src/bond_coeff.txt
View File

@ -56,25 +56,13 @@ corresponds to the 1st example above would be listed as
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
The list of all bond styles defined in LAMMPS is given on the
"bond_style"_bond_style.html doc page. They are also listed in more
compact form on the "Commands bond"_Commands_bond.html doc page.
Note that here are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond
"bond_style table"_bond_table.html - tabulated by bond length :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
bond_coeff command.
:line

2
doc/src/bond_oxdna.txt
View File

@ -52,7 +52,7 @@ hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparametrizing the entire model.
be changed without reparameterizing the entire model.
Example input and data files for DNA duplexes can be found in
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python

14
doc/src/bond_style.txt
View File

@ -65,9 +65,15 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that there are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the bond_style command, and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands bond"_Commands_bond.html
doc page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"none"_bond_none.html - turn off bonded interactions
"zero"_bond_zero.html - topology but no interactions
@ -83,7 +89,7 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page.
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"quartic"_bond_quartic.html - breakable quartic bond
"table"_bond_table.html - tabulated by bond length :ul

2
doc/src/comm_modify.txt
View File

@ -154,6 +154,6 @@ Communication mode {multi} is currently only available for
[Default:]
The option defauls are mode = single, group = all, cutoff = 0.0, vel =
The option defaults are mode = single, group = all, cutoff = 0.0, vel =
no. The cutoff default of 0.0 means that ghost cutoff = neighbor
cutoff = pairwise force cutoff + neighbor skin.

5
doc/src/comm_style.txt
View File

@ -51,7 +51,10 @@ decomposition will be the same, as described by
commands. The decomposition can be changed via the
"balance"_balance.html or "fix balance"_fix_balance.html commands.
[Restrictions:] none
[Restrictions:]
Communication style {tiled} cannot be used with {triclinic} simulation
cells.
[Related commands:]

129
doc/src/compute.txt
View File

@ -164,25 +164,20 @@ and what it does. Here is an alphabetic list of compute styles
available in LAMMPS. They are also listed in more compact form on the
"Commands compute"_Commands_compute.html doc page.
There are also additional compute styles (not listed here) submitted
by users which are included in the LAMMPS distribution. The full list
of all compute styles is on the "Commands
compute"_Commands_compute.html doc page.
There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
(g,i,k,o,t) to indicate which accelerated styles exist.
"ackland/atom"_compute_ackland_atom.html -
"adf"_compute_adf.html - angular distribution function
"ackland/atom"_compute_ackland_atom.html -
"adf"_compute_adf.html - angular distribution function of triples of atoms
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle/local"_compute_bond_local.html - theta and energy of each angle
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
"basal/atom"_compute_basal_atom.html -
"basal/atom"_compute_basal_atom.html -
"body/local"_compute_body_local.html - attributes of body sub-particles
"bond"_compute_bond.html - values computed by a bond style
"bond/local"_compute_bond_local.html - distance and energy of each bond
@ -191,48 +186,48 @@ compute"_Commands_compute.html doc page are followed by one or more of
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"cnp/atom"_compute_cnp_atom.html -
"cnp/atom"_compute_cnp_atom.html -
"com"_compute_com.html - center-of-mass of group of atoms
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
"dihedral"_compute_dihedral.html -
"dihedral"_compute_dihedral.html -
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
"dipole/chunk"_compute_dipole_chunk.html -
"dipole/chunk"_compute_dipole_chunk.html -
"displace/atom"_compute_displace_atom.html - displacement of each atom
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"event/displace"_compute_event_displace.html - detect event on atom displacement
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
"global/atom"_compute_global_atom.html -
"global/atom"_compute_global_atom.html -
"group/group"_compute_group_group.html - energy/force between two groups of atoms
"gyration"_compute_gyration.html - radius of gyration of group of atoms
"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"heat/flux/tally"_compute_tally.html -
"heat/flux/tally"_compute_tally.html -
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
"improper"_compute_improper.html -
"improper"_compute_improper.html -
"improper/local"_compute_improper_local.html - angle of each improper
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
"ke"_compute_ke.html - translational kinetic energy
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@ -242,74 +237,74 @@ compute"_Commands_compute.html doc page are followed by one or more of
"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
"pe"_compute_pe.html - potential energy
"pe/atom"_compute_pe_atom.html - potential energy for each atom
"pe/mol/tally"_compute_tally.html -
"pe/tally"_compute_tally.html -
"pe/mol/tally"_compute_tally.html -
"pe/tally"_compute_tally.html -
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"ptm/atom"_compute_ptm_atom.html -
"ptm/atom"_compute_ptm_atom.html -
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"saed"_compute_saed.html -
"saed"_compute_saed.html -
"slice"_compute_slice.html - extract values from global vector or array
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"spin"_compute_spin.html -
"spin"_compute_spin.html -
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/body"_compute_temp_body.html - temperature of body particles
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/cs"_compute_temp_cs.html -
"temp/cs"_compute_temp_cs.html -
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
"temp/uef"_compute_temp_uef.html -
"temp/uef"_compute_temp_uef.html -
"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
"xrd"_compute_xrd.html - :ul

62
doc/src/compute_adf.txt
View File

@ -33,22 +33,22 @@ keyword = {ordinate} :l
compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
1 1 2 0.0 1.2 0.0 1.5 &
1 2 2 0.0 1.5 0.0 1.5 &
1 2 2 0.0 1.5 0.0 1.5 &
2 1 1 0.0 1.2 0.0 1.2 &
2 1 2 0.0 1.5 2.0 3.5 &
2 2 2 2.0 3.5 2.0 3.5
2 2 2 2.0 3.5 2.0 3.5
compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5
compute 1 fluid adf 32 :pre
[Description:]
Define a computation that calculates one or more angular distribution functions
(ADF) for a group of particles. Each ADF is calculated in histogram form
(ADF) for a group of particles. Each ADF is calculated in histogram form
by measuring the angle formed by a central atom and two neighbor atoms and
binning these angles into {Nbin} bins.
Only neighbors for which {Rinner} < {R} < {Router} are counted, where
{Rinner} and {Router} are specified separately for the first and second
neighbor atom in each requested ADF.
neighbor atom in each requested ADF.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
@ -66,18 +66,18 @@ the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
NOTE: If you request any outer cutoff {Router} > force cutoff, or if no
NOTE: If you request any outer cutoff {Router} > force cutoff, or if no
pair style is defined, e.g. the "rerun"_rerun.html command is being used to
post-process a dump file of snapshots you must insure ghost atom information
out to the largest value of {Router} + {skin} is communicated, via the
"comm_modify cutoff"_comm_modify.html command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The {skin} value
is what is specified with the "neighbor"_neighbor.html command.
post-process a dump file of snapshots you must insure ghost atom information
out to the largest value of {Router} + {skin} is communicated, via the
"comm_modify cutoff"_comm_modify.html command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The {skin} value
is what is specified with the "neighbor"_neighbor.html command.
The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 1st example
above. Or a wild-card asterisk can be used to specify a range of atom
types as in the 2nd example above.
types as in the 2nd example above.
This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
@ -88,13 +88,13 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example
above, this means that the ADF is computed where atoms of type {itypeN}
are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN}
are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN}
are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN}
represent a range of values via
the wild-card asterisk, as in the 2nd example above, this means that the
ADF is computed where atoms of any of the range of types represented
by {itypeN} are the central atom, and the angle is formed by two neighbors,
one neighbor in the range of types represented by {jtypeN} and another neighbor
in the range of types represented by {ktypeN}.
one neighbor in the range of types represented by {jtypeN} and another neighbor
in the range of types represented by {ktypeN}.
If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then
LAMMPS will generate a single ADF for all atoms in the group.
@ -106,13 +106,13 @@ Such an ADF is both uninformative and
extremely expensive to compute. For example, with liquid water
with a 10 A force cutoff, there are 80,000 angles per atom.
In addition, most of the interesting angular structure occurs for
neighbors that are the closest to the central atom, involving
neighbors that are the closest to the central atom, involving
just a few dozen angles.
Angles for each ADF are generated by double-looping over the list of
neighbors of each central atom I,
just as they would be in the force calculation for
a threebody potential such as "Stillinger-Weber"_pair_sw.html.
Angles for each ADF are generated by double-looping over the list of
neighbors of each central atom I,
just as they would be in the force calculation for
a three-body potential such as "Stillinger-Weber"_pair_sw.html.
The angle formed by central atom I and neighbor atoms J and K is included in an
ADF if the following criteria are met:
@ -121,12 +121,12 @@ the distance between atoms I,J is between Rjinner and Rjouter
the distance between atoms I,K is between Rkinner and Rkouter
the type of the I atom matches itypeN (one or a range of types)
atoms I,J,K are distinct
the type of the J atom matches jtypeN (one or a range of types)
the type of the J atom matches jtypeN (one or a range of types)
the type of the K atom matches ktypeN (one or a range of types) :ul
Each unique angle satisfying the above criteria is counted only once, regardless
of whether either or both of the neighbor atoms making up the
angle appear in both the J and K lists.
angle appear in both the J and K lists.
It is OK if a particular angle is included in more than
one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN}
arguments are specified.
@ -146,15 +146,15 @@ number radial distribution function.
The {ordinate} optional keyword determines
whether the bins are of uniform angular size from zero
to 180 ({degree}), zero to Pi ({radian}), or the
to 180 ({degree}), zero to Pi ({radian}), or the
cosine of the angle uniform in the range \[-1,1\] ({cosine}).
{cosine} has the advantage of eliminating the {acos()} function
call, which speeds up the compute by 2-3x, and it is also preferred
on physical grounds, because the for uniformly distributed particles
on physical grounds, because the for uniformly distributed particles
in 3D, the angular probability density w.r.t dtheta is
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
the integral is 1.
The simplest way to output the results of the compute adf calculation
@ -170,7 +170,7 @@ This compute calculates a global array with the number of rows =
{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the
number of I,J,K triples specified. The first column has the bin
coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN})
the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN})
interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
the "Howto output"_Howto_output.html doc page for an overview of
@ -181,15 +181,15 @@ The array values calculated by this compute are all "intensive".
The first column of array values is the angle-related ordinate, either
the angle in degrees or radians, or the cosine of the angle. Each
subsequent pair of columns gives the first and second kinds of ADF
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
in the first ADF column are normalized numbers >= 0.0,
whose integral w.r.t. the ordinate is 1,
i.e. the first ADF is a normalized probability distribution.
i.e. the first ADF is a normalized probability distribution.
The values in the second ADF column are also numbers >= 0.0.
They are the cumulative density distribution of angles per atom.
By definition, this ADF is monotonically increasing from zero to
a maximum value equal to the average total number of
angles per atom satisfying the ADF criteria.
angles per atom satisfying the ADF criteria.
[Restrictions:]
@ -200,7 +200,7 @@ distances, you can use the "rerun"_rerun.html command to post-process
a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren't running dynamics and thus are not changing
your model.
your model.
[Related commands:]

2
doc/src/compute_angle_local.txt
View File

@ -29,7 +29,7 @@ keyword = {set} :l
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local eng theta
compute 1 all angle/local eng theta
compute 1 all angle/local theta v_cos set theta t :pre
[Description:]

2
doc/src/compute_basal_atom.txt
View File

@ -28,7 +28,7 @@ The results enable efficient identification and characterization of
twins and grains in hexagonal close-packed structures.
The output of the compute is thus the 3 components of a unit vector
associdate with each atom. The components are set to 0.0 for
associated with each atom. The components are set to 0.0 for
atoms not in the group.
Details of the calculation are given in "(Barrett)"_#Barrett.

2
doc/src/compute_bond_local.txt
View File

@ -68,7 +68,7 @@ in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms along the bond
direction, after the COM velocity has been subtracted from each.
The value {engrot} is the rotationsl kinetic energy of the two atoms
The value {engrot} is the rotational kinetic energy of the two atoms
in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms perpendicular to
the bond direction, after the COM velocity has been subtracted from

2
doc/src/compute_chunk_atom.txt
View File

@ -210,7 +210,7 @@ between {crmin} and {crmax}. For example, if {crmin} = 1.0 and
{crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r <
2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in
the radial dimensions is the same whether the simulation box is
orthogonal or triclinic; i.e. the concetric circles are not tilted or
orthogonal or triclinic; i.e. the concentric circles are not tilted or
scaled differently in the two different dimensions to transform them
into ellipses.

22
doc/src/compute_chunk_spread_atom.txt
View File

@ -74,7 +74,7 @@ produces a global vector or array.
:line
Each listed input is operated on independently.
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
@ -134,16 +134,16 @@ compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
thermo_style custom step etotal press v_ave :pre
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362 :pre
:line

2
doc/src/compute_cna_atom.txt
View File

@ -33,7 +33,7 @@ Currently, there are five kinds of CNA patterns LAMMPS recognizes:
fcc = 1
hcp = 2
bcc = 3
icosohedral = 4
icosahedral = 4
unknown = 5 :ul
The value of the CNA pattern will be 0 for atoms not in the specified

2
doc/src/compute_damage_atom.txt
View File

@ -26,7 +26,7 @@ in a group. This is a quantity relevant for "Peridynamics
models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf
for an overview of LAMMPS commands for Peridynamics modeling.
The "damage" of a Peridymaics particles is based on the bond breakage
The "damage" of a Peridynamics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged.

2
doc/src/compute_displace_atom.txt
View File

@ -57,7 +57,7 @@ correctly with time=0 atom coordinates from the restart file.
:line
The {refresh} option can be used in conjuction with the "dump_modify
The {refresh} option can be used in conjunction with the "dump_modify
refresh" command to generate incremental dump files.
The definition and motivation of an incremental dump file is as

2
doc/src/compute_edpd_temp_atom.txt
View File

@ -24,7 +24,7 @@ compute 1 all edpd/temp/atom :pre
Define a computation that calculates the per-atom temperature
for each eDPD particle in a group.
The temperature is a local temperature derived from the internal energy
The temperature is a local temperature derived from the internal energy
of each eDPD particle based on the local equilibrium hypothesis.
For more details please see "(Espanol1997)"_#Espanol1997 and
"(Li2014)"_#Li2014a.

34
doc/src/compute_entropy_atom.txt
View File

@ -35,11 +35,11 @@ compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
Define a computation that calculates the pair entropy fingerprint for
each atom in the group. The fingerprint is useful to distinguish between
ordered and disordered environments, for instance liquid and solid-like
environments, or glassy and crystalline-like environments. Some
applications could be the identification of grain boundaries, a
melt-solid interface, or a solid cluster emerging from the melt.
The advantage of this parameter over others is that no a priori
ordered and disordered environments, for instance liquid and solid-like
environments, or glassy and crystalline-like environments. Some
applications could be the identification of grain boundaries, a
melt-solid interface, or a solid cluster emerging from the melt.
The advantage of this parameter over others is that no a priori
information about the solid structure is required.
This parameter for atom i is computed using the following formula from
@ -47,8 +47,8 @@ This parameter for atom i is computed using the following formula from
:c,image(Eqs/pair_entropy.jpg)
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
atom i can be noisy and therefore it is smoothed using:
:c,image(Eqs/pair_entropy2.jpg)
@ -57,7 +57,7 @@ where the sum in j goes through the neighbors of atom i, and sigma is a
parameter to control the smoothing.
The input parameters are {sigma} the smoothing parameter, and the
{cutoff} for the calculation of g(r).
{cutoff} for the calculation of g(r).
If the keyword {avg} has the setting {yes}, then this compute also
averages the parameter over the neighbors of atom i according to:
@ -66,25 +66,25 @@ averages the parameter over the neighbors of atom i according to:
where the sum j goes over the neighbors of atom i and N is the number
of neighbors. This procedure provides a sharper distinction between
order and disorder environments. In this case the input parameter
{cutoff2} is the cutoff for the averaging over the neighbors and
order and disorder environments. In this case the input parameter
{cutoff2} is the cutoff for the averaging over the neighbors and
must also be specified.
If the {avg yes} option is used, the effective cutoff of the neighbor
list should be {cutoff}+{cutoff2} and therefore it might be necessary
list should be {cutoff}+{cutoff2} and therefore it might be necessary
to increase the skin of the neighbor list with:
neighbor skin bin :pre
See "neighbor"_neighbor.html for details.
If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
Here are typical input parameters for fcc aluminum (lattice
constant 4.05 Angstroms),
compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
@ -102,7 +102,7 @@ uses per-atom values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The pair entropy values have units of the Boltzmann constant. They are
The pair entropy values have units of the Boltzmann constant. They are
always negative, and lower values (lower entropy) correspond to more
ordered environments.

4
doc/src/compute_heat_flux.txt
View File

@ -82,11 +82,11 @@ first term in the equation for J above.
The heat flux can be output every so many timesteps (e.g. via the
"thermo_style custom"_thermo_style.html command). Then as a
post-processing operation, an autocorrelation can be performed, its
post-processing operation, an auto-correlation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.
The "fix ave/correlate"_fix_ave_correlate.html command can calculate
the autocorrelation. The trap() function in the
the auto-correlation. The trap() function in the
"variable"_variable.html command can calculate the integral.
An example LAMMPS input script for solid Ar is appended below. The

2
doc/src/compute_msd.txt
View File

@ -50,7 +50,7 @@ The value of the displacement will be
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
displacement of each atom is calculated.
If the {average} option is set to {yes} then the reference position of
an atom is based on the average position of that atom, corrected for

2
doc/src/compute_msd_nongauss.txt
View File

@ -48,7 +48,7 @@ others.
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
displacement of each atom is calculated.
See the "compute msd"_compute_msd.html doc page for further important
NOTEs, which also apply to this compute.

2
doc/src/compute_pair.txt
View File

@ -15,7 +15,7 @@ compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
pair = style name of this compute command :l
pstyle = style name of a pair style that calculates additional values :l
nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l
nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a hybrid style :l
{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l
:ule

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