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Merge branch 'master' into bond/react-new-examples-and-package

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This commit is contained in:
Jacob Gissinger
2020-03-05 20:08:19 -07:00
committed by GitHub
parent fe1ac99ae7 1fb54c307c
commit 21f2ec3a25
660 changed files with 8682 additions and 8165 deletions
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2
.github/CONTRIBUTING.md vendored
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@ -73,7 +73,7 @@ Here is a checklist of steps you need to follow to submit a single file or user
* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. * You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.

42
cmake/CMakeLists.txt
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@ -2,7 +2,7 @@
# CMake build system # CMake build system
# This file is part of LAMMPS # This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger # Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 2.8.12) cmake_minimum_required(VERSION 3.10)
project(lammps CXX) project(lammps CXX)
set(SOVERSION 0) set(SOVERSION 0)
@ -36,7 +36,6 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
include(PreventInSourceBuilds) include(PreventInSourceBuilds)
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
#release comes with -O3 by default
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@ -53,16 +52,19 @@ include(CheckCCompilerFlag)
include(CheckIncludeFileCXX) include(CheckIncludeFileCXX)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif() endif()
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF) if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
if(DISABLE_CXX11_REQUIREMENT) if(NOT ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug"))
add_definitions(-DLAMMPS_CXX98) set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -ftree-vectorize -fexpensive-optimizations")
# else() endif()
# set(CMAKE_CXX_STANDARD 11)
endif() endif()
# we require C++11
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# GNU compiler features # GNU compiler features
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable code coverage" OFF) option(ENABLE_COVERAGE "Enable code coverage" OFF)
@ -179,6 +181,7 @@ option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI) if(BUILD_MPI)
find_package(MPI REQUIRED) find_package(MPI REQUIRED)
include_directories(${MPI_CXX_INCLUDE_PATH}) include_directories(${MPI_CXX_INCLUDE_PATH})
add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1)
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES}) list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG) if(LAMMPS_LONGLONG_TO_LONG)
@ -356,9 +359,6 @@ endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library") set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES ) mark_as_advanced( MATH_LIBRARIES )
include(CheckLibraryExists) include(CheckLibraryExists)
if (CMAKE_VERSION VERSION_LESS "3.4")
enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
endif()
# RB: disabled this check because it breaks with KOKKOS CUDA enabled # RB: disabled this check because it breaks with KOKKOS CUDA enabled
#foreach(FUNC sin cos) #foreach(FUNC sin cos)
# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) # check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
@ -420,7 +420,7 @@ endforeach()
############################################## ##############################################
# add lib sources of (simple) enabled packages # add lib sources of (simple) enabled packages
############################################ ############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM) foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
if(PKG_${SIMPLE_LIB}) if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB) string(TOLOWER "${PKG_LIB}" PKG_LIB)
@ -682,7 +682,7 @@ endforeach()
get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS) get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
include(FeatureSummary) include(FeatureSummary)
feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND) feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
message(STATUS "<<< Build configuration >>> message(STATUS "<<< Build configuration >>>
Build type ${CMAKE_BUILD_TYPE} Build type ${CMAKE_BUILD_TYPE}
Install path ${CMAKE_INSTALL_PREFIX} Install path ${CMAKE_INSTALL_PREFIX}
@ -702,7 +702,7 @@ if (${_index} GREATER -1)
endif() endif()
list (FIND LANGUAGES "C" _index) list (FIND LANGUAGES "C" _index)
if (${_index} GREATER -1) if (${_index} GREATER -1)
message(STATUS "C Compiler ${CMAKE_C_COMPILER} message(STATUS "C compiler ${CMAKE_C_COMPILER}
Type ${CMAKE_C_COMPILER_ID} Type ${CMAKE_C_COMPILER_ID}
Version ${CMAKE_C_COMPILER_VERSION} Version ${CMAKE_C_COMPILER_VERSION}
C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}") C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
@ -712,22 +712,22 @@ if(CMAKE_EXE_LINKER_FLAGS)
Executable ${CMAKE_EXE_LINKER_FLAGS}") Executable ${CMAKE_EXE_LINKER_FLAGS}")
endif() endif()
if(BUILD_SHARED_LIBS) if(BUILD_SHARED_LIBS)
message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}") message(STATUS "Shared library flags: ${CMAKE_SHARED_LINKER_FLAGS}")
else() else()
message(STATUS "Static libraries ${CMAKE_STATIC_LINKER_FLAGS}") message(STATUS "Static library flags: ${CMAKE_STATIC_LINKER_FLAGS}")
endif() endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}") message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
if(BUILD_MPI) if(BUILD_MPI)
message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}") message(STATUS "Using MPI with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
endif() endif()
if(PKG_GPU) if(PKG_GPU)
message(STATUS "GPU Api: ${GPU_API}") message(STATUS "GPU API: ${GPU_API}")
if(GPU_API STREQUAL "CUDA") if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU Arch: ${GPU_ARCH}") message(STATUS "GPU architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OPENCL") elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OCL Tune: ${OCL_TUNE}") message(STATUS "OpenCL parameter tuning: ${OCL_TUNE}")
endif() endif()
message(STATUS "GPU Precision: ${GPU_PREC}") message(STATUS "GPU precision: ${GPU_PREC}")
endif() endif()
if(PKG_KOKKOS) if(PKG_KOKKOS)
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")

29
cmake/Modules/FindQE.cmake
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@ -1,29 +0,0 @@
# - Find quantum-espresso
# Find the native QE headers and libraries.
#
# QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
# QE_LIBRARIES - List of libraries when using quantum-espresso.
# QE_FOUND - True if quantum-espresso found.
#
find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
find_library(QECOUPLE_LIBRARY NAMES qecouple)
find_library(PW_LIBRARY NAMES pw)
find_library(QEMOD_LIBRARY NAMES qemod)
find_library(QEFFT_LIBRARY NAMES qefft)
find_library(QELA_LIBRARY NAMES qela)
find_library(CLIB_LIBRARY NAMES clib)
find_library(IOTK_LIBRARY NAMES iotk)
set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)

3
cmake/Modules/Packages/GPU.cmake
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@ -1,7 +1,4 @@
if(PKG_GPU) if(PKG_GPU)
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) set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h ${GPU_SOURCES_DIR}/fix_gpu.h

3
cmake/Modules/Packages/LATTE.cmake
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@ -8,9 +8,6 @@ if(PKG_LATTE)
endif() endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT}) option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE) if(DOWNLOAD_LATTE)
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()
if(CMAKE_GENERATOR STREQUAL "Ninja") if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool") message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
endif() endif()

3
cmake/Modules/Packages/MSCG.cmake
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@ -8,9 +8,6 @@ if(PKG_MSCG)
endif() endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT}) option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG) if(DOWNLOAD_MSCG)
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()
if(CMAKE_GENERATOR STREQUAL "Ninja") if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool") message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
endif() endif()

4
cmake/Modules/Packages/USER-MOLFILE.cmake
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@ -1,8 +1,4 @@
if(PKG_USER-MOLFILE) if(PKG_USER-MOLFILE)
if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
endif()
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers") set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE) add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})

14
cmake/Modules/Packages/USER-QMMM.cmake
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@ -1,9 +1,13 @@
if(PKG_USER-QMMM) if(PKG_USER-QMMM)
enable_language(Fortran)
enable_language(C) enable_language(C)
message(WARNING "Building QMMM with CMake is still experimental") if(NOT BUILD_LIB)
find_package(QE REQUIRED) message(FATAL_ERROR "Building a QM/MM executable with USER-QMMM requires BUILD_LIB=yes")
include_directories(${QE_INCLUDE_DIRS}) endif()
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES}) if(NOT BUILD_SHARED_LIBS)
message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
endif()
add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
list(APPEND LAMMPS_LINK_LIBS qmmm)
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
endif() endif()

2
doc/.gitignore vendored
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@ -1,6 +1,8 @@
/old /old
/html /html
/html-offline
/latex /latex
/mathjax
/spelling /spelling
/LAMMPS.epub /LAMMPS.epub
/LAMMPS.mobi /LAMMPS.mobi

50
doc/Makefile
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@ -4,6 +4,7 @@ SHELL = /bin/bash
BUILDDIR = ${CURDIR} BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src RSTDIR = $(BUILDDIR)/src
VENV = $(BUILDDIR)/docenv VENV = $(BUILDDIR)/docenv
MATHJAX = $(BUILDDIR)/mathjax
TXT2RST = $(VENV)/bin/txt2rst TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check ANCHORCHECK = $(VENV)/bin/rst_anchor_check
@ -28,50 +29,48 @@ endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check .PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
# ------------------------------------------ # ------------------------------------------
help: help:
@echo "Please use \`make <target>' where <target> is one of" @echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir" @echo " html create HTML doc pages in html dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir" @echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers" @echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)" @echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files" @echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment" @echo " clean-all reset the entire build environment"
@echo " anchor_check scan for duplicate anchor labels" @echo " anchor_check scan for duplicate anchor labels"
@echo " style_check check for complete and consistent style lists" @echo " style_check check for complete and consistent style lists"
@echo " spelling spell-check the manual" @echo " package_check check for complete and consistent package lists"
@echo " spelling spell-check the manual"
# ------------------------------------------ # ------------------------------------------
clean-all: clean clean-all: clean
rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax
clean: clean: clean-spelling
rm -rf html epub latex rm -rf html epub latex
rm -rf spelling
clean-spelling: clean-spelling:
rm -rf spelling rm -rf spelling
rst: clean $(ANCHORCHECK) html: $(ANCHORCHECK) $(MATHJAX)
html: $(ANCHORCHECK)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
echo "############################################" ;\ echo "############################################" ;\
rst_anchor_check src/*.rst ;\ rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\ python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\ echo "############################################" ;\
deactivate ;\ deactivate ;\
) )
-rm html/searchindex.js
@rm -rf html/_sources @rm -rf html/_sources
@rm -rf html/PDF @rm -rf html/PDF
@rm -rf html/USER @rm -rf html/USER
@ -84,9 +83,11 @@ html: $(ANCHORCHECK)
@rm -rf html/USER/.[sg]* @rm -rf html/USER/.[sg]*
@rm -rf html/USER/*/.[sg]* @rm -rf html/USER/*/.[sg]*
@rm -rf html/USER/*/*.[sg]* @rm -rf html/USER/*/*.[sg]*
@mkdir -p html/_static/mathjax
@cp -r $(MATHJAX)/es5 html/_static/mathjax/
@echo "Build finished. The HTML pages are in doc/html." @echo "Build finished. The HTML pages are in doc/html."
spelling: utils/sphinx-config/false_positives.txt spelling: $(VENV) utils/sphinx-config/false_positives.txt
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
pip install sphinxcontrib-spelling ;\ pip install sphinxcontrib-spelling ;\
@ -96,7 +97,7 @@ spelling: utils/sphinx-config/false_positives.txt
) )
@echo "Spell check finished." @echo "Spell check finished."
epub: epub: $(VENV)
@mkdir -p epub/JPG @mkdir -p epub/JPG
@rm -f LAMMPS.epub @rm -f LAMMPS.epub
@cp src/JPG/lammps-logo.png epub/ @cp src/JPG/lammps-logo.png epub/
@ -128,6 +129,7 @@ pdf: $(ANCHORCHECK)
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
echo "############################################" ;\ echo "############################################" ;\
rst_anchor_check src/*.rst ;\ rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\ python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\ echo "############################################" ;\
@ -171,13 +173,20 @@ anchor_check : $(ANCHORCHECK)
deactivate ;\ deactivate ;\
) )
style_check : style_check : $(VENV)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
python utils/check-styles.py -s ../src -d src ;\ python utils/check-styles.py -s ../src -d src ;\
deactivate ;\ deactivate ;\
) )
package_check : $(VENV)
@(\
. $(VENV)/bin/activate ;\
python utils/check-packages.py -s ../src -d src ;\
deactivate ;\
)
# ------------------------------------------ # ------------------------------------------
$(VENV): $(VENV):
@ -190,6 +199,9 @@ $(VENV):
deactivate;\ deactivate;\
) )
$(MATHJAX):
@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
$(TXT2RST) $(ANCHORCHECK): $(VENV) $(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \ @( \
. $(VENV)/bin/activate; \ . $(VENV)/bin/activate; \

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "18 February 2020" "2020-02-18" .TH LAMMPS "3 March 2020" "2020-03-03"
.SH NAME .SH NAME
.B LAMMPS .B LAMMPS
\- Molecular Dynamics Simulator. \- Molecular Dynamics Simulator.

399
doc/src/Build_basics.rst
View File

@ -19,94 +19,115 @@ CMake and make:
Serial vs parallel build Serial vs parallel build
------------------------------------- -------------------------------------
LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
library. Or it can built to run on a single processor (serial) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
without MPI. It can also be built with support for OpenMP threading for distributed memory parallel computation. You need to have such a
(see more discussion below). library installed for building and running LAMMPS in parallel using a
domain decomposition parallelization. It is compatible with the MPI
standard version 2.x and later. LAMMPS can also be built into a
"serial" executable for use with a single processor using the bundled
MPI STUBS library.
**CMake variables**\ : Independent of the distributed memory MPI parallelization, parts of
LAMMPS are also written with support for shared memory parallelization
using the OpenMP threading standard. A more detailed discussion of that
is below.
**CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no -D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no (default) -D BUILD_OMP=value # yes or no, default is yes if a compatible compiler is detected
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc -D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value # no default value
The executable created by CMake (after running make) is lmp\_name. If The executable created by CMake (after running make) is named *lmp* unless
the LAMMPS\_MACHINE variable is not specified, the executable is just the LAMMPS\_MACHINE option is set. When setting `LAMMPS_MACHINE=name`
lmp. Using BUILD\_MPI=no will produce a serial executable. the executable will be named *lmp\_name*\. Using `BUILD\_MPI=no` will
enforce building a serial executable using the MPI STUBS library.
**Traditional make**\ : **Traditional make**\ :
The build with traditional makefiles has to be done inside the source folder `src`.
.. parsed-literal:: .. code-block:: bash
cd lammps/src
make mpi # parallel build, produces lmp_mpi using Makefile.mpi make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox make mybox # uses Makefile.mybox to produce lmp_mybox
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal:: Any "make machine" command will look up the make settings from a file
Makefile.machine, create a folder Obj\_machine with all objects and
generated files and an executable called *lmp\_machine*\ . The standard
parallel build with `make mpi` assumes a standard MPI installation with
MPI compiler wrappers where all necessary compiler and linker flags to
get access and link with the suitable MPI headers and libraries are set
by the wrapper programs. For other cases or the serial build, you have
to adjust the make file variables MPI\_INC, MPI\_PATH, MPI\_LIB as well
as CC and LINK. To enable OpenMP threading usually a compiler specific
flag needs to be added to the compile and link commands. For the GNU
compilers, this is *-fopenmp*\ , which can be added to the CC and LINK
makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
.. code-block:: make
CC = g++
LINK = g++
MPI_INC = -I../STUBS MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs MPI_LIB = -lmpi_stubs
For a parallel build, if MPI is installed on your system in the usual You also need to build the STUBS library for your platform before making
place (e.g. under /usr/local), you do not need to specify the 3 LAMMPS itself. A "make serial" build does this for you automatically,
variables MPI\_INC, MPI\_PATH, MPI\_LIB. The MPI wrapper on the compiler otherwise, type "make mpi-stubs" from the src directory, or "make" from
(e.g. mpicxx, mpiCC) knows where to find the needed include and the src/STUBS dir. If the build fails, you will need to edit the
library files. Failing this, these 3 variables can be used to specify STUBS/Makefile for your platform. The stubs library does not provide
where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH) MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
are found, and the name of the library files (MPI\_LIB). and thus is not compatible with those packages.
For a serial build, you need to specify the 3 variables, as shown .. note::
above.
For a serial LAMMPS build, use the dummy MPI library provided in The file STUBS/mpi.c provides a CPU timer function called
src/STUBS. You also need to build the STUBS library for your platform MPI\_Wtime() that calls gettimeofday() . If your operating system
before making LAMMPS itself. A "make serial" build does this for. does not support gettimeofday() , you will need to insert code to
Otherwise, type "make mpi-stubs" from the src directory, or "make" call another timer. Note that the ANSI-standard function clock()
from the src/STUBS dir. If the build fails, you will need to edit the rolls over after an hour or so, and is therefore insufficient for
STUBS/Makefile for your platform. timing long LAMMPS simulations.
The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime() **MPI and OpenMP support info**\ :
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
**CMake and make info**\ : If you are installing MPI yourself to build a parallel LAMMPS
executable, we recommend either MPICH or OpenMPI which are regularly
used and tested with LAMMPS by the LAMMPS developers. MPICH can be
downloaded from the `MPICH home page <https://www.mpich.org>`_ and
OpenMPI can be downloaded correspondingly from the `OpenMPI home page
<https://www.open-mpi.org>`_. Other MPI packages should also work. No
specific vendor provided and standard compliant MPI library is currently
known to be incompatible with LAMMPS. If you are running on a large
parallel machine, your system admins or the vendor should have already
installed a version of MPI, which is likely to be faster than a
self-installed MPICH or OpenMPI, so you should study the provided
documentation to find out how to build and link with it.
If you are installing MPI yourself, we recommend MPICH2 from Argonne The majority of OpenMP (threading) support in LAMMPS is provided by the
National Laboratory or OpenMPI. MPICH can be downloaded from the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_. details. The USER-INTEL package also includes OpenMP threading (it is
OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_. Other MPI packages should also work.
If you are running on a large parallel machine, your system admins or
the vendor should have already installed a version of MPI, which is
likely to be faster than a self-installed MPICH or OpenMPI, so find
out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by
the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
details. The USER-INTEL package also provides OpenMP support (it is
compatible with USER-OMP) and adds vectorization support when compiled compatible with USER-OMP) and adds vectorization support when compiled
with the Intel compilers on top of that. Also, the KOKKOS package can with compatible compilers, in particular the Intel compilers on top of
be compiled for using OpenMP threading. OpenMP. Also, the KOKKOS package can be compiled to include OpenMP
threading.
However, there are a few commands in LAMMPS that have native OpenMP In addition, there are a few commands in LAMMPS that have native OpenMP
support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and support included as well. These are commands in the MPIIO, SNAP,
USER-DPD packages. In addition some packages support OpenMP threading USER-DIFFRACTION, and USER-DPD packages. In addition some packages
indirectly through the libraries they interface to: e.g. LATTE and support OpenMP threading indirectly through the libraries they interface
USER-COLVARS. See the :doc:`Packages details <Packages_details>` doc to: e.g. LATTE and USER-COLVARS. See the :doc:`Packages details
page for more info on these packages and the doc pages for their <Packages_details>` doc page for more info on these packages and the doc
respective commands for OpenMP threading info. pages for their respective commands for OpenMP threading info.
For CMake, if you use BUILD\_OMP=yes, you can use these packages and For CMake, if you use BUILD\_OMP=yes, you can use these packages and
turn on their native OpenMP support and turn on their native OpenMP turn on their native OpenMP support and turn on their native OpenMP
@ -143,22 +164,37 @@ Choice of compiler and compile/link options
--------------------------------------------------------- ---------------------------------------------------------
The choice of compiler and compiler flags can be important for The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than performance. Vendor provided compilers for a specific hardware can
open-source compilers like GNU. On boxes with Intel CPUs, we suggest produce faster code than open-source compilers like the GNU compilers.
trying the `Intel C++ compiler <intel_>`_. On x86 hardware most popular compilers are quite similar in performance
of C/C++ code at high optimization levels. When using the USER-INTEL
package, there is a distinct advantage in using the `Intel C++ compiler
<intel_>`_ due to much improved vectorization through SSE and AVX
instructions on compatible hardware as the source code includes changes
and compiler directives to enable high degrees of vectorization.
.. _intel: https://software.intel.com/en-us/intel-compilers .. _intel: https://software.intel.com/en-us/intel-compilers
On parallel clusters or supercomputers which use "environment modules"
for their compile/link environments, you can often access different
compilers by simply loading the appropriate module before building
LAMMPS.
**CMake build**\ :
On parallel clusters or supercomputers which use "modules" for their By default CMake will use a compiler it finds and it will add
compile/link environments, you can often access different compilers by optimization flags appropriate to that compiler and any
simply loading the appropriate module before building LAMMPS. :doc:`accelerator packages <Speed_packages>` you have included in the
build.
**CMake variables**\ : You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
.. code-block:: bash
.. parsed-literal::
-D CMAKE_CXX_COMPILER=name # name of C++ compiler -D CMAKE_CXX_COMPILER=name # name of C++ compiler
-D CMAKE_C_COMPILER=name # name of C compiler -D CMAKE_C_COMPILER=name # name of C compiler
@ -168,42 +204,42 @@ simply loading the appropriate module before building LAMMPS.
-D CMAKE_C_FLAGS=string # flags to use with C compiler -D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler -D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
You can tell CMake to look for a specific compiler with these variable A few example command lines are:
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
.. code-block:: bash
.. parsed-literal:: # Building with GNU Compilers:
Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
Building with Intel Compilers: # Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
Building with LLVM/Clang Compilers: # Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
For compiling with the Clang/LLVM compilers a special CMake preset is
included that can be loaded with `-C ../cmake/presets/clang.cmake`.
.. note:: .. note::
When the cmake command completes, it prints info to the screen When the cmake command completes, it prints a summary to the screen
as to which compilers it is using, and what flags will be used in the which compilers it is using and what flags and settings will be used
compilation. Note that if the top-level compiler is mpicxx, it is for the compilation. Note that if the top-level compiler is mpicxx,
simply a wrapper on a real compiler. The underlying compiler info is it is simply a wrapper on a real compiler. The underlying compiler
what will be listed in the CMake output. You should check to insure info is what CMake will try to determine and report. You should check
you are using the compiler and optimization flags are the ones you to confirm you are using the compiler and optimization flags you want.
want.
**Makefile.machine settings**\ : **Makefile.machine settings for traditional make**\ :
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. For a parallel build it is recommended to use
mpicxx or mpiCC, since these compiler wrappers will include a variety of
settings appropriate for your MPI installation and thus avoiding the
guesswork of finding the right flags.
Parallel build (see src/MAKE/Makefile.mpi): Parallel build (see src/MAKE/Makefile.mpi):
.. code-block:: bash
.. parsed-literal::
CC = mpicxx CC = mpicxx
CCFLAGS = -g -O3 CCFLAGS = -g -O3
@ -212,33 +248,26 @@ Parallel build (see src/MAKE/Makefile.mpi):
Serial build (see src/MAKE/Makefile.serial): Serial build (see src/MAKE/Makefile.serial):
.. code-block:: make
.. parsed-literal::
CC = g++ CC = g++
CCFLAGS = -g -O3 CCFLAGS = -g -O3
LINK = g++ LINK = g++
LINKFLAGS = -g -O LINKFLAGS = -g -O
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. You should always use mpicxx or mpiCC for
a parallel build, since these compiler wrappers will include
a variety of settings appropriate for your MPI installation.
.. note:: .. note::
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>`
optimization flags that are either required or recommended for optimal included, there may be specific optimization flags that are either
performance. You need to include these in the CCFLAGS and LINKFLAGS required or recommended to enable required features and to achieve
settings above. For details, see the individual package doc pages optimal performance. You need to include these in the CCFLAGS and
listed on the :doc:`Speed packages <Speed_packages>` doc page. Or LINKFLAGS settings above. For details, see the individual package
examine these files in the src/MAKE/OPTIONS directory. They doc pages listed on the :doc:`Speed packages <Speed_packages>` doc
correspond to each of the 5 accelerator packages and their hardware page. Or examine these files in the src/MAKE/OPTIONS directory.
variants: They correspond to each of the 5 accelerator packages and their
hardware variants:
.. code-block:: bash
.. parsed-literal::
Makefile.opt # OPT package Makefile.opt # OPT package
Makefile.omp # USER-OMP package Makefile.omp # USER-OMP package
@ -249,10 +278,8 @@ a variety of settings appropriate for your MPI installation.
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP) Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)
Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP)
---------- ----------
.. _exe: .. _exe:
Build LAMMPS as an executable or a library Build LAMMPS as an executable or a library
@ -265,10 +292,13 @@ page for more info on coupling LAMMPS to other codes. See the
:doc:`Python <Python_head>` doc page for more info on wrapping and :doc:`Python <Python_head>` doc page for more info on wrapping and
running LAMMPS from Python via its library interface. running LAMMPS from Python via its library interface.
**CMake variables**\ : **CMake build**\ :
For CMake builds, you can select through setting CMake variables which
files the compilation produces during the configuration step. If none
are set, defaults are applied.
.. parsed-literal:: .. code-block:: bash
-D BUILD_EXE=value # yes (default) or no -D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default) -D BUILD_LIB=value # yes or no (default)
@ -277,24 +307,32 @@ running LAMMPS from Python via its library interface.
# no default value # no default value
Setting BUILD\_EXE=no will not produce an executable. Setting Setting BUILD\_EXE=no will not produce an executable. Setting
BUILD\_LIB=yes will produce a static library named liblammps.a. BUILD\_LIB=yes will produce a static library named *liblammps.a*\ .
Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated shared library named *liblammps.so* instead. If LAMMPS\_LIB\_SUFFIX is
libraries will be named liblammps\_name.a or liblammps\_name.so instead. set to *name* in addition, the name of the generated libraries will be
changed to either *liblammps\_name.a* or *liblammps\_name.so*\ ,
respectively.
**Traditional make**\ : **Traditional make**\ :
With the traditional makefile based build process, the choice of
the generated executable or library depends on the "mode" setting.
Several options are available and "mode=exe" is the default.
.. parsed-literal:: .. code-block:: bash
cd lammps/src
make machine # build LAMMPS executable lmp_machine make machine # build LAMMPS executable lmp_machine
mkae mode=exe machine # same as "make machine"
make mode=lib machine # build LAMMPS static lib liblammps_machine.a make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
make mode=shexe machine # same as "mode=exe" but uses objects from "mode=shlib"
The two library builds also create generic soft links, named The two "exe" builds will generate and executable *lmp\_machine*\ ,
liblammps.a and liblammps.so, which point to the liblammps\_machine while the two library builds will create a file *liblammps\_machine.a*
files. or *liblammps\_machine.so*\ . They will also create generic soft links,
named *liblammps.a* and *liblammps.so*\ , which point to the specific
*liblammps\_machine.a/so* files.
**CMake and make info**\ : **CMake and make info**\ :
@ -302,32 +340,40 @@ Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS, libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built as shared the lib/packages directory, since they are always built in a shared
libraries using the -fPIC switch. However, if a library like MPI or library compatible way using the -fPIC switch. However, if a library
FFTW does not exist as a shared library, the shared library build will like MPI or FFTW does not exist as a shared library, the shared library
generate an error. This means you will need to install a shared build may generate an error. This means you will need to install a
library version of the auxiliary library. The build instructions for shared library version of the auxiliary library. The build instructions
the library should tell you how to do this. for the library should tell you how to do this.
As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
Argonne National Lab, as a shared library in the default
/usr/local/lib location:
.. _mpich: http://www-unix.mcs.anl.gov/mpi
As an example, here is how to build and install the `MPICH library
<mpich_>`_, a popular open-source version of MPI, as a shared library
in the default /usr/local/lib location:
.. _mpich: https://www.mpich.org
.. parsed-literal:: .. code-block:: bash
./configure --enable-shared ./configure --enable-shared
make make
make install make install
You may need to use "sudo make install" in place of the last line if You may need to use "sudo make install" in place of the last line if you
you do not have write privileges for /usr/local/lib. The end result do not have write privileges for /usr/local/lib. The end result should
should be the file /usr/local/lib/libmpich.so. be the file /usr/local/lib/libmpich.so. On many Linux installations the
folder "${HOME}/.local" is an alternative to using /usr/local and does
not require superuser or sudo access. In that case the configuration
step becomes:
.. code-block:: bash
./configure --enable-shared --prefix=${HOME}/.local
Avoiding using "sudo" for custom software installation (i.e. from source
and not through a package manager tool provided by the OS) is generally
recommended to ensure the integrity of the system software installation.
---------- ----------
@ -337,30 +383,39 @@ should be the file /usr/local/lib/libmpich.so.
Build the LAMMPS documentation Build the LAMMPS documentation
---------------------------------------- ----------------------------------------
**CMake variable**\ : The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
can be translated to different output format using the `Sphinx <sphinx_>`_
document generator tool. Currently the translation to HTML and PDF (via
LaTeX) are supported. For that to work a Python 3 interpreter and
internet access is required. For the documentation build a python
based virtual environment is set up in the folder doc/docenv and various
python packages are installed into that virtual environment via the pip
tool. The actual translation is then done via make commands.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://sphinx-doc.org
**Documentation make option**\ :
The following make commands can be issued in the doc folder of the
LAMMPS source distribution.
.. code-block:: bash
make html # create HTML doc pages in html directory
make pdf # create Developer.pdf and Manual.pdf in this directory
make fetch # fetch HTML and PDF files from LAMMPS web site
make clean # remove all intermediate files
make clean-all # reset the entire doc build environment
make anchor_check # scan for duplicate anchor labels
make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
make spelling # spell-check the manual
.. parsed-literal:: Thus "make html" will create a "doc/html" directory with the HTML format
manual pages so that you can browse them with a web browser locally on
-D BUILD_DOC=value # yes or no (default) your system.
This will create the HTML doc pages within the CMake build directory.
The reason to do this is if you want to "install" LAMMPS on a system
after the CMake build via "make install", and include the doc pages in
the install.
**Traditional make**\ :
.. parsed-literal::
cd lammps/doc
make html # html doc pages
make pdf # single Manual.pdf file
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:: .. note::
@ -369,6 +424,19 @@ lammps/doc dir to see other options.
`download page <http://lammps.sandia.gov/download.html>`_. `download page <http://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :
It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this
option is to include the installation of the HTML manual pages into
the "install" step when installing LAMMPS after the CMake build via
"make install".
.. code-block:: bash
-D BUILD_DOC=value # yes or no (default)
---------- ----------
@ -380,19 +448,20 @@ Build LAMMPS tools
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make. using CMake or Make.
**CMake variable**\ : **CMake build3**\ :
.. parsed-literal:: .. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default) -D BUILD_TOOLS=value # yes or no (default)
The generated binaries will also become part of the LAMMPS installation (see below) The generated binaries will also become part of the LAMMPS installation
(see below).
**Traditional make**\ : **Traditional make**\ :
.. parsed-literal:: .. code-block:: bash
cd lammps/tools cd lammps/tools
make all # build all binaries of tools make all # build all binaries of tools
@ -416,10 +485,10 @@ a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected. you want to copy files to is protected.
**CMake variable**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
make # perform make after CMake command make # perform make after CMake command

26
doc/src/Build_cmake.rst
View File

@ -20,7 +20,7 @@ make command to build LAMMPS, which uses the created
Makefile(s). Example: Makefile(s). Example:
.. parsed-literal:: .. code-block:: bash
cd lammps # change to the LAMMPS distribution directory 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
@ -52,7 +52,7 @@ After compilation, you may optionally install the LAMMPS executable into
your system with: your system with:
.. parsed-literal:: .. code-block:: bash
make install # optional, copy LAMMPS executable & library elsewhere make install # optional, copy LAMMPS executable & library elsewhere
@ -95,10 +95,8 @@ this directory or sub-directories within it that CMake creates.
directory to un-install all packages. The purge removes all the \*.h directory to un-install all packages. The purge removes all the \*.h
files auto-generated by make. files auto-generated by make.
You must have CMake version 2.8 or later on your system to build You must have CMake version 3.10 or later on your system to build
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a LAMMPS. Installation instructions for CMake are below.
later version. CMake will print a message telling you if a later
version is required. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from own new files to the source directory, you can just re-type make from
@ -115,7 +113,7 @@ folder, recreate the directory and start over.
**Command-line version of CMake**\ : **Command-line version of CMake**\ :
.. parsed-literal:: .. code-block:: bash
cmake [options ...] /path/to/lammps/cmake # build from any dir cmake [options ...] /path/to/lammps/cmake # build from any dir
cmake [options ...] ../cmake # build from lammps/build cmake [options ...] ../cmake # build from lammps/build
@ -127,7 +125,7 @@ The argument can be preceeded or followed by various CMake
command-line options. Several useful ones are: command-line options. Several useful ones are:
.. parsed-literal:: .. code-block:: bash
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired -D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug -D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
@ -177,7 +175,7 @@ directory.
**Curses version (terminal-style menu) of CMake**\ : **Curses version (terminal-style menu) of CMake**\ :
.. parsed-literal:: .. code-block:: bash
ccmake ../cmake ccmake ../cmake
@ -195,7 +193,7 @@ more information.
**GUI version of CMake**\ : **GUI version of CMake**\ :
.. parsed-literal:: .. code-block:: bash
cmake-gui ../cmake cmake-gui ../cmake
@ -216,7 +214,7 @@ for more information.
Check if your machine already has CMake installed: Check if your machine already has CMake installed:
.. parsed-literal:: .. code-block:: bash
which cmake # do you have it? which cmake # do you have it?
which cmake3 # version 3 may have this name which cmake3 # version 3 may have this name
@ -226,10 +224,10 @@ On clusters or supercomputers which use environment modules to manage
software packages, do this: software packages, do this:
.. parsed-literal:: .. code-block:: bash
module list # is a cmake module already loaded? module list # is a module for cmake already loaded?
module avail # is a cmake module available? module avail # is a module for cmake available?
module load cmake3 # load cmake module with appropriate name module load cmake3 # load cmake module with appropriate name
Most Linux distributions offer pre-compiled cmake packages through Most Linux distributions offer pre-compiled cmake packages through

16
doc/src/Build_development.rst
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@ -18,14 +18,14 @@ generated by the CMake build. To enable a more verbose output during
compilation you can use the following option. compilation you can use the following option.
.. parsed-literal:: .. code-block:: bash
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes -D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1: Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
.. parsed-literal:: .. code-block:: bash
make VERBOSE=1 make VERBOSE=1
@ -48,7 +48,7 @@ it. Please note that they come with a performance hit. However, they are
usually faster than using tools like Valgrind. usually faster than using tools like Valgrind.
.. parsed-literal:: .. code-block:: bash
-D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes -D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes -D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes
@ -72,7 +72,7 @@ developers can run the tests directly on their workstation.
this is incomplete and only represents a small subset of tests that we run this is incomplete and only represents a small subset of tests that we run
.. parsed-literal:: .. code-block:: bash
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes -D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location) -D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
@ -81,7 +81,7 @@ developers can run the tests directly on their workstation.
If you enable testing in the CMake build it will create an additional target called "test". You can run them with: If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
.. parsed-literal:: .. code-block:: bash
make test make test
@ -93,14 +93,14 @@ You can also collect code coverage metrics while running the tests by enabling
coverage support during building. coverage support during building.
.. parsed-literal:: .. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes -D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
This will also add the following targets to generate coverage reports after running the LAMMPS executable: This will also add the following targets to generate coverage reports after running the LAMMPS executable:
.. parsed-literal:: .. code-block:: bash
make test # run tests first! make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format make gen_coverage_html # generate coverage report in HTML format
@ -109,6 +109,6 @@ This will also add the following targets to generate coverage reports after runn
These reports require GCOVR to be installed. The easiest way to do this to install it via pip: These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
.. parsed-literal:: .. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git pip install git+https://github.com/gcovr/gcovr.git

366
doc/src/Build_extras.rst
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@ -5,10 +5,15 @@ When building with some packages, additional steps may be required,
in addition to: in addition to:
.. parsed-literal:: .. code-block:: bash
-D PKG_NAME=yes # CMake $ cmake -D PKG_NAME=yes
make yes-name # make
or
.. code-block:: bash
$ make yes-name
as described on the :doc:`Build\_package <Build_package>` doc page. as described on the :doc:`Build\_package <Build_package>` doc page.
@ -20,18 +25,35 @@ You may need to tell LAMMPS where it is found on your system.
This is the list of packages that may require additional steps. This is the list of packages that may require additional steps.
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ .. table_from_list::
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` | :columns: 6
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MESSAGE <message>`
* :ref:`MSCG <mscg>`
* :ref:`OPT <opt>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`VORONOI <voronoi>`
* :ref:`USER-ADIOS <user-adios>`
* :ref:`USER-ATC <user-atc>`
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
* :ref:`USER-QUIP <user-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`USER-SMD <user-smd>`
* :ref:`USER-VTK <user-vtk>`
---------- ----------
@ -49,15 +71,15 @@ available on your system.
If CMake cannot find the library, you can set these variables: If CMake cannot find the library, you can set these variables:
.. parsed-literal:: .. code-block:: bash
-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 -D ZLIB_LIBRARIES=path # path to libz.a (.so) file
**Traditional make**\ : **Traditional make**\ :
If make cannot find the library, you can edit the If make cannot find the library, you can edit the file
lib/compress/Makefile.lammps file to specify the paths and library lib/compress/Makefile.lammps to specify the paths and library
name. name.
@ -75,7 +97,7 @@ which GPU hardware to build for.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D GPU_API=value # value = opencl (default) or cuda -D GPU_API=value # value = opencl (default) or cuda
-D GPU_PREC=value # precision setting -D GPU_PREC=value # precision setting
@ -125,12 +147,12 @@ using a command like these, which simply invoke the lib/gpu/Install.py
script with the specified args: script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-gpu # print help message $ make lib-gpu # print help message
make lib-gpu args="-b" # build GPU library with default Makefile.linux $ make lib-gpu args="-b" # build GPU library with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision $ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
Note that this procedure starts with a Makefile.machine in lib/gpu, as Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles specified by the "-m" switch. For your convenience, machine makefiles
@ -181,7 +203,8 @@ use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
command, you also need to have libcurl installed with the matching command, you also need to have libcurl installed with the matching
development headers and the curl-config tool. development headers and the curl-config tool.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
web page to
learn how to install a pre-build binary of the OpenKIM Repository of Models. learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models See the list of all KIM models here: https://openkim.org/browse/models
@ -192,7 +215,7 @@ minutes to hours) to build. Of course you only need to do that once.)
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes -D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on -D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
@ -203,7 +226,7 @@ inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
environment variable so that libkim-api can be found. environment variable so that libkim-api can be found.
For using OpenKIM web queries in LAMMPS. *For using OpenKIM web queries in LAMMPS*\ :
If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
libcurl calls within the KIM web query display a lot of information about libcurl calls within the KIM web query display a lot of information about
@ -229,16 +252,23 @@ step from the lammps/src dir, using a command like these, which simply
invoke the lib/kim/Install.py script with the specified args. invoke the lib/kim/Install.py script with the specified args.
.. parsed-literal:: .. code-block:: bash
make lib-kim # print help message $ make lib-kim # print help message
make lib-kim args="-b " # (re-)install KIM API lib with only example models $ make lib-kim args="-b " # (re-)install KIM API lib with only example models
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models $ make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
Settings for OpenKIM web queries discussed above need to be applied by adding
them to the LMP\_INC variable through editing the Makefile.machine you are
using. For example:
.. code-block:: make
LMP_INC = -DLMP_NO_SSL_CHECK
---------- ----------
@ -257,22 +287,29 @@ KOKKOS\_ARCH settings described below. Note that for CMake, these are
really Kokkos variables, not LAMMPS variables. Hence you must use really Kokkos variables, not LAMMPS variables. Hence you must use
case-sensitive values, e.g. BDW, not bdw. case-sensitive values, e.g. BDW, not bdw.
* AMDAVX = AMD 64-bit x86 CPUs
* EPYC = AMD EPYC Zen class CPUs
* ARMv80 = ARMv8.0 Compatible CPU * ARMv80 = ARMv8.0 Compatible CPU
* ARMv81 = ARMv8.1 Compatible CPU * ARMv81 = ARMv8.1 Compatible CPU
* ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU * ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
* BGQ = IBM Blue Gene/Q CPUs * ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU
* Power8 = IBM POWER8 CPUs * WSM = Intel Westmere CPUs
* Power9 = IBM POWER9 CPUs
* SNB = Intel Sandy/Ivy Bridge CPUs * SNB = Intel Sandy/Ivy Bridge CPUs
* HSW = Intel Haswell CPUs * HSW = Intel Haswell CPUs
* BDW = Intel Broadwell Xeon E-class CPUs * BDW = Intel Broadwell Xeon E-class CPUs
* SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) * SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
* KNC = Intel Knights Corner Xeon Phi * KNC = Intel Knights Corner Xeon Phi
* KNL = Intel Knights Landing Xeon Phi * KNL = Intel Knights Landing Xeon Phi
* BGQ = IBM Blue Gene/Q CPUs
* Power7 = IBM POWER8 CPUs
* Power8 = IBM POWER8 CPUs
* Power9 = IBM POWER9 CPUs
* Kepler = NVIDIA Kepler default (generation CC 3.5)
* Kepler30 = NVIDIA Kepler generation CC 3.0 * Kepler30 = NVIDIA Kepler generation CC 3.0
* Kepler32 = NVIDIA Kepler generation CC 3.2 * Kepler32 = NVIDIA Kepler generation CC 3.2
* Kepler35 = NVIDIA Kepler generation CC 3.5 * Kepler35 = NVIDIA Kepler generation CC 3.5
* Kepler37 = NVIDIA Kepler generation CC 3.7 * Kepler37 = NVIDIA Kepler generation CC 3.7
* Maxwell = NVIDIA Maxwell default (generation CC 5.0)
* Maxwell50 = NVIDIA Maxwell generation CC 5.0 * Maxwell50 = NVIDIA Maxwell generation CC 5.0
* Maxwell52 = NVIDIA Maxwell generation CC 5.2 * Maxwell52 = NVIDIA Maxwell generation CC 5.2
* Maxwell53 = NVIDIA Maxwell generation CC 5.3 * Maxwell53 = NVIDIA Maxwell generation CC 5.3
@ -287,7 +324,7 @@ case-sensitive values, e.g. BDW, not bdw.
For multicore CPUs using OpenMP, set these 2 variables. For multicore CPUs using OpenMP, set these 2 variables.
.. parsed-literal:: .. code-block:: bash
-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above -D KOKKOS_ARCH=archCPU # archCPU = CPU from list above
-D KOKKOS_ENABLE_OPENMP=yes -D KOKKOS_ENABLE_OPENMP=yes
@ -295,7 +332,7 @@ For multicore CPUs using OpenMP, set these 2 variables.
For Intel KNLs using OpenMP, set these 2 variables: For Intel KNLs using OpenMP, set these 2 variables:
.. parsed-literal:: .. code-block:: bash
-D KOKKOS_ARCH=KNL -D KOKKOS_ARCH=KNL
-D KOKKOS_ENABLE_OPENMP=yes -D KOKKOS_ENABLE_OPENMP=yes
@ -303,7 +340,7 @@ For Intel KNLs using OpenMP, set these 2 variables:
For NVIDIA GPUs using CUDA, set these 4 variables: For NVIDIA GPUs using CUDA, set these 4 variables:
.. parsed-literal:: .. code-block:: bash
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU -D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
# archGPU = GPU from list above # archGPU = GPU from list above
@ -316,7 +353,7 @@ Kokkos library: lib/kokkos/bin/nvcc\_wrapper. The setting should
include the full path name to the wrapper, e.g. include the full path name to the wrapper, e.g.
.. parsed-literal:: .. code-block:: bash
-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper -D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper
@ -329,7 +366,7 @@ src/MAKE/OPTIONS/Makefile.kokkos\* files for examples.
For multicore CPUs using OpenMP: For multicore CPUs using OpenMP:
.. parsed-literal:: .. code-block:: make
KOKKOS_DEVICES = OpenMP KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = archCPU # archCPU = CPU from list above KOKKOS_ARCH = archCPU # archCPU = CPU from list above
@ -337,7 +374,7 @@ For multicore CPUs using OpenMP:
For Intel KNLs using OpenMP: For Intel KNLs using OpenMP:
.. parsed-literal:: .. code-block:: make
KOKKOS_DEVICES = OpenMP KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNL KOKKOS_ARCH = KNL
@ -345,7 +382,7 @@ For Intel KNLs using OpenMP:
For NVIDIA GPUs using CUDA: For NVIDIA GPUs using CUDA:
.. parsed-literal:: .. code-block:: make
KOKKOS_DEVICES = Cuda KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU
@ -360,7 +397,7 @@ compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
files. files.
.. parsed-literal:: .. code-block:: make
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
@ -381,7 +418,7 @@ library.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) -D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
@ -401,12 +438,12 @@ simply invokes the lib/latte/Install.py script with the specified
args: args:
.. parsed-literal:: .. code-block:: bash
make lib-latte # print help message $ make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master $ 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="-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 # copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, "includelink" and "liblink" and Note that 3 symbolic (soft) links, "includelink" and "liblink" and
@ -431,7 +468,7 @@ be installed on your system.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes -D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location) -D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location)
@ -446,11 +483,11 @@ one step from the lammps/src dir, using a command like these, which
simply invoke the lib/message/Install.py script with the specified args: simply invoke the lib/message/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-message # print help message $ make lib-message # print help message
make lib-message args="-m -z" # build with MPI and socket (ZMQ) support $ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
make lib-message args="-s" # build as serial lib with no ZMQ support $ make lib-message args="-s" # build as serial lib with no ZMQ support
The build should produce two files: lib/message/cslib/src/libmessage.a The build should produce two files: lib/message/cslib/src/libmessage.a
and lib/message/Makefile.lammps. The latter is copied from an and lib/message/Makefile.lammps. The latter is copied from an
@ -475,7 +512,7 @@ lib/mscg/README and MSCG/Install files for more details.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes -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)
@ -496,14 +533,14 @@ step from the lammps/src dir, using a command like these, which simply
invoke the lib/mscg/Install.py script with the specified args: invoke the lib/mscg/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-mscg # print help message $ make lib-mscg # print help message
make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial" # with the settings compatible with "make serial"
make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi" # with the settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
Note that 2 symbolic (soft) links, "includelink" and "liblink", will Note that 2 symbolic (soft) links, "includelink" and "liblink", will
be created in lib/mscg to point to the MS-CG src/installation dir. be created in lib/mscg to point to the MS-CG src/installation dir.
@ -552,12 +589,12 @@ dir, using a command like these, which simply invoke the
lib/poems/Install.py script with the specified args: lib/poems/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-poems # print help message $ make lib-poems # print help message
make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") $ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") $ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m icc" # build with Intel icc compiler $ make lib-poems args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/poems/libpoems.a and The build should produce two files: lib/poems/libpoems.a and
lib/poems/Makefile.lammps. The latter is copied from an existing lib/poems/Makefile.lammps. The latter is copied from an existing
@ -584,7 +621,7 @@ lib/python/README for more details.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D PYTHON_EXECUTABLE=path # path to Python executable to use -D PYTHON_EXECUTABLE=path # path to Python executable to use
@ -620,7 +657,7 @@ To build with this package, you must download and build the `Voro++ library <vor
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes -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)
@ -642,12 +679,12 @@ simply invoke the lib/voronoi/Install.py script with the specified
args: args:
.. parsed-literal:: .. code-block:: bash
make lib-voronoi # print help message $ make lib-voronoi # print help message
make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version> $ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ $ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
Note that 2 symbolic (soft) links, "includelink" and "liblink", are Note that 2 symbolic (soft) links, "includelink" and "liblink", are
created in lib/voronoi to point to the Voro++ src dir. When LAMMPS created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
@ -673,7 +710,7 @@ installation and the instructions below are followed for the respective build sy
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed -D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes -D PKG_USER-ADIOS=yes
@ -683,16 +720,16 @@ installation and the instructions below are followed for the respective build sy
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
.. parsed-literal:: .. code-block:: bash
make yes-user-adios $ make yes-user-adios
otherwise, set ADIOS2\_DIR environment variable when turning on the package: otherwise, set ADIOS2\_DIR environment variable when turning on the package:
.. parsed-literal:: .. code-block:: bash
ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed $ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
---------- ----------
@ -719,12 +756,12 @@ dir, using a command like these, which simply invoke the
lib/atc/Install.py script with the specified args: lib/atc/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-atc # print help message $ make lib-atc # print help message
make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") $ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") $ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m icc" # build with Intel icc compiler $ make lib-atc args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/atc/libatc.a and The build should produce two files: lib/atc/libatc.a and
lib/atc/Makefile.lammps. The latter is copied from an existing lib/atc/Makefile.lammps. The latter is copied from an existing
@ -741,12 +778,12 @@ lib/linalg. In the latter case you also need to build the library in
lib/linalg with a command like these: lib/linalg with a command like these:
.. parsed-literal:: .. code-block:: bash
make lib-linalg # print help message $ make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") $ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") $ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler $ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
---------- ----------
@ -770,12 +807,12 @@ dir, using a command like these, which simply invoke the
lib/awpmd/Install.py script with the specified args: lib/awpmd/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-awpmd # print help message $ make lib-awpmd # print help message
make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") $ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") $ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m icc" # build with Intel icc compiler $ make lib-awpmd args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/awpmd/libawpmd.a and The build should produce two files: lib/awpmd/libawpmd.a and
lib/awpmd/Makefile.lammps. The latter is copied from an existing lib/awpmd/Makefile.lammps. The latter is copied from an existing
@ -792,12 +829,12 @@ provided in lib/linalg. In the latter case you also need to build the
library in lib/linalg with a command like these: library in lib/linalg with a command like these:
.. parsed-literal:: .. code-block:: bash
make lib-linalg # print help message $ make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") $ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") $ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler $ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
---------- ----------
@ -844,12 +881,12 @@ command like these, which simply invoke the lib/colvars/Install.py script with
the specified args: the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-colvars # print help message $ make lib-colvars # print help message
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") $ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") $ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled $ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
The "machine" argument of the "-m" flag is used to find a Makefile.machine to The "machine" argument of the "-m" flag is used to find a Makefile.machine to
use as build recipe. If it does not already exist in lib/colvars, it will be use as build recipe. If it does not already exist in lib/colvars, it will be
@ -858,8 +895,10 @@ core LAMMPS makefiles.
Optional flags may be specified as environment variables: Optional flags may be specified as environment variables:
COLVARS\_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) .. code-block:: bash
COLVARS\_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
The build should produce two files: the library lib/colvars/libcolvars.a The build should produce two files: the library lib/colvars/libcolvars.a
(which also includes Lepton objects if enabled) and the specification file (which also includes Lepton objects if enabled) and the specification file
@ -921,7 +960,7 @@ your environment. There are then two additional commands that control
the manner in which PLUMED is obtained and linked into LAMMPS. the manner in which PLUMED is obtained and linked into LAMMPS.
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes -D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime -D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime
@ -957,12 +996,12 @@ Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args: from the src folder through the following make args:
.. parsed-literal:: .. code-block:: bash
make lib-plumed # print help message $ make lib-plumed # print help message
make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2 $ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local $ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in $ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode # /usr/local and use shared linkage mode
Note that 2 symbolic (soft) links, "includelink" and "liblink" are Note that 2 symbolic (soft) links, "includelink" and "liblink" are
@ -973,10 +1012,10 @@ mode. After this step is completed, you can install the USER-PLUMED
package and compile LAMMPS in the usual manner: package and compile LAMMPS in the usual manner:
.. parsed-literal:: .. code-block:: bash
make yes-user-plumed $ make yes-user-plumed
make machine $ make machine
Once this compilation completes you should be able to run LAMMPS in the Once this compilation completes you should be able to run LAMMPS in the
usual way. For shared linkage mode, libplumed.so must be found by the usual way. For shared linkage mode, libplumed.so must be found by the
@ -1024,10 +1063,10 @@ dir, using a command like these, which simply invoke the
lib/h5md/Install.py script with the specified args: lib/h5md/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-h5md # print help message $ make lib-h5md # print help message
make lib-h5md args="-m h5cc" # build with h5cc compiler $ make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: lib/h5md/libch5md.a and The build should produce two files: lib/h5md/libch5md.a and
lib/h5md/Makefile.lammps. The latter is copied from an existing lib/h5md/Makefile.lammps. The latter is copied from an existing
@ -1055,7 +1094,7 @@ on the :doc:`Speed intel <Speed_intel>` doc page.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D INTEL_ARCH=value # value = cpu (default) or knl -D INTEL_ARCH=value # value = cpu (default) or knl
-D INTEL_LRT_MODE=value # value = threads, none, or c++11 -D INTEL_LRT_MODE=value # value = threads, none, or c++11
@ -1082,7 +1121,7 @@ additional information.
For CPUs: For CPUs:
.. parsed-literal:: .. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
@ -1092,7 +1131,7 @@ For CPUs:
For KNLs: For KNLs:
.. parsed-literal:: .. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
@ -1111,7 +1150,7 @@ USER-MOLFILE package
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed -D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes -D PKG_USER-MOLFILE=yes
@ -1191,9 +1230,9 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
.. parsed-literal:: .. parsed-literal::
CCFLAGS: -fopenmp # for GNU Compilers CCFLAGS: -fopenmp # for GNU and Clang Compilers
CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux
LINKFLAGS: -fopenmp # for GNU Compilers LINKFLAGS: -fopenmp # for GNU and Clang Compilers
LINKFLAGS: -qopenmp # for Intel compilers on Linux LINKFLAGS: -qopenmp # for Intel compilers on Linux
For other platforms and compilers, please consult the documentation For other platforms and compilers, please consult the documentation
@ -1209,25 +1248,40 @@ how to address compatibility :ref:`issues with the 'default(none)' directive <de
USER-QMMM package USER-QMMM package
--------------------------------- ---------------------------------
.. note:: For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
need to build LAMMPS as a library. A LAMMPS executable with fix qmmm
The LAMMPS executable these steps produce is not yet functional included can be built, but will not be able to do a QM/MM simulation
for a QM/MM simulation. You must also build Quantum ESPRESSO and on as such. You must also build a QM code - currently only Quantum
create a new executable (pwqmmm.x) which links LAMMPS and Quantum ESPRESSO (QE) is supported - and create a new executable which links
ESPRESSO together. These are steps 3 and 4 described in the LAMMPS and the QM code together. Details are given in the
lib/qmmm/README file. Unfortunately, the Quantum ESPRESSO developers lib/qmmm/README file. It is also recommended to read the instructions
have been breaking the interface that the QM/MM code in LAMMPS is using, for :doc:`linking with LAMMPS as a library <Build_link>` for
so that currently (Summer 2018) using this feature requires either background information. This requires compatible Quantum Espresso
correcting the library interface feature in recent Quantum ESPRESSO and LAMMPS versions. The current interface and makefiles have last
releases, or using an outdated version of QE. The last version of been verified to work in February 2020 with Quantum Espresso versions
Quantum ESPRESSO known to work with this QM/MM interface was version 6.3 to 6.5.
5.4.1 from 2016.
**CMake build**\ : **CMake build**\ :
The CMake build system currently does not support building the full When using CMake, building a LAMMPS library is required and it is
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. recommended to build a shared library, since any libraries built from
You must use the traditional make build for this package. the sources in the *lib* folder (including the essential libqmmm.a)
are not included in the static LAMMPS library and (currently) not
installed, while their code is included in the shared LAMMPS library.
Thus a typical command line to configure building LAMMPS for USER-QMMM
would be:
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
-D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
After completing the LAMMPS build and also configuring and compiling
Quantum ESPRESSO with external library support (via "make couple"),
go back to the lib/qmmm folder and follow the instructions on the
README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder. You need to make certain, that
**Traditional make**\ : **Traditional make**\ :
@ -1238,12 +1292,12 @@ lammps/src dir, using a command like these, which simply invoke the
lib/qmmm/Install.py script with the specified args: lib/qmmm/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-qmmm # print help message $ make lib-qmmm # print help message
make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") $ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") $ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler $ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
The build should produce two files: lib/qmmm/libqmmm.a and The build should produce two files: lib/qmmm/libqmmm.a and
lib/qmmm/Makefile.lammps. The latter is copied from an existing lib/qmmm/Makefile.lammps. The latter is copied from an existing
@ -1255,10 +1309,10 @@ a corresponding Makefile.lammps.machine file.
You can then install QMMM package and build LAMMPS in the usual You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support, go back to the lib/qmmm folder ESPRESSO with external library support (via "make couple"), go back to
and follow the instructions on the README file to build the combined the lib/qmmm folder and follow the instructions in the README file to
LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder. build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
lib/qmmm folder.
---------- ----------
@ -1277,7 +1331,7 @@ lib/quip/README file for details on how to do this.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
@ -1313,7 +1367,7 @@ To build with this package, you must download and build the `ScaFaCoS Coulomb so
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes -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)
@ -1358,7 +1412,7 @@ Eigen3 is a template library, so you do not need to build it.
**CMake build**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
@ -1376,11 +1430,11 @@ the lammps/src dir, using a command like these, which simply invoke
the lib/smd/Install.py script with the specified args: the lib/smd/Install.py script with the specified args:
.. parsed-literal:: .. code-block:: bash
make lib-smd # print help message $ make lib-smd # print help message
make lib-smd args="-b" # download to lib/smd/eigen3 $ make lib-smd args="-b" # download to lib/smd/eigen3
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 $ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named "includelink" is created in Note that a symbolic (soft) link named "includelink" is created in
lib/smd to point to the Eigen dir. When LAMMPS builds it will use lib/smd to point to the Eigen dir. When LAMMPS builds it will use

230
doc/src/Build_link.rst
View File

@ -3,62 +3,228 @@ Link LAMMPS as a library to another code
LAMMPS can be used as a library by another application, including LAMMPS can be used as a library by another application, including
Python scripts. The files src/library.cpp and library.h define the Python scripts. The files src/library.cpp and library.h define the
C-style API for using LAMMPS as a library. See the :doc:`Howto library <Howto_library>` doc page for a description of the C-style API for using LAMMPS as a library. See the :doc:`Howto
interface and how to extend it for your needs. library <Howto_library>` doc page for a description of the interface
and how to extend it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in one of LAMMPS as either a shared or static library. This results in one of
these 2 files: these 2 files:
liblammps.so # shared library .. parsed-literal::
liblammps.a # static library
liblammps.so # shared library
liblammps.a # static library
.. note::
Care should be taken to use the same MPI library for the calling
code and the LAMMPS library. The library.h file includes mpi.h and
uses definitions from it so those need to be available and
consistent. When LAMMPS is compiled with the MPI STUBS library,
then its mpi.h file needs to be included. While it is technically
possible to use a full MPI library in the calling code and link to
a serial LAMMPS library compiled with MPI STUBS, it is recommended
to use the *same* MPI library for both, and then use MPI\_Comm\_split()
in the calling code to pass a suitable communicator with a subset
of MPI ranks to the function creating the LAMMPS instance.
---------- ----------
**Link with LAMMPS as a static library**\ : **Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with a The calling application can link to LAMMPS as a static library with
link command like this: compilation and link commands as in the examples shown below. These
are examples for a code written in C in the file *caller.c*.
The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required
executable code from the library is copied into the calling executable.
g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller *CMake build*\ :
The -L argument is the path to where the liblammps.a file is. The This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
-llammps argument is shorthand for the file liblammps.a. and installed with "make install" and the PKG\_CONFIG\_PATH environment
variable updated to include the *liblammps.pc* file installed into the
configured destination folder, if needed. The commands to compile and
link the coupled executable are then:
.. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
This assumes that LAMMPS has been compiled in the folder
"${HOME}/lammps/src" with "make mode=lib mpi". The commands to compile
and link the coupled executable are then:
.. code-block:: bash
mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps
The *-I* argument is the path to the location of the *library.h*
header file containing the interface to the LAMMPS C-style library
interface. The *-L* argument is the path to where the *liblammps.a*
file is located. The *-llammps* argument is shorthand for telling the
compiler to link the file *liblammps.a*\ .
However, it is only as simple as shown above for the case of a plain
LAMMPS library without any optional packages that depend on libraries
(bundled or external). Otherwise, you need to include all flags,
libraries, and paths for the coupled executable, that are also
required to link the LAMMPS executable.
*CMake build*\ :
When using CMake, additional libraries with sources in the lib folder
are built, but not included in liblammps.a and (currently) not
installed with "make install" and not included in the *pkgconfig*
configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is
therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared
library instead.
*Traditional make*\ :
After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=lib serial". And you also
have installed the POEMS package after building its bundled library in
lib/poems. Then the commands to build and link the coupled executable
change to:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since LAMMPS
is C++ code. You can display the currently applied settings for building
LAMMPS for the "serial" machine target by using the command:
.. code-block:: bash
make mode=print serial
Which should output something like:
.. code-block:: bash
# Compiler:
CXX=g++
# Linker:
LD=g++
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS
# Linking:
LDFLAGS=-g -O
# Libraries:
LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the
equivalent and replace "serial" with the corresponding *machine* name
of the makefile.
---------- ----------
**Link with LAMMPS as a shared library**\ : **Link with LAMMPS as a shared library**\ :
If you wish to link to liblammps.so, the operating system finds shared When linking to LAMMPS built as a shared library, the situation
libraries to load at run-time using the environment variable becomes much simpler, as all dependent libraries and objects are
LD\_LIBRARY\_PATH. To enable this you can do one of two things: included in the shared library, which is - technically speaking -
effectively a regular LAMMPS executable that is missing the `main()`
function. Thus those libraries need not to be specified when linking
the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library
with the POEMS package installed becomes:
(1) Copy the liblammps.so file to a location the system can find it, *CMake build*\ :
such as /usr/local/lib. I.e. a directory already listed in your
LD\_LIBRARY\_PATH variable. You can type
The commands with a shared LAMMPS library compiled with the CMake
build process are the same as for the static library.
.. parsed-literal:: .. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
*Traditional make*\ :
The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shlib serial" becomes:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/src -llammps
*Locating liblammps.so at runtime*\ :
However, now the `liblammps.so` file is required at runtime and needs
to be in a folder, where the shared linker program of the operating
system can find it. This would be either a folder like "/usr/local/lib64"
or "${HOME}/.local/lib64" or a folder pointed to by the LD\_LIBRARY\_PATH
environment variable. You can type
.. code-block:: bash
printenv LD_LIBRARY_PATH printenv LD_LIBRARY_PATH
to see what directories are in that list. to see what directories are in that list.
(2) Add the LAMMPS src directory (or the directory you perform CMake Or you can add the LAMMPS src directory (or the directory you performed
build in) to your LD\_LIBRARY\_PATH, so that the current version of the a CMake style build in) to your LD\_LIBRARY\_PATH, so that the current
shared library is always available to programs that use it. version of the shared library is always available to programs that use it.
For the csh or tcsh shells, you would add something like this to your For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
~/.cshrc file: would add something like this to your ~/.profile file:
.. code-block:: bash
LD_LIBRARY_PATH ${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/lammps/src
export LD_LIBRARY_PATH
For the csh or tcsh shells, you would equivalently add something like this
to your ~/.cshrc file:
.. parsed-literal:: .. code-block:: csh
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
You can verify whether all required shared libraries are found with the
`ldd` tool. Example:
.. code-block:: bash
$ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
linux-vdso.so.1 (0x00007ffe729e0000)
liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
libm.so.6 => /lib64/libm.so.6 (0x00007fc91b83e000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc91b824000)
libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash
$ ldd caller
linux-vdso.so.1 (0x00007ffd672fe000)
liblammps.so => not found
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb7c7d40000)
libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fb7c7d26000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
---------- ----------
@ -67,18 +233,20 @@ For the csh or tcsh shells, you would add something like this to your
**Calling the LAMMPS library**\ : **Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a LAMMPS\_NS namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS To be compatible with C, Fortran, Python programs, the library has a simple
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.
When used from a C or Fortran program, the library has a simple
C-style interface, provided in src/library.cpp and src/library.h. C-style interface, provided in src/library.cpp and src/library.h.
See the :doc:`Python library <Python_library>` doc page for a See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style description of the Python interface to LAMMPS, which wraps the C-style
interface. interface from a shared library through the ctypes python module.
See the sample codes in examples/COUPLE/simple for examples of C++ and See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface. C and Fortran codes that invoke LAMMPS through its library interface.

58
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@ -7,18 +7,33 @@ src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
below). It can include various options for customizing your LAMMPS below). It can include various options for customizing your LAMMPS
build with a number of global compilation options and features. build with a number of global compilation options and features.
Those makefiles are written for and tested with GNU make and may not
be compatible with other make programs. In most cases, if the "make"
program is not GNU make, then there will be a GNU make program
available under the name "gmake". If GNU make or a compatible make is
not available, you may have to first install it or switch to building
with :doc:`CMake <Build_cmake>`. The makefiles of the traditional
make based build process and the scripts they are calling expect a few
additional tools to be available and functioning.
* a Bourne shell compatible "Unix" shell program (often this is bash)
* a few shell utilities: ls, mv, ln, rm, grep, sed, tr, cat, touch, diff, dirname
* python (optional, required for "make lib-XXX" in the src folder)
To include LAMMPS packages (i.e. optional commands and styles) you To include LAMMPS packages (i.e. optional commands and styles) you
must install them first, as discussed on the :doc:`Build package <Build_package>` doc page. If the packages require must enable them first, as discussed on the :doc:`Build package
provided or external libraries, you must build those libraries before <Build_package>` doc page. If a packages requires (provided or
building LAMMPS. Building :doc:`LAMMPS with CMake <Build_cmake>` can external) libraries, you must configure and build those libraries
automate all of this for many types of machines, especially **before** building LAMMPS itself and especially **before** enabling
workstations, desktops and laptops, so we suggest you try it first. such a package with "make yes-<package>". Building :doc:`LAMMPS
with CMake <Build_cmake>` can automate much of this for many types of
machines, especially workstations, desktops, and laptops, so we suggest
you try it first when building LAMMPS in those cases.
These commands perform a default LAMMPS build, producing the LAMMPS The commands below perform a default LAMMPS build, producing the LAMMPS
executable lmp\_serial or lmp\_mpi in lammps/src: executable lmp\_serial and lmp\_mpi in lammps/src:
.. code-block:: bash
.. parsed-literal::
cd lammps/src cd lammps/src
make serial # build a serial LAMMPS executable make serial # build a serial LAMMPS executable
@ -42,18 +57,21 @@ re-compiled.
.. note:: .. note::
When you build LAMMPS for the first time, a long list of \*.d Before the actual compilation starts, LAMMPS will perform several
files will be printed out rapidly. This is not an error; it is the steps to collect information from the configuration and setup that
Makefile doing its normal creation of dependencies. is then embedded into the executable. When you build LAMMPS for
the first time, it will also compile a tool to quickly assemble
a list of dependencies, that are required for the make program to
correctly detect which parts need to be recompiled after changes
were made to the sources.
---------- ----------
The lammps/src/MAKE tree contains the Makefile.machine files included
The lammps/src/MAKE tree contains all the Makefile.machine files in the LAMMPS distribution. Typing "make machine" uses
included in the LAMMPS distribution. Typing "make machine" uses *Makefile.machine*\ . Thus the "make serial" or "make mpi" lines above
Makefile.machine. Thus the "make serial" or "make mpi" lines above use Makefile.serial and Makefile.mpi, respectively. Other makefiles
use Makefile.serial and Makefile.mpi. Others are in these dirs: are in these directories:
.. parsed-literal:: .. parsed-literal::
@ -64,7 +82,7 @@ use Makefile.serial and Makefile.mpi. Others are in these dirs:
Typing "make" lists all the available Makefile.machine files. A file Typing "make" lists all the available Makefile.machine files. A file
with the same name can appear in multiple folders (not a good idea). with the same name can appear in multiple folders (not a good idea).
The order the dirs are searched is as follows: src/MAKE/MINE, The order the directories are searched is as follows: src/MAKE/MINE,
src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference
to a customized file you put in src/MAKE/MINE. to a customized file you put in src/MAKE/MINE.
@ -76,7 +94,7 @@ compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated: settings may become outdated:
.. parsed-literal:: .. code-block:: bash
make mac # build serial LAMMPS on a Mac make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac make mac_mpi # build parallel LAMMPS on a Mac

103
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@ -14,10 +14,13 @@ package. In general there is no need to include a package if you
never plan to use its features. never plan to use its features.
If you get a run-time error that a LAMMPS command or style is If you get a run-time error that a LAMMPS command or style is
"Unknown", it is often because the command is contained in a package, "unknown", it is often because the command is contained in a package,
and your build did not include that package. Running LAMMPS with the and your build did not include that package. If the command or style
:doc:`-h command-line switch <Run_options>` will print all the included *is* available in a package included in the LAMMPS distribution,
packages and commands for that executable. the error message will indicate which package would be needed.
Running LAMMPS with the :doc:`-h command-line switch <Run_options>`
will print *all* optional commands and packages that were enabled
when building that executable.
For the majority of packages, if you follow the single step below to For the majority of packages, if you follow the single step below to
include it, you can then build LAMMPS exactly the same as you would include it, you can then build LAMMPS exactly the same as you would
@ -42,17 +45,17 @@ packages:
The mechanism for including packages is simple but different for CMake The mechanism for including packages is simple but different for CMake
versus make. versus make.
**CMake variables**\ : **CMake build**\ :
.. parsed-literal:: .. code-block:: bash
-D PKG_NAME=value # yes or no (default) -D PKG_NAME=value # yes or no (default)
Examples: Examples:
.. parsed-literal:: .. code-block:: bash
-D PKG_MANYBODY=yes -D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes -D PKG_USER-INTEL=yes
@ -74,7 +77,7 @@ once with CMake.
**Traditional make**\ : **Traditional make**\ :
.. parsed-literal:: .. code-block:: bash
cd lammps/src cd lammps/src
make ps # check which packages are currently installed make ps # check which packages are currently installed
@ -85,7 +88,7 @@ once with CMake.
Examples: Examples:
.. parsed-literal:: .. code-block:: bash
make no-rigid make no-rigid
make yes-user-intel make yes-user-intel
@ -119,7 +122,7 @@ are already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded. dependent on that package are also excluded.
When you download a LAMMPS tarball or download LAMMPS source files When you download a LAMMPS tarball or download LAMMPS source files
from the Git or SVN repositories, no packages are pre-installed in the from the git repository, no packages are pre-installed in the
src directory. src directory.
.. note:: .. note::
@ -136,9 +139,10 @@ src directory.
**CMake shortcuts for installing many packages**\ : **CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line, Instead of specifying all the CMake options via the command-line,
CMake allows initializing the variable cache using script files. These CMake allows initializing its settings cache using script files.
are regular CMake files which can manipulate and set variables, and These are regular CMake files which can manipulate and set CMake
can also contain control flow constructs. variables (which represent selected options), and can also contain
control flow constructs for more complex operations.
LAMMPS includes several of these files to define configuration LAMMPS includes several of these files to define configuration
"presets", similar to the options that exist for the Make based "presets", similar to the options that exist for the Make based
@ -146,25 +150,19 @@ system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs. one of them as a starting point and customize it to your needs.
+-------------------------------------------------------------+-----------------------------------------------------------+ .. code-block:: bash
| cmake -C ../cmake/presets/all\_on.cmake [OPTIONS] ../cmake | enable all packages |
+-------------------------------------------------------------+-----------------------------------------------------------+ cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages | cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
+-------------------------------------------------------------+-----------------------------------------------------------+ cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake | enable just a few core packages | cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most common packages
+-------------------------------------------------------------+-----------------------------------------------------------+ cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
| cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake | enable most common packages | cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
+-------------------------------------------------------------+-----------------------------------------------------------+ cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake # enable all packages compatible with MinGW compilers
| cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake | disable packages that do require extra libraries or tools |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake | change settings to use the Clang compilers by default |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake | enable all packages compatible with MinGW compilers |
+-------------------------------------------------------------+-----------------------------------------------------------+
.. note:: .. note::
Running cmake this way manipulates the variable cache in your Running cmake this way manipulates the CMake settings cache in your
current build directory. You can combine multiple presets and options current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running in a single cmake run, or change settings incrementally by running
cmake with new flags. cmake with new flags.
@ -172,7 +170,7 @@ one of them as a starting point and customize it to your needs.
**Example:** **Example:**
.. parsed-literal:: .. code-block:: bash
# build LAMMPS with most commonly used packages, but then remove # build LAMMPS with most commonly used packages, but then remove
# those requiring additional library or tools, but still enable # those requiring additional library or tools, but still enable
@ -200,37 +198,30 @@ Just type "make" in lammps/src to see a one-line summary.
These commands install/un-install sets of packages: These commands install/un-install sets of packages:
+-----------------------------------+-----------------------------------------------------+ .. code-block:: bash
| make yes-all | install all packages |
+-----------------------------------+-----------------------------------------------------+ make yes-all # install all packages
| make no-all | un-install all packages | make no-all # uninstall all packages
+-----------------------------------+-----------------------------------------------------+ make yes-standard or make yes-std # install standard packages
| make yes-standard or make yes-std | install standard packages | make no-standard or make no-std # uninstall standard packages
+-----------------------------------+-----------------------------------------------------+ make yes-user # install user packages
| make no-standard or make no-std | un-install standard packages | make no-user # uninstall user packages
+-----------------------------------+-----------------------------------------------------+ make yes-lib # install packages that require extra libraries
| make yes-user | install user packages | make no-lib # uninstall packages that require extra libraries
+-----------------------------------+-----------------------------------------------------+ make yes-ext # install packages that require external libraries
| make no-user | un-install user packages | make no-ext # uninstall packages that require external libraries
+-----------------------------------+-----------------------------------------------------+
| make yes-lib | install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-lib | un-install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make yes-ext | install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-ext | un-install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
which install/un-install various sets of packages. Typing "make which install/un-install various sets of packages. Typing "make
package" will list all the these commands. package" will list all the these commands.
.. note:: .. note::
Installing or un-installing a package works by simply copying Installing or un-installing a package for the make based build process
files back and forth between the main src directory and works by simply copying files back and forth between the main source
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), directory src and the sub-directories with the package name (e.g.
so that the files are included or excluded when LAMMPS is built. src/KSPACE, src/USER-ATC), so that the files are included or excluded
when LAMMPS is built. Only source files in the src folder will be
compiled.
The following make commands help manage files that exist in both the The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally src directory and in package sub-directories. You do not normally
@ -257,4 +248,4 @@ Type "make package-overwrite" to overwrite files in the package
sub-directories with src files. sub-directories with src files.
Type "make package-diff" to list all differences between pairs of Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir. files in both the source directory and the package directory.

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@ -4,16 +4,15 @@ Optional build settings
LAMMPS can be built with several optional settings. Each sub-section LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make. explain how to do this for building both with CMake and make.
| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS * :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command * :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
| :ref:`Size of LAMMPS data types <size>` * :ref:`Size of LAMMPS data types <size>`
| :ref:`Read or write compressed files <gzip>` * :ref:`Read or write compressed files <gzip>`
| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command * :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command * :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
| :ref:`Memory allocation alignment <align>` * :ref:`Memory allocation alignment <align>`
| :ref:`Workaround for long long integers <longlong>` * :ref:`Workaround for long long integers <longlong>`
| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library * :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
|
---------- ----------
@ -21,45 +20,16 @@ explain how to do this for building both with CMake and make.
.. _cxx11: .. _cxx11:
C++11 standard compliance test C++11 standard compliance
------------------------------------------ ------------------------------------------
The LAMMPS developers plan to transition to make the C++11 standard the A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
minimum requirement for compiling LAMMPS. Currently this only applies to LAMMPS version 3 March 2020 is the last version compatible with the previous
some packages like KOKKOS while the rest aims to be compatible with the C++98 C++98 standard for the core code and most packages. Most currently used
standard. Most currently used compilers are compatible with C++11; some need C++ compilers are compatible with C++11, but some older ones may need extra
to set extra flags to switch. To determine the impact of requiring C++11, flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
we have added a simple compliance test to the source code, that will cause
the compilation to abort, if C++11 compliance is not available or enabled.
To bypass this check, you need to change a setting in the makefile or
when calling CMake.
**CMake variable**\ : .. code-block:: make
.. parsed-literal::
-D DISABLE_CXX11_REQUIREMENT=yes
You can set additional C++ compiler flags (beyond those selected by CMake)
through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
.. parsed-literal::
-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
**Makefile.machine setting**\ to bypass the C++11 test and compile in C++98 mode:
.. parsed-literal::
LMP_INC = -DLAMMPS_CXX98
**Makefile.machine setting**\ to enable the C++11 with older (but not too old) GNU c++ (e.g. on CentOS 7):
.. parsed-literal::
CCFLAGS = -g -O3 -std=c++11 CCFLAGS = -g -O3 -std=c++11
@ -80,7 +50,7 @@ LAMMPS can use them if they are available on your system.
**CMake variables**\ : **CMake variables**\ :
.. parsed-literal:: .. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS -D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision -D FFT_SINGLE=value # yes or no (default), no = double precision
@ -100,7 +70,7 @@ used. If CMake cannot detect the FFT library, you can set these variables
to assist: to assist:
.. parsed-literal:: .. code-block:: bash
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files -D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
-D FFTW3_LIBRARIES=path # path to FFTW3 libraries -D FFTW3_LIBRARIES=path # path to FFTW3 libraries
@ -112,7 +82,7 @@ to assist:
**Makefile.machine settings**\ : **Makefile.machine settings**\ :
.. parsed-literal:: .. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified # default is KISS if not specified
@ -124,7 +94,7 @@ to assist:
# default is FFT\_PACK\_ARRAY if not specified # default is FFT\_PACK\_ARRAY if not specified
.. parsed-literal:: .. code-block:: make
FFT_INC = -I/usr/local/include FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib FFT_PATH = -L/usr/local/lib
@ -190,7 +160,7 @@ For FFTW3, do the following, which should produce the additional
library libfftw3f.a or libfftw3f.so. library libfftw3f.a or libfftw3f.so.
.. parsed-literal:: .. code-block:: bash
make clean make clean
./configure --enable-single; make; make install ./configure --enable-single; make; make install
@ -218,14 +188,14 @@ adequate.
**CMake variable**\ : **CMake variable**\ :
.. parsed-literal:: .. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall -D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ : **Makefile.machine setting**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
@ -296,21 +266,21 @@ following settings:
**CMake variables**\ : **CMake variables**\ :
.. parsed-literal:: .. code-block:: bash
-D WITH_JPEG=value # yes or no -D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no # default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no -D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no # default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no -D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no # default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot find Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these the graphics header, library, executable files, you can set these
variables: variables:
.. parsed-literal:: .. code-block:: bash
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file -D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file -D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
@ -323,7 +293,7 @@ variables:
**Makefile.machine settings**\ : **Makefile.machine settings**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_JPEG LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG LMP_INC = -DLAMMPS_PNG
@ -337,7 +307,7 @@ As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
find the graphics header and library files. You must specify JPG\_LIB find the graphics header and library files. You must specify JPG\_LIB
with a list of graphics libraries to include in the link. You must with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime, insure ffmpeg is in a directory where LAMMPS can find it at runtime,
i.e. a dir in your PATH environment variable. that is a directory in your PATH environment variable.
**CMake and make info**\ : **CMake and make info**\ :
@ -347,7 +317,7 @@ supports the "popen" function in the standard runtime library.
.. note:: .. note::
On some clusters with high-speed networks, using the fork() On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast library call (required by popen()) can interfere with the fast
communication library and lead to simulations using ffmpeg to hang or communication library and lead to simulations using ffmpeg to hang or
crash. crash.
@ -367,7 +337,7 @@ gzip compression by several LAMMPS commands, including
**CMake variables**\ : **CMake variables**\ :
.. parsed-literal:: .. code-block:: bash
-D WITH_GZIP=value # yes or no -D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no # default is yes if CMake can find gzip, else no
@ -376,7 +346,7 @@ gzip compression by several LAMMPS commands, including
**Makefile.machine setting**\ : **Makefile.machine setting**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_GZIP LMP_INC = -DLAMMPS_GZIP
@ -389,7 +359,7 @@ found by LAMMPS during a run.
.. note:: .. note::
On some clusters with high-speed networks, using the fork() On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast library call (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which is I/O is also available using a compression library instead, which is
@ -416,7 +386,7 @@ aligned on 64-byte boundaries.
**CMake variable**\ : **CMake variable**\ :
.. parsed-literal:: .. code-block:: bash
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) -D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
@ -428,7 +398,7 @@ and this setting ignored.
**Makefile.machine setting**\ : **Makefile.machine setting**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
@ -455,14 +425,14 @@ those systems:
**CMake variable**\ : **CMake variable**\ :
.. parsed-literal:: .. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) -D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ : **Makefile.machine setting**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
@ -476,20 +446,21 @@ Exception handling when using LAMMPS as a library
------------------------------------------------------------------ ------------------------------------------------------------------
This setting is useful when external codes drive LAMMPS as a library. This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller. With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller, Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. e.g. to Python. Of course the calling code has to be set up to
*catch* exceptions from within LAMMPS.
**CMake variable**\ : **CMake variable**\ :
.. parsed-literal:: .. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default) -D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ : **Makefile.machine setting**\ :
.. parsed-literal:: .. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS LMP_INC = -DLAMMPS_EXCEPTIONS

2
doc/src/Commands_all.rst
View File

@ -17,7 +17,7 @@ General commands
An alphabetic list of all general LAMMPS commands. An alphabetic list of all general LAMMPS commands.
.. table_from_list:: .. table_from_list::
:columns: 6 :columns: 5
* :doc:`angle_coeff <angle_coeff>` * :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>` * :doc:`angle_style <angle_style>`

233
doc/src/Commands_category.rst
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@ -7,126 +7,163 @@ alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically. have their own pages where they are listed alphabetically.
Initialization: Initialization:
------------------------------
* :doc:`newton <newton>`, .. table_from_list::
* :doc:`package <package>`, :columns: 5
* :doc:`processors <processors>`,
* :doc:`suffix <suffix>`, * :doc:`newton <newton>`
* :doc:`units <units>` * :doc:`package <package>`
* :doc:`processors <processors>`
* :doc:`suffix <suffix>`
* :doc:`units <units>`
Setup simulation box: Setup simulation box:
------------------------------
* :doc:`boundary <boundary>`, .. table_from_list::
* :doc:`box <box>`, :columns: 4
* :doc:`change_box <change_box>`,
* :doc:`create_box <create_box>`, * :doc:`boundary <boundary>`
* :doc:`dimension <dimension>`, * :doc:`box <box>`
* :doc:`lattice <lattice>`, * :doc:`change_box <change_box>`
* :doc:`region <region>` * :doc:`create_box <create_box>`
* :doc:`dimension <dimension>`
* :doc:`lattice <lattice>`
* :doc:`region <region>`
Setup atoms: Setup atoms:
------------------------------
* :doc:`atom_modify <atom_modify>`, .. table_from_list::
* :doc:`atom_style <atom_style>`, :columns: 4
* :doc:`balance <balance>`,
* :doc:`create_atoms <create_atoms>`, * :doc:`atom_modify <atom_modify>`
* :doc:`create_bonds <create_bonds>`, * :doc:`atom_style <atom_style>`
* :doc:`delete_atoms <delete_atoms>`, * :doc:`balance <balance>`
* :doc:`delete_bonds <delete_bonds>`, * :doc:`create_atoms <create_atoms>`
* :doc:`displace_atoms <displace_atoms>`, * :doc:`create_bonds <create_bonds>`
* :doc:`group <group>`, * :doc:`delete_atoms <delete_atoms>`
* :doc:`mass <mass>`, * :doc:`delete_bonds <delete_bonds>`
* :doc:`molecule <molecule>`, * :doc:`displace_atoms <displace_atoms>`
* :doc:`read_data <read_data>`, * :doc:`group <group>`
* :doc:`read_dump <read_dump>`, * :doc:`mass <mass>`
* :doc:`read_restart <read_restart>`, * :doc:`molecule <molecule>`
* :doc:`replicate <replicate>`, * :doc:`read_data <read_data>`
* :doc:`set <set>`, * :doc:`read_dump <read_dump>`
* :doc:`velocity <velocity>` * :doc:`read_restart <read_restart>`
* :doc:`replicate <replicate>`
* :doc:`set <set>`
* :doc:`velocity <velocity>`
Force fields: Force fields:
------------------------------
* :doc:`angle_coeff <angle_coeff>`, .. table_from_list::
* :doc:`angle_style <angle_style>`, :columns: 4
* :doc:`bond_coeff <bond_coeff>`,
* :doc:`bond_style <bond_style>`, * :doc:`angle_coeff <angle_coeff>`
* :doc:`bond_write <bond_write>`, * :doc:`angle_style <angle_style>`
* :doc:`dielectric <dielectric>`, * :doc:`bond_coeff <bond_coeff>`
* :doc:`dihedral_coeff <dihedral_coeff>`, * :doc:`bond_style <bond_style>`
* :doc:`dihedral_style <dihedral_style>`, * :doc:`bond_write <bond_write>`
* :doc:`improper_coeff <improper_coeff>`, * :doc:`dielectric <dielectric>`
* :doc:`improper_style <improper_style>`, * :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`kspace_modify <kspace_modify>`, * :doc:`dihedral_style <dihedral_style>`
* :doc:`kspace_style <kspace_style>`, * :doc:`improper_coeff <improper_coeff>`
* :doc:`pair_coeff <pair_coeff>`, * :doc:`improper_style <improper_style>`
* :doc:`pair_modify <pair_modify>`, * :doc:`kspace_modify <kspace_modify>`
* :doc:`pair_style <pair_style>`, * :doc:`kspace_style <kspace_style>`
* :doc:`pair_write <pair_write>`, * :doc:`pair_coeff <pair_coeff>`
* :doc:`special_bonds <special_bonds>` * :doc:`pair_modify <pair_modify>`
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`special_bonds <special_bonds>`
Settings: Settings:
------------------------------
* :doc:`comm_modify <comm_modify>`, .. table_from_list::
* :doc:`comm_style <comm_style>`, :columns: 4
* :doc:`info <info>`,
* :doc:`min_modify <min_modify>`, * :doc:`comm_modify <comm_modify>`
* :doc:`min_style <min_style>`, * :doc:`comm_style <comm_style>`
* :doc:`neigh_modify <neigh_modify>`, * :doc:`info <info>`
* :doc:`neighbor <neighbor>`, * :doc:`min_modify <min_modify>`
* :doc:`partition <partition>`, * :doc:`min_style <min_style>`
* :doc:`reset_timestep <reset_timestep>`, * :doc:`neigh_modify <neigh_modify>`
* :doc:`run_style <run_style>`, * :doc:`neighbor <neighbor>`
* :doc:`timer <timer>`, * :doc:`partition <partition>`
* :doc:`timestep <timestep>` * :doc:`reset_timestep <reset_timestep>`
* :doc:`run_style <run_style>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes): Operations within timestepping (fixes) and diagnostics (computes):
------------------------------------------------------------------------------------------
* :doc:`compute <compute>`, .. table_from_list::
* :doc:`compute_modify <compute_modify>`, :columns: 4
* :doc:`fix <fix>`,
* :doc:`fix_modify <fix_modify>`, * :doc:`compute <compute>`
* :doc:`uncompute <uncompute>`, * :doc:`compute_modify <compute_modify>`
* :doc:`unfix <unfix>` * :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`uncompute <uncompute>`
* :doc:`unfix <unfix>`
Output: Output:
------------------------------
* :doc:`dump image <dump_image>`, .. table_from_list::
* :doc:`dump movie <dump_image>`, :columns: 4
* :doc:`dump <dump>`,
* :doc:`dump_modify <dump_modify>`, * :doc:`dump image <dump_image>`
* :doc:`restart <restart>`, * :doc:`dump movie <dump_image>`
* :doc:`thermo <thermo>`, * :doc:`dump <dump>`
* :doc:`thermo_modify <thermo_modify>`, * :doc:`dump_modify <dump_modify>`
* :doc:`thermo_style <thermo_style>`, * :doc:`restart <restart>`
* :doc:`undump <undump>`, * :doc:`thermo <thermo>`
* :doc:`write_coeff <write_coeff>`, * :doc:`thermo_modify <thermo_modify>`
* :doc:`write_data <write_data>`, * :doc:`thermo_style <thermo_style>`
* :doc:`write_dump <write_dump>`, * :doc:`undump <undump>`
* :doc:`write_restart <write_restart>` * :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
Actions: Actions:
------------------------------
* :doc:`minimize <minimize>`, .. table_from_list::
* :doc:`neb <neb>`, :columns: 6
* :doc:`neb_spin <neb_spin>`,
* :doc:`prd <prd>`, * :doc:`minimize <minimize>`
* :doc:`rerun <rerun>`, * :doc:`neb <neb>`
* :doc:`run <run>`, * :doc:`neb_spin <neb_spin>`
* :doc:`tad <tad>`, * :doc:`prd <prd>`
* :doc:`temper <temper>` * :doc:`rerun <rerun>`
* :doc:`run <run>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
Input script control: Input script control:
------------------------------
* :doc:`clear <clear>`, .. table_from_list::
* :doc:`echo <echo>`, :columns: 7
* :doc:`if <if>`,
* :doc:`include <include>`, * :doc:`clear <clear>`
* :doc:`jump <jump>`, * :doc:`echo <echo>`
* :doc:`label <label>`, * :doc:`if <if>`
* :doc:`log <log>`, * :doc:`include <include>`
* :doc:`next <next>`, * :doc:`info <info>`
* :doc:`print <print>`, * :doc:`jump <jump>`
* :doc:`python <python>`, * :doc:`label <label>`
* :doc:`quit <quit>`, * :doc:`log <log>`
* :doc:`shell <shell>`, * :doc:`next <next>`
* :doc:`variable <variable>` * :doc:`print <print>`
* :doc:`python <python>`
* :doc:`quit <quit>`
* :doc:`shell <shell>`
* :doc:`variable <variable>`

2
doc/src/Commands_compute.rst
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@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT. KOKKOS, o = USER-OMP, t = OPT.
.. table_from_list:: .. table_from_list::
:columns: 6 :columns: 5
* :doc:`ackland/atom <compute_ackland_atom>` * :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>` * :doc:`adf <compute_adf>`

2
doc/src/Commands_fix.rst
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@ -20,7 +20,7 @@ parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT. OPT.
.. table_from_list:: .. table_from_list::
:columns: 6 :columns: 5
* :doc:`adapt <fix_adapt>` * :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>` * :doc:`adapt/fep <fix_adapt_fep>`

6
doc/src/Commands_pair.rst
View File

@ -26,6 +26,10 @@ OPT.
* :doc:`zero <pair_zero>` * :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>` * :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>` * :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
*
*
* *
* *
* *
@ -108,14 +112,12 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>` * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>` * :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>` * :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>` * :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>` * :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>` * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>` * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>` * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`

221
doc/src/Commands_parse.rst
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@ -9,134 +9,151 @@ file names or user-chosen ID strings.
Here are 6 rules for how each line in the input script is parsed by Here are 6 rules for how each line in the input script is parsed by
LAMMPS: LAMMPS:
(1) If the last printable character on the line is a "&" character, .. _one:
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the "&" character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using "&" characters.
(2) All characters from the first "#" character onward are treated as 1. If the last printable character on the line is a "&" character, the
comment and discarded. See an exception in (6). Note that a command is assumed to continue on the next line. The next line is
comment after a trailing "&" character will prevent the command from concatenated to the previous line by removing the "&" character and
continuing on the next line. Also note that for multi-line commands a line break. This allows long commands to be continued across two or
single leading "#" will comment out the entire command. more lines. See the discussion of triple quotes in :ref:`6 <six>`
for how to continue a command across multiple line without using "&"
characters.
.. code-block:: LAMMPS .. _two:
# this is a comment 2. All characters from the first "#" character onward are treated as
comment and discarded. The exception to this rule is described in
:ref:`6 <six>`. Note that a comment after a trailing "&" character
will prevent the command from continuing on the next line. Also note
that for multi-line commands a single leading "#" will comment out
the entire command.
(3) The line is searched repeatedly for $ characters, which indicate .. code-block:: LAMMPS
variables that are replaced with a text string. See an exception in
(6).
If the $ is followed by curly brackets, then the variable name is the # this is a comment
text inside the curly brackets. If no curly brackets follow the $, timestep 1.0 # this is also a comment
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
"x".
How the variable is converted to a text string depends on what style .. _three:
of variable it is; see the :doc:`variable <variable>` doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
As a special case, if the $ is followed by parenthesis, then the text 3. The line is searched repeatedly for $ characters, which indicate
inside the parenthesis is treated as an "immediate" variable and variables that are replaced with a text string. The exception to
evaluated as an :doc:`equal-style variable <variable>`. This is a way this rule is described in :ref:`6 <six>`.
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines: If the $ is followed by text in curly brackets '{}', then the
variable name is the text inside the curly brackets. If no curly
brackets follow the $, then the variable name is the single character
immediately following the $. Thus ${myTemp} and $x refer to variables
named "myTemp" and "x", while "$xx" will be interpreted as a variable
named "x" followed by an "x" character.
How the variable is converted to a text string depends on what style
of variable it is; see the :doc:`variable <variable>` doc page for
details. It can be a variable that stores multiple text strings, and
return one of them. The returned text string can be multiple "words"
(space separated) which will then be interpreted as multiple
arguments in the input command. The variable can also store a
numeric formula which will be evaluated and its numeric result
returned as a string.
As a special case, if the $ is followed by parenthesis "()", then the
text inside the parenthesis is treated as an "immediate" variable and
evaluated as an :doc:`equal-style variable <variable>`. This is a
way to use numeric formulas in an input script without having to
assign them to variable names. For example, these 3 input script
lines:
.. code-block:: LAMMPS
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
can be replaced by:
.. code-block:: LAMMPS
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
so that you do not have to define (or discard) a temporary variable,
"X" in this case.
Additionally, the "immediate" variable expression may be followed by
a colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
The format string must be appropriate for a double-precision
floating-point value. The format string is used to output the result
of the variable expression evaluation. If a format string is not
specified a high-precision "%.20g" is used as the default.
This can be useful for formatting print output to a desired precision:
.. code-block:: LAMMPS .. code-block:: LAMMPS
variable X equal (xlo+xhi)/2+sqrt(v_area) print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
can be replaced by Note that neither the curly-bracket or immediate form of variables
can contain nested $ characters for other variables to substitute
for. Thus you may **NOT** do this:
.. code-block:: LAMMPS
.. code-block:: LAMMPS variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE Nor can you specify an expression like "$($x-1.0)" for an immediate
variable, but you could use $(v\_x-1.0), since the latter is valid
syntax for an :doc:`equal-style variable <variable>`.
so that you do not have to define (or discard) a temporary variable X. See the :doc:`variable <variable>` command for more details of how
strings are assigned to variables and evaluated, and how they can
be used in input script commands.
Additionally, the "immediate" variable expression may be followed by a .. _four:
colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
The format string must be appropriate for a double-precision
floating-point value. The format string is used to output the result
of the variable expression evaluation. If a format string is not
specified a high-precision "%.20g" is used as the default.
This can be useful for formatting print output to a desired precision: 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.
.. _five:
5. The first word is the command name. All successive words in the line
are arguments.
.. code-block:: LAMMPS .. _six:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" 6. If you want text with spaces to be treated as a single argument, it
can be enclosed in either single or double or triple quotes. A long
single argument enclosed in single or double quotes can span multiple
lines if the "&" character is used, as described above. When the
lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are
not needed. For example:
Note that neither the curly-bracket or immediate form of variables can .. code-block:: LAMMPS
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
print "Volume = $v"
.. code-block:: LAMMPS print 'Volume = $v'
if "${steps} > 1000" then quit
variable a equal 2 variable a string "red green blue &
variable b2 equal 4
print "B2 = ${b$a}"
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v\_x-1.0), since the latter is valid syntax for an
:doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` 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 white-space (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the "&" character is used, as described above. When
the lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
.. code-block:: LAMMPS
print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan" purple orange cyan"
print """ print """
System volume = $v System volume = $v
System temperature = $t System temperature = $t
""" """
In each case, the single, double, or triple quotes are removed when In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally. the single argument they enclose is stored internally.
See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`, See the :doc:`dump modify format <dump_modify>`, :doc:`print
:doc:`if <if>`, and :doc:`python <python>` commands for examples. <print>`, :doc:`if <if>`, and :doc:`python <python>` commands for
examples.
A "#" or "$" character that is between quotes will not be treated as a A "#" or "$" character that is between quotes will not be treated as
comment indicator in (2) or substituted for as a variable in (3). a comment indicator in :ref:`2 <two>` or substituted for as a
variable in :ref:`3 <three>`.
.. note:: .. note::

52
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@ -8,17 +8,20 @@ page.
A LAMMPS input script typically has 4 parts: A LAMMPS input script typically has 4 parts:
1. Initialization 1. :ref:`Initialization <init>`
2. Atom definition 2. :ref:`System definition <system>`
3. Settings 3. :ref:`Simulation settings <settings>`
4. Run a simulation 4. :ref:`Run a simulation <run>`
The last 2 parts can be repeated as many times as desired. I.e. run a The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4 simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all parts is now described in more detail. Remember that almost all
commands need only be used if a non-default value is desired. commands need only be used if a non-default value is desired.
(1) Initialization .. _init:
Initialization
------------------------------
Set parameters that need to be defined before atoms are created or Set parameters that need to be defined before atoms are created or
read-in from a file. read-in from a file.
@ -34,23 +37,33 @@ commands tell LAMMPS what kinds of force fields are being used:
:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`, :doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
:doc:`improper_style <improper_style>`. :doc:`improper_style <improper_style>`.
(2) Atom definition .. _system:
There are 3 ways to define atoms in LAMMPS. Read them in from a data System definition
or restart file via the :doc:`read_data <read_data>` or ------------------------------
:doc:`read_restart <read_restart>` commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: :doc:`lattice <lattice>`,
:doc:`region <region>`, :doc:`create_box <create_box>`,
:doc:`create_atoms <create_atoms>`. The entire set of atoms can be
duplicated to make a larger simulation using the
:doc:`replicate <replicate>` command.
(3) Settings There are 3 ways to define the simulation cell and reserve space for
force field info and fill it with atoms in LAMMPS. Read them in from
(1) a data file or (2) a restart file via the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands,
respectively. These files can also contain molecular topology
information. Or (3) create a simulation cell and fill it with atoms on
a lattice (with no molecular topology), using these commands:
:doc:`lattice <lattice>`, :doc:`region <region>`, :doc:`create_box
<create_box>`, :doc:`create_atoms <create_atoms>` or
:doc:`read_dump <read_dump>`.
The entire set of atoms can be duplicated to make a larger simulation
using the :doc:`replicate <replicate>` command.
.. _settings:
Simulation settings
------------------------------
Once atoms and molecular topology are defined, a variety of settings Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters, can be specified: force field coefficients, simulation parameters,
output options, etc. output options, and more.
Force field coefficients are set by these commands (they can also be Force field coefficients are set by these commands (they can also be
set in the read-in files): :doc:`pair_coeff <pair_coeff>`, set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
@ -77,7 +90,10 @@ commands.
Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`, Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
and :doc:`restart <restart>` commands. and :doc:`restart <restart>` commands.
(4) Run a simulation .. _run:
Run a simulation
------------------------------
A molecular dynamics simulation is run using the :doc:`run <run>` A molecular dynamics simulation is run using the :doc:`run <run>`
command. Energy minimization (molecular statics) is performed using command. Energy minimization (molecular statics) is performed using

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\documentclass[12pt]{article}
\usepackage{amsmath}
\begin{document}
\begin{align*}
E =& E_2 \sum_{i,j}e^{-k_2 r_{ij}} + E_A \sum_{\substack{i,j,k,\ell \\\in \textrm{type A}}} f(r_{ij})f(r_{k\ell}) + E_B \sum_{\substack{i,j,k,\ell \\\in \textrm{type B}}} f(r_{ij})f(r_{k\ell}) + E_C \sum_{\substack{i,j,k,\ell \\\in \textrm{type C}}} f(r_{ij})f(r_{k\ell}) \\
f(r) =& e^{-k_3 r}s(r) \\
s(r) =& \begin{cases}
1 & r<R_s \\
\displaystyle\frac{(R_f-r)^2(R_f-3R_s+2r)}{(R_f-R_s)^3} & R_s\leq r\leq R_f \\
0 & r>R_f\\
\end{cases}
\end{align*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E_{Pauli(ECP_s)}=p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right)
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right]
$$

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\documentclass[12pt]{article}
\begin{document}
$$
E_{KE} = \frac{\hbar^2 }{{m_{e} }}\sum\limits_i {\frac{3}{{2s_i^2 }}}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E_{NN} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{{Z_i Z_j }}{{R_{ij} }}}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E_{Ne} = - \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i,j} {\frac{{Z_i }}{{R_{ij} }}Erf\left( {\frac{{\sqrt 2 R_{ij} }}{{s_j }}} \right)}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E_{Pauli} = \sum\limits_{\sigma _i = \sigma _j } {E\left( { \uparrow \uparrow } \right)_{ij}} + \sum\limits_{\sigma _i \ne \sigma _j } {E\left( { \uparrow \downarrow } \right)_{ij}}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E_{ee} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{1}{{r_{ij} }}Erf\left( {\frac{{\sqrt 2 r_{ij} }}{{\sqrt {s_i^2 + s_j^2 } }}} \right)}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right)
$$
\end{document}

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\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left(
\vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i}
\times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber
\end{equation}
\end{varwidth}
\end{document}

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\documentclass[12pt]{article}
\usepackage{amsmath}
\begin{document}
$$
F = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
\lambda(\tau) = \tau
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
\lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right)
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
F^{H} = -R_{FU}(U-U^{\infty}) + R_{FE}E^{\infty}
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
-R_{FU}(U-U^{\infty}) = -R_{FE}E^{\infty} - F^{rest}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
\mathbf{J} & = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \mathbf{v}_j \right) \mathbf{x}_{ij} \right] \\
& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) \right) \mathbf{x}_{ij} \right]
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
\kappa = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0) J_x(t) \rangle \, dt
= \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot \mathbf{J}(t) \rangle \, dt
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left( r_{ij} \right) - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\sigma,ij} \left( r_{ij} \right) \cdot \Theta_{\sigma,ij} - \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \beta_{\pi,ij} \left( r_{ij} \right) \cdot \Theta_{\pi,ij} + U_{prom}
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E = A \exp \left(\frac{\sigma - r}{\rho} \right) -
\frac{C}{r^6} + \frac{D}{r^8} \qquad r < r_c
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = A e^{-r / \rho} - \frac{C}{r^6} \qquad r < r_c
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\pagestyle{empty}
\begin{eqnarray*}
E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
E & = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
& = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
& = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E & = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
& = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
& = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) & = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
\left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
\end{eqnarray*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
3 \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
\left(\frac{\sigma}{r}\right)^6 \right] &
\qquad r < r_c \\
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right] &
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] &
\qquad r < r_c
\end{eqnarray*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{eqnarray}
U_A &=& - \frac{A_{cc}}{6} \left[
\frac{2 a_1 a_2}{r^2-\left(a_1+a_2\right)^2}
+ \frac{2 a_1 a_2}{r^2 - \left(a_1 - a_2\right)^2}
+ \mathrm{ln}
\left(
\frac{r^2-\left(a_1+a_2\right)^2}{r^2-\left(a_1-a_2\right)^2}
\right)
\right] \nonumber \\
\nonumber \\
U_R &=& \frac{A_{cc}}{37800} \frac{\sigma^6}{r}
\left[ \frac{}{} \right. \nonumber \\
&&\qquad \frac{r^2-7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
{\left(r-a_1-a_2\right)^7} \nonumber \\
&&\qquad +\frac{r^2+7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
{\left(r+a_1+a_2\right)^7} \nonumber \\
&&\qquad -\frac{r^2+7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
{\left(r+a_1-a_2\right)^7} \nonumber \\
&&\qquad \left. -\frac{r^2-7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
{\left(r-a_1+a_2\right)^7}
\right] \nonumber \\
\nonumber \\
U &=& U_A + U_R, \qquad r < r_c \nonumber
\end{eqnarray}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{eqnarray}
U &=& \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3}
\left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6}
{15 \left(a-r\right)^6 \left( a+r \right)^6} \right], ~~ r < r_c \nonumber
\end{eqnarray}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{eqnarray}
U &=& \frac{A_{ss}}{36} \left[ \left( \frac{\sigma}{r}
\right)^{12} - \left( \frac{ \sigma}{r} \right)^6 \right], ~~
r < r_c \nonumber
\end{eqnarray}
\end{document}

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\documentclass[12pt]{article}
\begin{document} \large
\begin{eqnarray*}
E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\
&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\
\end{eqnarray*}
\end{document}

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\documentclass[10pt]{article}
\begin{document}
\begin{table}[h]
\begin{tabular}{|c|c|c|c|c|c|c|c|c|}
\hline
& $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ & $Zr$ \\ \hline
$O$ & F & F & F & F & F & F & F & F\\ \hline
$Cu$ & F & F & P & F & F & P & F & P \\ \hline
$N$ & F & P & F & M & F & P & P & P \\ \hline
$C$ & F & F & M & F & F & M & M & M \\ \hline
$H$ & F & F & F & F & F & M & M & F \\ \hline
$Ti$ & F & P & P & M & M & F & P & P \\ \hline
$Zn$ & F & F & P & M & M & P & F & P \\ \hline
$Zr$ & F & P & P & M & F & P & P & F \\ \hline
\multicolumn{9}{l}{F: Fully optimized} \\
\multicolumn{9}{l}{M: Only optimized for dimer molecule} \\
\multicolumn{9}{l}{P: in Progress but have it from mixing rule} \\
\end{tabular}
\end{table}
\end{document}

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\documentclass[12pt]{article}
\usepackage{amsmath}
\begin{document}
\begin{align*}
E =
\begin{cases}
-\epsilon& \quad r < \sigma \\
-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
0& \quad r \geq r_c
\end{cases}
\end{align*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
2\left(\frac{\sigma}{r}\right)^6 + 1\right]
, \quad r < \sigma
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
E & = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\
\epsilon_D(r) & = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right)
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

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\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
\begin{document}
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\[15pt]
{\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
\end{eqnarray*}
\endgroup
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
\begin{eqnarray*}
E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
\end{eqnarray*}
\end{document}

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