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Merge branch 'master' into feature-cnt

This commit is contained in:
iafoss 2020-03-06 18:41:38 -05:00
parent 8c82c60f2f 8c580c1d47
commit bdbbe00ec7
1003 changed files with 21321 additions and 10773 deletions
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2
.github/CONTRIBUTING.md vendored
View File

@ -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-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.
* 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
* 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.

48
cmake/CMakeLists.txt
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@ -2,7 +2,7 @@
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 2.8.12)
cmake_minimum_required(VERSION 3.10)
project(lammps CXX)
set(SOVERSION 0)
@ -36,7 +36,6 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
include(PreventInSourceBuilds)
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
#release comes with -O3 by default
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@ -53,16 +52,19 @@ include(CheckCCompilerFlag)
include(CheckIncludeFileCXX)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
if(DISABLE_CXX11_REQUIREMENT)
add_definitions(-DLAMMPS_CXX98)
# else()
# set(CMAKE_CXX_STANDARD 11)
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
if(NOT ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug"))
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -ftree-vectorize -fexpensive-optimizations")
endif()
endif()
# we require C++11
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# GNU compiler features
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable code coverage" OFF)
@ -132,9 +134,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
@ -179,6 +181,7 @@ option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI)
find_package(MPI REQUIRED)
include_directories(${MPI_CXX_INCLUDE_PATH})
add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1)
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
@ -356,9 +359,6 @@ endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
include(CheckLibraryExists)
if (CMAKE_VERSION VERSION_LESS "3.4")
enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
endif()
# RB: disabled this check because it breaks with KOKKOS CUDA enabled
#foreach(FUNC sin cos)
# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
@ -420,7 +420,7 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
@ -682,7 +682,7 @@ endforeach()
get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
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 >>>
Build type ${CMAKE_BUILD_TYPE}
Install path ${CMAKE_INSTALL_PREFIX}
@ -702,7 +702,7 @@ if (${_index} GREATER -1)
endif()
list (FIND LANGUAGES "C" _index)
if (${_index} GREATER -1)
message(STATUS "C Compiler ${CMAKE_C_COMPILER}
message(STATUS "C compiler ${CMAKE_C_COMPILER}
Type ${CMAKE_C_COMPILER_ID}
Version ${CMAKE_C_COMPILER_VERSION}
C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
@ -712,22 +712,22 @@ if(CMAKE_EXE_LINKER_FLAGS)
Executable ${CMAKE_EXE_LINKER_FLAGS}")
endif()
if(BUILD_SHARED_LIBS)
message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}")
message(STATUS "Shared library flags: ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message(STATUS "Static libraries ${CMAKE_STATIC_LINKER_FLAGS}")
message(STATUS "Static library flags: ${CMAKE_STATIC_LINKER_FLAGS}")
endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
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()
if(PKG_GPU)
message(STATUS "GPU Api: ${GPU_API}")
message(STATUS "GPU API: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU Arch: ${GPU_ARCH}")
message(STATUS "GPU architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OCL Tune: ${OCL_TUNE}")
message(STATUS "OpenCL parameter tuning: ${OCL_TUNE}")
endif()
message(STATUS "GPU Precision: ${GPU_PREC}")
message(STATUS "GPU precision: ${GPU_PREC}")
endif()
if(PKG_KOKKOS)
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
View File

@ -1,7 +1,4 @@
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 ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

3
cmake/Modules/Packages/LATTE.cmake
View File

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

3
cmake/Modules/Packages/MSCG.cmake
View File

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

4
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

@ -1,8 +1,4 @@
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")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})

4
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
message(STATUS "PLUMED download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
URL_MD5 de30d6e7c2dcc0973298e24a6da24286
URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
URL_MD5 204d2edae58d9b10ba3ad460cad64191
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}

14
cmake/Modules/Packages/USER-QMMM.cmake
View File

@ -1,9 +1,13 @@
if(PKG_USER-QMMM)
enable_language(Fortran)
enable_language(C)
message(WARNING "Building QMMM with CMake is still experimental")
find_package(QE REQUIRED)
include_directories(${QE_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
if(NOT BUILD_LIB)
message(FATAL_ERROR "Building a QM/MM executable with USER-QMMM requires BUILD_LIB=yes")
endif()
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()

2
doc/.gitignore vendored
View File

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

53
doc/Makefile
View File

@ -4,6 +4,7 @@ SHELL = /bin/bash
BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src
VENV = $(BUILDDIR)/docenv
MATHJAX = $(BUILDDIR)/mathjax
TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
@ -28,62 +29,65 @@ endif
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:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " html create HTML doc pages in html dir"
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " anchor_check scan for duplicate anchor labels"
@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
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 spelling
clean-spelling:
rm -rf spelling
rst: clean $(ANCHORCHECK)
html: $(ANCHORCHECK)
html: $(ANCHORCHECK) $(MATHJAX)
@(\
. $(VENV)/bin/activate ;\
sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
echo "############################################" ;\
rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
)
-rm html/searchindex.js
@rm -rf html/_sources
@rm -rf html/PDF
@rm -rf html/USER
@rm -rf html/JPG
@cp -r src/PDF html/PDF
@cp -r src/USER html/USER
@mkdir -p html/JPG
@cp `grep -A2 '\.\. image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@rm -rf html/PDF/.[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."
spelling: utils/sphinx-config/false_positives.txt
spelling: $(VENV) utils/sphinx-config/false_positives.txt
@(\
. $(VENV)/bin/activate ;\
pip install sphinxcontrib-spelling ;\
@ -93,7 +97,7 @@ spelling: utils/sphinx-config/false_positives.txt
)
@echo "Spell check finished."
epub:
epub: $(VENV)
@mkdir -p epub/JPG
@rm -f LAMMPS.epub
@cp src/JPG/lammps-logo.png epub/
@ -125,6 +129,7 @@ pdf: $(ANCHORCHECK)
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
echo "############################################" ;\
rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
@ -168,13 +173,20 @@ anchor_check : $(ANCHORCHECK)
deactivate ;\
)
style_check :
style_check : $(VENV)
@(\
. $(VENV)/bin/activate ;\
python utils/check-styles.py -s ../src -d src ;\
deactivate ;\
)
package_check : $(VENV)
@(\
. $(VENV)/bin/activate ;\
python utils/check-packages.py -s ../src -d src ;\
deactivate ;\
)
# ------------------------------------------
$(VENV):
@ -187,6 +199,9 @@ $(VENV):
deactivate;\
)
$(MATHJAX):
@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
$(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \

11
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "4 February 2020" "2020-02-04"
.TH LAMMPS "3 March 2020" "2020-03-03"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
@ -11,13 +11,18 @@ or
mpirun \-np 2
.B lmp
<input file> [OPTIONS] ...
\-in <input file> [OPTIONS] ...
or
.B lmp
\-r2data file.restart file.data
or
.B lmp
\-h
.SH DESCRIPTION
.B LAMMPS
is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
@ -249,7 +254,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2019 Sandia Corporation
© 2003--2020 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

399
doc/src/Build_basics.rst
View File

@ -19,94 +19,115 @@ CMake and make:
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>`_
library. Or it can built to run on a single processor (serial)
without MPI. It can also be built with support for OpenMP threading
(see more discussion below).
LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
for distributed memory parallel computation. You need to have such a
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_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
# no default value
The executable created by CMake (after running make) is lmp\_name. If
the LAMMPS\_MACHINE variable is not specified, the executable is just
lmp. Using BUILD\_MPI=no will produce a serial executable.
The executable created by CMake (after running make) is named *lmp* unless
the LAMMPS\_MACHINE option is set. When setting `LAMMPS_MACHINE=name`
the executable will be named *lmp\_name*\. Using `BUILD\_MPI=no` will
enforce building a serial executable using the MPI STUBS library.
**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 serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Serial build (see src/MAKE/Makefile.serial):
make mybox # uses Makefile.mybox to produce lmp_mybox
.. 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_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
For a parallel build, if MPI is installed on your system in the usual
place (e.g. under /usr/local), you do not need to specify the 3
variables MPI\_INC, MPI\_PATH, MPI\_LIB. The MPI wrapper on the compiler
(e.g. mpicxx, mpiCC) knows where to find the needed include and
library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
are found, and the name of the library files (MPI\_LIB).
You also need to build the STUBS library for your platform before making
LAMMPS itself. A "make serial" build does this for you automatically,
otherwise, type "make mpi-stubs" from the src directory, or "make" from
the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform. The stubs library does not provide
MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
and thus is not compatible with those packages.
For a serial build, you need to specify the 3 variables, as shown
above.
.. note::
For a serial LAMMPS build, use the dummy MPI library provided in
src/STUBS. You also need to build the STUBS library for your platform
before making LAMMPS itself. A "make serial" build does this for.
Otherwise, type "make mpi-stubs" from the src directory, or "make"
from the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.c provides a CPU timer function called
MPI\_Wtime() that calls gettimeofday() . If your operating system
does not support gettimeofday() , you will 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.
The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
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.
**MPI and OpenMP support info**\ :
**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
National Laboratory or OpenMPI. MPICH can be downloaded from the
`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
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
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 includes OpenMP threading (it is
compatible with USER-OMP) and adds vectorization support when compiled
with the Intel compilers on top of that. Also, the KOKKOS package can
be compiled for using OpenMP threading.
with compatible compilers, in particular the Intel compilers on top of
OpenMP. Also, the KOKKOS package can be compiled to include OpenMP
threading.
However, there are a few commands in LAMMPS that have native OpenMP
support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
USER-DPD packages. In addition some packages support OpenMP threading
indirectly through the libraries they interface to: e.g. LATTE and
USER-COLVARS. See the :doc:`Packages details <Packages_details>` doc
page for more info on these packages and the doc pages for their
respective commands for OpenMP threading info.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the MPIIO, SNAP,
USER-DIFFRACTION, and USER-DPD packages. In addition some packages
support OpenMP threading indirectly through the libraries they interface
to: e.g. LATTE and USER-COLVARS. See the :doc:`Packages details
<Packages_details>` doc page for more info on these packages and the doc
pages for their respective commands for OpenMP threading info.
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
@ -143,22 +164,37 @@ Choice of compiler and compile/link options
---------------------------------------------------------
The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than
open-source compilers like GNU. On boxes with Intel CPUs, we suggest
trying the `Intel C++ compiler <intel_>`_.
performance. Vendor provided compilers for a specific hardware can
produce faster code than open-source compilers like the GNU compilers.
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
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
compile/link environments, you can often access different compilers by
simply loading the appropriate module before building LAMMPS.
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.
**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:
.. parsed-literal::
.. code-block:: bash
-D CMAKE_CXX_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_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
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:
A few example command lines are:
.. 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
Building with Intel Compilers:
# Building with Intel Compilers:
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
For compiling with the Clang/LLVM compilers a special CMake preset is
included that can be loaded with `-C ../cmake/presets/clang.cmake`.
.. note::
When the cmake command completes, it prints info to the screen
as to which compilers it is using, and what flags will be used in the
compilation. Note that if the top-level compiler is mpicxx, it is
simply a wrapper on a real compiler. The underlying compiler info is
what will be listed in the CMake output. You should check to insure
you are using the compiler and optimization flags are the ones you
want.
When the cmake command completes, it prints a summary to the screen
which compilers it is using and what flags and settings will be used
for the compilation. Note that if the top-level compiler is mpicxx,
it is simply a wrapper on a real compiler. The underlying compiler
info is what CMake will try to determine and report. You should check
to confirm you are using the compiler and optimization flags you 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):
.. parsed-literal::
.. code-block:: bash
CC = mpicxx
CCFLAGS = -g -O3
@ -212,33 +248,26 @@ Parallel build (see src/MAKE/Makefile.mpi):
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal::
.. code-block:: make
CC = g++
CCFLAGS = -g -O3
LINK = g++
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::
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
optimization flags that are either required or recommended for optimal
performance. You need to include these in the CCFLAGS and LINKFLAGS
settings above. For details, see the individual package doc pages
listed on the :doc:`Speed packages <Speed_packages>` doc page. Or
examine these files in the src/MAKE/OPTIONS directory. They
correspond to each of the 5 accelerator packages and their hardware
variants:
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>`
included, there may be specific optimization flags that are either
required or recommended to enable required features and to achieve
optimal performance. You need to include these in the CCFLAGS and
LINKFLAGS settings above. For details, see the individual package
doc pages listed on the :doc:`Speed packages <Speed_packages>` doc
page. Or examine these files in the src/MAKE/OPTIONS directory.
They correspond to each of the 5 accelerator packages and their
hardware variants:
.. parsed-literal::
.. code-block:: bash
Makefile.opt # OPT 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_phi # KOKKOS package for KNLs (OpenMP)
----------
.. _exe:
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
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_LIB=value # yes or no (default)
@ -277,24 +307,32 @@ running LAMMPS from Python via its library interface.
# no default value
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
shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
libraries will be named liblammps\_name.a or liblammps\_name.so instead.
shared library named *liblammps.so* instead. If LAMMPS\_LIB\_SUFFIX is
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**\ :
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
mkae mode=exe machine # same as "make machine"
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
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
liblammps.a and liblammps.so, which point to the liblammps\_machine
files.
The two "exe" builds will generate and executable *lmp\_machine*\ ,
while the two library builds will create a file *liblammps\_machine.a*
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**\ :
@ -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
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
the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
library version of the auxiliary library. The build instructions 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
the lib/packages directory, since they are always built in a shared
library compatible way using the -fPIC switch. However, if a library
like MPI or FFTW does not exist as a shared library, the shared library
build may generate an error. This means you will need to install a
shared library version of the auxiliary library. The build instructions
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, as a shared library
in the default /usr/local/lib location:
.. _mpich: https://www.mpich.org
.. parsed-literal::
.. code-block:: bash
./configure --enable-shared
make
make install
You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
You may need to use "sudo make install" in place of the last line if you
do not have write privileges for /usr/local/lib. The end result should
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
----------------------------------------
**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::
-D BUILD_DOC=value # yes or no (default)
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.
Thus "make html" will create a "doc/html" directory with the HTML format
manual pages so that you can browse them with a web browser locally on
your system.
.. note::
@ -369,6 +424,19 @@ lammps/doc dir to see other options.
`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
using CMake or Make.
**CMake variable**\ :
**CMake build3**\ :
.. parsed-literal::
.. code-block:: bash
-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**\ :
.. parsed-literal::
.. code-block:: bash
cd lammps/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
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
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:
.. parsed-literal::
.. code-block:: bash
cd lammps # change to the LAMMPS distribution directory
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:
.. parsed-literal::
.. code-block:: bash
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
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
later version. CMake will print a message telling you if a later
version is required. Installation instructions for CMake are below.
You must have CMake version 3.10 or later on your system to build
LAMMPS. Installation instructions for CMake are below.
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
@ -115,7 +113,7 @@ folder, recreate the directory and start over.
**Command-line version of CMake**\ :
.. parsed-literal::
.. code-block:: bash
cmake [options ...] /path/to/lammps/cmake # build from any dir
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:
.. parsed-literal::
.. code-block:: bash
-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
@ -177,7 +175,7 @@ directory.
**Curses version (terminal-style menu) of CMake**\ :
.. parsed-literal::
.. code-block:: bash
ccmake ../cmake
@ -195,7 +193,7 @@ more information.
**GUI version of CMake**\ :
.. parsed-literal::
.. code-block:: bash
cmake-gui ../cmake
@ -216,7 +214,7 @@ for more information.
Check if your machine already has CMake installed:
.. parsed-literal::
.. code-block:: bash
which cmake # do you have it?
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:
.. parsed-literal::
.. code-block:: bash
module list # is a cmake module already loaded?
module avail # is a cmake module available?
module list # is a module for cmake already loaded?
module avail # is a module for cmake available?
module load cmake3 # load cmake module with appropriate name
Most Linux distributions offer pre-compiled cmake packages through

16
doc/src/Build_development.rst
View File

@ -18,14 +18,14 @@ generated by the CMake build. To enable a more verbose output during
compilation you can use the following option.
.. parsed-literal::
.. code-block:: bash
-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:
.. parsed-literal::
.. code-block:: bash
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.
.. parsed-literal::
.. code-block:: bash
-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
@ -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
.. parsed-literal::
.. code-block:: bash
-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)
@ -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:
.. parsed-literal::
.. code-block:: bash
make test
@ -93,14 +93,14 @@ You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
.. parsed-literal::
.. code-block:: bash
-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:
.. parsed-literal::
.. code-block:: bash
make test # run tests first!
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:
.. parsed-literal::
.. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git

369
doc/src/Build_extras.rst
View File

@ -5,10 +5,15 @@ When building with some packages, additional steps may be required,
in addition to:
.. parsed-literal::
.. code-block:: bash
-D PKG_NAME=yes # CMake
make yes-name # make
$ cmake -D PKG_NAME=yes
or
.. code-block:: bash
$ make yes-name
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.
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :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>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
.. table_from_list::
:columns: 6
* :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:
.. parsed-literal::
.. code-block:: bash
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
**Traditional make**\ :
If make cannot find the library, you can edit the
lib/compress/Makefile.lammps file to specify the paths and library
If make cannot find the library, you can edit the file
lib/compress/Makefile.lammps to specify the paths and library
name.
@ -75,7 +97,7 @@ which GPU hardware to build for.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-D GPU_API=value # value = opencl (default) or cuda
-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:
.. parsed-literal::
.. code-block:: bash
make lib-gpu # print help message
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 mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
$ make lib-gpu # print help message
$ 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 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
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
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.
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**\ :
.. parsed-literal::
.. code-block:: bash
-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
@ -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
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
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.
.. parsed-literal::
.. code-block:: bash
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 -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="-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 -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
$ 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 -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="-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 -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
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
* ARMv81 = ARMv8.1 Compatible CPU
* ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
* BGQ = IBM Blue Gene/Q CPUs
* Power8 = IBM POWER8 CPUs
* Power9 = IBM POWER9 CPUs
* ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU
* WSM = Intel Westmere CPUs
* SNB = Intel Sandy/Ivy Bridge CPUs
* HSW = Intel Haswell CPUs
* BDW = Intel Broadwell Xeon E-class CPUs
* SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
* KNC = Intel Knights Corner 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
* Kepler32 = NVIDIA Kepler generation CC 3.2
* Kepler35 = NVIDIA Kepler generation CC 3.5
* Kepler37 = NVIDIA Kepler generation CC 3.7
* Maxwell = NVIDIA Maxwell default (generation CC 5.0)
* Maxwell50 = NVIDIA Maxwell generation CC 5.0
* Maxwell52 = NVIDIA Maxwell generation CC 5.2
* 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.
.. parsed-literal::
.. code-block:: bash
-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above
-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:
.. parsed-literal::
.. code-block:: bash
-D KOKKOS_ARCH=KNL
-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:
.. parsed-literal::
.. code-block:: bash
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
# 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.
.. parsed-literal::
.. code-block:: bash
-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:
.. parsed-literal::
.. code-block:: make
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = archCPU # archCPU = CPU from list above
@ -337,7 +374,7 @@ For multicore CPUs using OpenMP:
For Intel KNLs using OpenMP:
.. parsed-literal::
.. code-block:: make
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNL
@ -345,7 +382,7 @@ For Intel KNLs using OpenMP:
For NVIDIA GPUs using CUDA:
.. parsed-literal::
.. code-block:: make
KOKKOS_DEVICES = Cuda
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.
.. parsed-literal::
.. code-block:: make
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
@ -381,7 +418,7 @@ library.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -401,12 +438,12 @@ simply invokes the lib/latte/Install.py script with the specified
args:
.. parsed-literal::
.. code-block:: bash
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
$ make lib-latte # print help message
$ make lib-latte args="-b" # download and build in lib/latte/LATTE-master
$ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
@ -431,7 +468,7 @@ be installed on your system.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -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:
.. parsed-literal::
.. code-block:: bash
make lib-message # print help message
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 # print help message
$ 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
The build should produce two files: lib/message/cslib/src/libmessage.a
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**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -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:
.. parsed-literal::
.. code-block:: bash
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 # print help message
$ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# 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"
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
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:
.. parsed-literal::
.. code-block:: bash
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 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 # print help message
$ 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 icc" # build with Intel icc compiler
The build should produce two files: lib/poems/libpoems.a and
lib/poems/Makefile.lammps. The latter is copied from an existing
@ -584,7 +621,7 @@ lib/python/README for more details.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-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**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -642,12 +679,12 @@ simply invoke the lib/voronoi/Install.py script with the specified
args:
.. parsed-literal::
.. code-block:: bash
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="-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 # print help message
$ 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="-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
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**\ :
.. parsed-literal::
.. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-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:
.. parsed-literal::
.. code-block:: bash
make yes-user-adios
$ make yes-user-adios
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:
.. parsed-literal::
.. code-block:: bash
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 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 # 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 mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/atc/libatc.a and
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:
.. parsed-literal::
.. code-block:: bash
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 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 # print help message
$ 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 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:
.. parsed-literal::
.. code-block:: bash
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 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 # 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 mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler
The build should produce two files: lib/awpmd/libawpmd.a and
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:
.. parsed-literal::
.. code-block:: bash
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 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 # print help message
$ 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 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:
.. parsed-literal::
.. code-block:: bash
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 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 # print help message
$ 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 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
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:
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)
.. code-block:: bash
$ 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
(which also includes Lepton objects if enabled) and the specification file
@ -880,6 +919,9 @@ USER-PLUMED package
Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
The USER-PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
PLUMED can be linked into MD codes in three different modes: static,
@ -918,7 +960,7 @@ your environment. There are then two additional commands that control
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 PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime
@ -954,12 +996,12 @@ Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args:
.. parsed-literal::
.. code-block:: bash
make lib-plumed # print help message
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 /usr/local -m shared" # use existing PLUMED installation in
$ make lib-plumed # print help message
$ 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 /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
Note that 2 symbolic (soft) links, "includelink" and "liblink" are
@ -970,10 +1012,10 @@ mode. After this step is completed, you can install the USER-PLUMED
package and compile LAMMPS in the usual manner:
.. parsed-literal::
.. code-block:: bash
make yes-user-plumed
make machine
$ make yes-user-plumed
$ make machine
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
@ -1021,10 +1063,10 @@ dir, using a command like these, which simply invoke the
lib/h5md/Install.py script with the specified args:
.. parsed-literal::
.. code-block:: bash
make lib-h5md # print help message
make lib-h5md args="-m h5cc" # build with h5cc compiler
$ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: lib/h5md/libch5md.a and
lib/h5md/Makefile.lammps. The latter is copied from an existing
@ -1052,7 +1094,7 @@ on the :doc:`Speed intel <Speed_intel>` doc page.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-D INTEL_ARCH=value # value = cpu (default) or knl
-D INTEL_LRT_MODE=value # value = threads, none, or c++11
@ -1079,7 +1121,7 @@ additional information.
For CPUs:
.. parsed-literal::
.. code-block:: make
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)
@ -1089,7 +1131,7 @@ For CPUs:
For KNLs:
.. parsed-literal::
.. code-block:: make
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)
@ -1108,7 +1150,7 @@ USER-MOLFILE package
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
-D PKG_USER-MOLFILE=yes
@ -1188,9 +1230,9 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
.. parsed-literal::
CCFLAGS: -fopenmp # for GNU Compilers
CCFLAGS: -fopenmp # for GNU and Clang Compilers
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
For other platforms and compilers, please consult the documentation
@ -1206,25 +1248,40 @@ how to address compatibility :ref:`issues with the 'default(none)' directive <de
USER-QMMM package
---------------------------------
.. note::
The LAMMPS executable these steps produce is not yet functional
for a QM/MM simulation. You must also build Quantum ESPRESSO and
create a new executable (pwqmmm.x) which links LAMMPS and Quantum
ESPRESSO together. These are steps 3 and 4 described in the
lib/qmmm/README file. Unfortunately, the Quantum ESPRESSO developers
have been breaking the interface that the QM/MM code in LAMMPS is using,
so that currently (Summer 2018) using this feature requires either
correcting the library interface feature in recent Quantum ESPRESSO
releases, or using an outdated version of QE. The last version of
Quantum ESPRESSO known to work with this QM/MM interface was version
5.4.1 from 2016.
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
included can be built, but will not be able to do a QM/MM simulation
on as such. You must also build a QM code - currently only Quantum
ESPRESSO (QE) is supported - and create a new executable which links
LAMMPS and the QM code together. Details are given in the
lib/qmmm/README file. It is also recommended to read the instructions
for :doc:`linking with LAMMPS as a library <Build_link>` for
background information. This requires compatible Quantum Espresso
and LAMMPS versions. The current interface and makefiles have last
been verified to work in February 2020 with Quantum Espresso versions
6.3 to 6.5.
**CMake build**\ :
The CMake build system currently does not support building the full
QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.
You must use the traditional make build for this package.
When using CMake, building a LAMMPS library is required and it is
recommended to build a shared library, since any libraries built from
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**\ :
@ -1235,12 +1292,12 @@ lammps/src dir, using a command like these, which simply invoke the
lib/qmmm/Install.py script with the specified args:
.. parsed-literal::
.. code-block:: bash
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 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 # print help message
$ 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 gfortran" # build with GNU Fortran compiler
The build should produce two files: lib/qmmm/libqmmm.a and
lib/qmmm/Makefile.lammps. The latter is copied from an existing
@ -1252,10 +1309,10 @@ a corresponding Makefile.lammps.machine file.
You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support, 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.
ESPRESSO with external library support (via "make couple"), go back to
the lib/qmmm folder and follow the instructions in the README file to
build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
lib/qmmm folder.
----------
@ -1274,7 +1331,7 @@ lib/quip/README file for details on how to do this.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
@ -1310,7 +1367,7 @@ To build with this package, you must download and build the `ScaFaCoS Coulomb so
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -1355,7 +1412,7 @@ Eigen3 is a template library, so you do not need to build it.
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-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)
@ -1373,11 +1430,11 @@ the lammps/src dir, using a command like these, which simply invoke
the lib/smd/Install.py script with the specified args:
.. parsed-literal::
.. code-block:: bash
make lib-smd # print help message
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 # print help message
$ 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
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

230
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@ -3,62 +3,228 @@ Link LAMMPS as a library to another code
LAMMPS can be used as a library by another application, including
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
interface and how to extend it for your needs.
C-style API for using LAMMPS as a library. See the :doc:`Howto
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
LAMMPS as either a shared or static library. This results in one of
these 2 files:
liblammps.so # shared library
liblammps.a # static library
.. parsed-literal::
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**\ :
The calling application can link to LAMMPS as a static library with a
link command like this:
The calling application can link to LAMMPS as a static library with
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
-llammps argument is shorthand for the file liblammps.a.
This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
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**\ :
If you wish to link to liblammps.so, the operating system finds shared
libraries to load at run-time using the environment variable
LD\_LIBRARY\_PATH. To enable this you can do one of two things:
When linking to LAMMPS built as a shared library, the situation
becomes much simpler, as all dependent libraries and objects are
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,
such as /usr/local/lib. I.e. a directory already listed in your
LD\_LIBRARY\_PATH variable. You can type
*CMake build*\ :
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
to see what directories are in that list.
(2) Add the LAMMPS src directory (or the directory you perform CMake
build in) to your LD\_LIBRARY\_PATH, so that the current version of the
shared library is always available to programs that use it.
Or you can add the LAMMPS src directory (or the directory you performed
a CMake style build in) to your LD\_LIBRARY\_PATH, so that the current
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
~/.cshrc file:
For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
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**\ :
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
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
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in src/library.cpp and src/library.h.
See the :doc:`Python library <Python_library>` doc page for a
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
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
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
must install them first, as discussed on the :doc:`Build package <Build_package>` doc page. If the packages require
provided or external libraries, you must build those libraries before
building LAMMPS. Building :doc:`LAMMPS with CMake <Build_cmake>` can
automate all of this for many types of machines, especially
workstations, desktops and laptops, so we suggest you try it first.
must enable them first, as discussed on the :doc:`Build package
<Build_package>` doc page. If a packages requires (provided or
external) libraries, you must configure and build those libraries
**before** building LAMMPS itself and especially **before** enabling
such a package with "make yes-<package>". 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
executable lmp\_serial or lmp\_mpi in lammps/src:
The commands below perform a default LAMMPS build, producing the LAMMPS
executable lmp\_serial and lmp\_mpi in lammps/src:
.. parsed-literal::
.. code-block:: bash
cd lammps/src
make serial # build a serial LAMMPS executable
@ -42,18 +57,21 @@ re-compiled.
.. note::
When you build LAMMPS for the first time, a long list of \*.d
files will be printed out rapidly. This is not an error; it is the
Makefile doing its normal creation of dependencies.
Before the actual compilation starts, LAMMPS will perform several
steps to collect information from the configuration and setup that
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 all the Makefile.machine files
included in the LAMMPS distribution. Typing "make machine" uses
Makefile.machine. Thus the "make serial" or "make mpi" lines above
use Makefile.serial and Makefile.mpi. Others are in these dirs:
The lammps/src/MAKE tree contains the Makefile.machine files included
in the LAMMPS distribution. Typing "make machine" uses
*Makefile.machine*\ . Thus the "make serial" or "make mpi" lines above
use Makefile.serial and Makefile.mpi, respectively. Other makefiles
are in these directories:
.. 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
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
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:
.. parsed-literal::
.. code-block:: bash
make mac # build serial 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.
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,
and your build did not include that package. Running LAMMPS with the
:doc:`-h command-line switch <Run_options>` will print all the included
packages and commands for that executable.
"unknown", it is often because the command is contained in a package,
and your build did not include that package. If the command or style
*is* available in a package included in the LAMMPS distribution,
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
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
versus make.
**CMake variables**\ :
**CMake build**\ :
.. parsed-literal::
.. code-block:: bash
-D PKG_NAME=value # yes or no (default)
Examples:
.. parsed-literal::
.. code-block:: bash
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
@ -74,7 +77,7 @@ once with CMake.
**Traditional make**\ :
.. parsed-literal::
.. code-block:: bash
cd lammps/src
make ps # check which packages are currently installed
@ -85,7 +88,7 @@ once with CMake.
Examples:
.. parsed-literal::
.. code-block:: bash
make no-rigid
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.
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.
.. note::
@ -136,9 +139,10 @@ src directory.
**CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line,
CMake allows initializing the variable cache using script files. These
are regular CMake files which can manipulate and set variables, and
can also contain control flow constructs.
CMake allows initializing its settings cache using script files.
These are regular CMake files which can manipulate and set CMake
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
"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
one of them as a starting point and customize it to your needs.
+-------------------------------------------------------------+-----------------------------------------------------------+
| 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/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/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 |
+-------------------------------------------------------------+-----------------------------------------------------------+
.. code-block:: bash
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/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/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::
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
in a single cmake run, or change settings incrementally by running
cmake with new flags.
@ -172,7 +170,7 @@ one of them as a starting point and customize it to your needs.
**Example:**
.. parsed-literal::
.. code-block:: bash
# build LAMMPS with most commonly used packages, but then remove
# 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:
+-----------------------------------+-----------------------------------------------------+
| make yes-all | install all packages |
+-----------------------------------+-----------------------------------------------------+
| make no-all | un-install all packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-standard or make yes-std | install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make no-standard or make no-std | un-install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-user | install user packages |
+-----------------------------------+-----------------------------------------------------+
| make no-user | un-install user packages |
+-----------------------------------+-----------------------------------------------------+
| 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 |
+-----------------------------------+-----------------------------------------------------+
.. code-block:: bash
make yes-all # install all packages
make no-all # uninstall all 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-user # uninstall user packages
make yes-lib # install packages that require extra libraries
make no-lib # uninstall packages that require extra libraries
make yes-ext # install packages that require external libraries
make no-ext # uninstall packages that require external libraries
which install/un-install various sets of packages. Typing "make
package" will list all the these commands.
.. note::
Installing or un-installing a package works by simply copying
files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are included or excluded when LAMMPS is built.
Installing or un-installing a package for the make based build process
works by simply copying files back and forth between the main source
directory src and the sub-directories with the package name (e.g.
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
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.
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.

115
doc/src/Build_settings.rst
View File

@ -4,16 +4,15 @@ Optional build settings
LAMMPS can be built with several optional settings. Each sub-section
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:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
| :ref:`Size of LAMMPS data types <size>`
| :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 movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
| :ref:`Memory allocation alignment <align>`
| :ref:`Workaround for long long integers <longlong>`
| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
|
* :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:`Size of LAMMPS data types <size>`
* :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 movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
* :ref:`Memory allocation alignment <align>`
* :ref:`Workaround for long long integers <longlong>`
* :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:
C++11 standard compliance test
C++11 standard compliance
------------------------------------------
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to switch. To determine the impact of requiring C++11,
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.
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
C++98 standard for the core code and most packages. Most currently used
C++ compilers are compatible with C++11, but some older ones may need extra
flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
**CMake variable**\ :
.. 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::
.. code-block:: make
CCFLAGS = -g -O3 -std=c++11
@ -80,7 +50,7 @@ LAMMPS can use them if they are available on your system.
**CMake variables**\ :
.. parsed-literal::
.. code-block:: bash
-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
@ -100,7 +70,7 @@ used. If CMake cannot detect the FFT library, you can set these variables
to assist:
.. parsed-literal::
.. code-block:: bash
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
-D FFTW3_LIBRARIES=path # path to FFTW3 libraries
@ -112,7 +82,7 @@ to assist:
**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
# default is KISS if not specified
@ -124,7 +94,7 @@ to assist:
# default is FFT\_PACK\_ARRAY if not specified
.. parsed-literal::
.. code-block:: make
FFT_INC = -I/usr/local/include
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.
.. parsed-literal::
.. code-block:: bash
make clean
./configure --enable-single; make; make install
@ -218,14 +188,14 @@ adequate.
**CMake variable**\ :
.. parsed-literal::
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
.. parsed-literal::
.. code-block:: make
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
@ -296,21 +266,21 @@ following settings:
**CMake variables**\ :
.. parsed-literal::
.. code-block:: bash
-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
# 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
# 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
the graphics header, library, executable files, you can set these
variables:
.. parsed-literal::
.. code-block:: bash
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
@ -323,7 +293,7 @@ variables:
**Makefile.machine settings**\ :
.. parsed-literal::
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
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
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,
i.e. a dir in your PATH environment variable.
that is a directory in your PATH environment variable.
**CMake and make info**\ :
@ -347,7 +317,7 @@ supports the "popen" function in the standard runtime library.
.. note::
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
crash.
@ -367,7 +337,7 @@ gzip compression by several LAMMPS commands, including
**CMake variables**\ :
.. parsed-literal::
.. code-block:: bash
-D WITH_GZIP=value # yes or 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**\ :
.. parsed-literal::
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
@ -389,7 +359,7 @@ found by LAMMPS during a run.
.. note::
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
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which is
@ -416,7 +386,7 @@ aligned on 64-byte boundaries.
**CMake variable**\ :
.. parsed-literal::
.. code-block:: bash
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
@ -428,7 +398,7 @@ and this setting ignored.
**Makefile.machine setting**\ :
.. parsed-literal::
.. code-block:: make
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
@ -455,14 +425,14 @@ those systems:
**CMake variable**\ :
.. parsed-literal::
.. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
.. code-block:: make
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.
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,
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**\ :
.. parsed-literal::
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS

28
doc/src/Build_windows.rst
View File

@ -17,9 +17,9 @@ General remarks
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
Thus portability to other platforms is desired, but not always achieved.
While portability to other platforms is desired, it is not always achieved.
The LAMMPS developers strongly rely on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This particularly
providing assistance in resolving portability issues. This is particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences with some low-level functionality.
@ -31,18 +31,20 @@ Running Linux on Windows
So before trying to build LAMMPS on Windows, please consider if using
the pre-compiled Windows binary packages are sufficient for your needs
(as an aside, those packages themselves are build on a Linux machine
using cross-compilers). If it is necessary for your to compile LAMMPS
using cross-compilers). If it is necessary for you to compile LAMMPS
on a Windows machine (e.g. because it is your main desktop), please also
consider using a virtual machine software and run a Linux virtual machine,
or - if have a recently updated Windows 10 installation - consider using
the Windows subsystem for Linux, which allows to run a bash shell from
Ubuntu and from there on, you can pretty much use that shell like you
are running on an Ubuntu Linux machine (e.g. installing software via
apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
consider using a virtual machine software and compile and run LAMMPS in
a Linux virtual machine, or - if you have a recently updated Windows 10
installation - consider using the Windows subsystem for Linux. This
optional Windows feature allows you to run the bash shell from Ubuntu
from within Windows and from there on, you can pretty much use that
shell like you are running on an Ubuntu Linux machine (e.g. installing
software via apt-get and more). For more details on that, please
see :doc:`this tutorial <Howto_bash>`
.. _gnu:
Using GNU GCC ported to Windows
Using a GNU GCC ported to Windows
-----------------------------------------
One option for compiling LAMMPS on Windows natively, that has been known
@ -83,13 +85,13 @@ traditional build system, but CMake has also been successfully tested
using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines. A CMake preset
selecting all packages compatible with this cross-compilation build
is provided. You likely need to disable the GPU package unless you
is provided. You will likely need to disable the GPU package unless you
download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
into your MinGW64 cross-compiler environment. The cross-compilation
currently will only produce non-MPI serial binaries.
Please keep in mind, though, that this only applies to compiling LAMMPS.
Whether the resulting binaries do work correctly is no tested by the
Please keep in mind, though, that this only applies to **compiling** LAMMPS.
Whether the resulting binaries do work correctly is not tested by the
LAMMPS developers. We instead rely on the feedback of the users
of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However

2
doc/src/Commands_all.rst
View File

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

233
doc/src/Commands_category.rst
View File

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

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

6
doc/src/Commands_pair.rst
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@ -26,6 +26,10 @@ OPT.
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
*
*
*
*
*
@ -109,14 +113,12 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`

221
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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
LAMMPS:
(1) If the last printable character on the line is a "&" character,
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.
.. _one:
(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). 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.
1. If the last printable character on the line is a "&" character, 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 :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
variables that are replaced with a text string. See an exception in
(6).
.. code-block:: LAMMPS
If the $ is followed by 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 variable names "myTemp" and
"x".
# this is a comment
timestep 1.0 # this is also a comment
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.
.. _three:
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:
3. The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. The exception to
this rule is described in :ref:`6 <six>`.
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)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
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
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.
.. _four:
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
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
.. code-block:: LAMMPS
.. code-block:: LAMMPS
variable a equal 2
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 &
print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
print """
System volume = $v
System temperature = $t
"""
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
:doc:`if <if>`, and :doc:`python <python>` commands for examples.
See the :doc:`dump modify format <dump_modify>`, :doc:`print
<print>`, :doc:`if <if>`, and :doc:`python <python>` commands for
examples.
A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
A "#" or "$" character that is between quotes will not be treated as
a comment indicator in :ref:`2 <two>` or substituted for as a
variable in :ref:`3 <three>`.
.. note::

52
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@ -8,17 +8,20 @@ page.
A LAMMPS input script typically has 4 parts:
1. Initialization
2. Atom definition
3. Settings
4. Run a simulation
1. :ref:`Initialization <init>`
2. :ref:`System definition <system>`
3. :ref:`Simulation settings <settings>`
4. :ref:`Run a simulation <run>`
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
parts is now described in more detail. Remember that almost all
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
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:`improper_style <improper_style>`.
(2) Atom definition
.. _system:
There are 3 ways to define atoms in LAMMPS. Read them in from a data
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.
System definition
------------------------------
(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
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
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>`,
and :doc:`restart <restart>` commands.
(4) Run a simulation
.. _run:
Run a simulation
------------------------------
A molecular dynamics simulation is run using the :doc:`run <run>`
command. Energy minimization (molecular statics) is performed using

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\documentclass[12pt]{article}
\begin{document}
$$
CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
$$
\end{document}

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\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\begin{document}
\begin{eqnarray*}
r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
\end{eqnarray*}
\end{document}

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\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\begin{document}
$$
Rc + Rs > 2*{\rm cutoff}
$$
\end{document}

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\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\begin{document}
\begin{eqnarray*}
r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
\end{eqnarray*}
\end{document}

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\documentclass[12pt,article]{article}
\usepackage{indentfirst}
\usepackage{amsmath}
\begin{document}
$$
Rc + Rs > 2*{\rm cutoff}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2
$$
\end{document}

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\documentstyle[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\
U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
U^{chem} = \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\
\theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
\end{eqnarray*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
A(\lambda_i)}{\delta} \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{eqnarray*}
\lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
\lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1
\end{eqnarray*}
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
\frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
{R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
I=\frac{F^{*}F}{N}
$$
\end{document}

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doc/src/Eqs/compute_saed2.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
$$
\end{document}

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doc/src/Eqs/compute_saed3.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
$$
\end{document}

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doc/src/Eqs/compute_shape_parameters.tex
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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
c = l_z - 0.5(l_y+l_x) \\
b = l_y - l_x \\
k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
\end{eqnarray*}
\end{document}

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doc/src/Eqs/compute_sna_atom1.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
\end{eqnarray*}
\end{document}

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doc/src/Eqs/compute_sna_atom2.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
\end{eqnarray*}
\end{document}

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doc/src/Eqs/compute_sna_atom3.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
\begin{equation}
B_{j_1,j_2,j} = \\
\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
\end{equation}
\end{document}

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doc/src/Eqs/compute_sna_atom4.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
\label{eqn:f_c}
f_c(r) & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
& = & 0, r > R_{ii'}
\end{eqnarray*}
\end{document}

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doc/src/Eqs/compute_sna_atom5.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\begin{equation}
- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i}
\end{equation}
\end{document}

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doc/src/Eqs/compute_sna_atom6.tex
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\documentclass[24pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
\end{eqnarray*}
\end{document}

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doc/src/Eqs/compute_xrd1.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
I=Lp(\theta)\frac{F^{*}F}{N}
$$
\end{document}

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doc/src/Eqs/compute_xrd2.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
$$
\end{document}

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doc/src/Eqs/compute_xrd3.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)}
$$
\end{document}

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doc/src/Eqs/compute_xrd4.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
\frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2}
$$
\end{document}

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doc/src/Eqs/compute_xrd5.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4}
a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
$$
\end{document}

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doc/src/Eqs/e3b.tex
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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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doc/src/Eqs/eff_ECP1.tex
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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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doc/src/Eqs/eff_ECP2.tex
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\documentstyle[12pt]{article}
\begin{document}
$$
E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right]
$$
\end{document}

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doc/src/Eqs/eff_KE.tex
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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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doc/src/Eqs/eff_NN.tex
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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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